2024-03-28T15:21:39Z
http://www.diagnosticpathology.eu/content/index.php/dpath/oai
oai:ojs2.localhost:article/272
2019-08-23T07:16:49Z
dpath:SHO
Expression of PTEN and pAKT in Non-Small Cell Lung Cancer
Antfang, Carina
Csanadi, Agnes
Kayser, Gian
Background: Alterations in the PTEN-AKT pathway play important roles indifferent solid carcinomas, e. g. of the breast, prostate and GI-tract. Since contradictory results have been reported for lung cancer mostly studying only one of the two proteins, we aim to elucidate the biological effects of alterations in this pathway in a large and well characterized cohort of non-small cell lung cancer.Material and Methods: We established an immunohistochemical double stain for PTEN and p-AKT in non-small cell lung carcinomas (NSCLC). This was applied to tissue-microarrays (TMA) including 44 patients.Results: Our results indicate, that not only alterations in one marker are of biological significance but rather the combination of PTEN-loss and p-AKT overexpression, as well as the intracellular localization of the protein staining. Patients with low-grade histological differentiation, negative lymphonodal status and PTEN-expression showed a significant better overall survival.Conclusion: We conclude, that PTEN-(over-)expression leads to p-AKT downregulation with better overall survival in nodal negative NSCLC patients.Virtual Slides:
DiagnomX GmbH
2019-08-22
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/272
10.17629/www.diagnosticpathology.eu-2019-5:272
Diagnostic Pathology; Vol 5 No 1 (2019): Vol. 5 No. 1 2019
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/272/566
Copyright (c) 2019 Gian Kayser, MD, Carina Antfang, M.D., Agnes Csanadi, M.D.
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/144
2018-06-19T09:27:28Z
dpath:SY01
A Graph-Based Digital Pathology Approach To Describe Lymphocyte Clustering Patterns After Renal Transplantation
Schaadt, N. S.
Uvarovskii, A.
Meyer-Hermann, M.
Schönmeyer, R.
Brieu, N.
Bräsen, J.H.
Gwinner, W.
Feuerhake, F.
Introduction/ BackgroundRenal transplantation (rTx) induces an adaptive immune response against foreign donor antigens mediated by lymphocytes of the recipient. Local accumulation of B- and T-cells is an important component of this response enabling and controlling immune cell interactions [1]. Combining digital microscopic images with network analysis [2][3] opens new perspectives to study the spa- tial dimension of lymphocyte clustering and to model their potential interactions. AimsThe aim of this study is to characterize the range of B- and T-lymphocytic infiltrates below the threshold of rejection defined by theBanffclassification [4][5] and to propose a mathematical description of immune cell clustering for use in systems medicine approaches. MethodsWe established a workflow to comprehensively characterize lymphocyte clusters and compare their morphological features with organized structures such as secondary or tertiary lymphoid organs (TLO/SLO) [6]. 51 renal protocol and indication biopsies from 13 patients without evidence for severe rejection over 10 years were stained by CD3/CD20 duplex immunohisto- chemistry. Whole slide images (WSIs) were acquired to automatically detect biologically relevant regions of in- terest (ROIs) by means of density maps for lymphocytes (image analysis workflow illustrated in Fig. 1a). They are generated from single nuclei identification using an au- to-adaptive random forest pixelwise classifier (“nucleus container†module [7],Definiens,Germany). We imple- mented a graph-based tool in Java using individual cell coordinates to identify cell compartments (Fig. 1b) and applied it to each selected ROI. For this, a neighborhood graph is built by Delaunay triangulation and Euclidean distances. This analysis allows describing their specific clustering behavior based on features as described in [8]. The convex hull of the neighborhood graph allows a visualization of B- and T-cell compartments. ResultsWe identified B-cell rich compartments in about 55% of 150 ROIs in kidney tissue after successful transplantation (examples in Fig. 2). The B-cell compartments in rTx tended towards smaller overall size with on average about 90 cells in a B-cell cluster compared to more than 600 B-cells observed in mature TLOs and SLOs and they showed less prominent spatial organization (average degree on average 3.92 instead of 4.97; degree shows generally Poisson distribution as illustrated in Fig. 3A). Further, the graph analysis confirmed lower B-cell density (Fig. 3B displays the exponential character of the spatial B-cell distribution in a selected ROI), a different ratio between T- and B-cell compartments, and more frequent overlap between both regions than in mature lymphoid structures. We conclude that the graph-based approach is feasible to distinguish relevant immune cell patterns in rTx and provides a useful mathematical description of neighborhood relationships between immune cells and their spatial organization. The workflow has the potential to improve throughput and robustness of immune cell evaluation for use in translational science.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/144
10.17629/www.diagnosticpathology.eu-2016-8:144
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/144/322
Copyright (c) 2016 N. S. Schaadt, A. Uvarovskii, M. Meyer-Hermann, R. Schönmeyer, N. Brieu, J.H. Bräsen, W. Gwinner, F. FeuerHake
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/160
2018-06-19T09:10:31Z
dpath:DA
Evolution And Revolution In Contemporary Pathology
Duglio, Giampiero
Introduction/ BackgroundCloud Pathology Group participated in the XI European Congress on Telepathology presenting the results of its great “in vitro research†about the use of HTS scanners in surgical pathology and in the XII European Congress on Digital Pathology presenting the preliminary results of its “in vivo research†done at the Busto Arsizio Multihospital Pathology Department, ended on June 30,2015.AimsThe aim of this abstract is to complete the Paris presentation and to highlight the conclusions of the three years and a half research work on the application of digital pathology in surgical activities. These conclusions became the base of the CPG software prototype (digital suite) put on the market by the Company.MethodsThe methods applied during the “in vitro research†and the “in vivo research†were described in 2012 and 2014 presentations. Afterwards, the work done consists indefining of specific tests to be executed on surgical specific diagnoses,defining the expected results of the tests,tests execution and validation of results,comparing expected and effective results,defining an evaluating the deviationsdefining how to proceed further.This Loup method was applied n times until a definitive specific conclusion was found.ResultsThere is no evidence that digital diagnoses present more risks than the microscopes’ ones. The costs per diagnosis increase due to new investments and new running costs, however the level of the increase depends on the organizational model adopted. The higher is the volume of the slides treated, the lower are the costs per diagnosis. The higher is the standardization of the slides that the Laboratory produces, the higher is the accuracy of the diagnosis. The greater is the number of the pathologists involved in the network entitled to a diagnosis, the higher is the accuracy of the diagnosis (side effect of the specialization). The second opinion solution is a slow process; it is better to produce the diagnosis by involving more pathologists in the same process in the same time (collaborative diagnosis). The Data Base on work’ tracking is the main requirement for the quality control procedure, for the evaluation process of the professional skills and for the work assignments. The electronic repository of the images instead of the physical stock of slides cuts relevant costs. The organization of Data Base, its flexibility and its multi-proprietary approach are the keys of the quality of the entire solution. At all, digital pathology is a total change process. The fundamentals of its success are:clear comprehension of the organizational effects to be put on place,massive educational programs on new technologies and on change management, for pathologist, technicians and therapists,strong change management assistance,coherent behaviour in all people involved.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/160
10.17629/www.diagnosticpathology.eu-2016-8:160
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/160/283
Copyright (c) 2016 G. Duglio
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/176
2018-06-19T09:09:06Z
dpath:STD
Typing, Grading, Staging - The Ultimate Goals Of Pathology Reports Modelled In HL7V3/CDA
Haroske, Gunter
Oemig, F.
Introduction/ BackgroundClinicians want pathologists to provide their reports fast, understandable, and useable for clinical decision making. Reports without a concise diagnostic conclusion in terms of typing, grading and staging of a disease are of low value. Therefore Anatomic Pathology Structured Reports (APSR) should have those keystones also reflected.AimsInstead to define very long lists with specific TNM-formulas, grading values, and tumor classifications information models have been developed which allow a flexible use in the diagnostic reporting approach and a compact programming.MethodsExemplarily for any diagnostic conclusion a model for TNM- as well as ICD-O-classification of malignant tumors for HL7 reporting to cancer registries in Germany was modified and completed with codes and value sets by means of Art-Decor. Additionally, an assessment score model was developed applicable for a wide variety of grading systems used in neoplastic as well as non-neoplastic diseases. ART-DECOR is a toolkit allowing for maintaining information models designated to data exchange facilitating communication standards.ResultsAn information model for TNM as well as ICD-O-classification of malignant tumors for reporting to cancer registries in Germany supporting the required data set was developed and filled with appropriate codes and value sets by means of ART-DECOR. The IHE APSR Trial implementation with its templates and value sets was mirrored in ART-DECOR and completed by templates for TNM-, ICD-O-3 and Assessment-Scores, based on the German HL7 Oncology Reporting requirements. A model based approach for structured reporting of complex problems is the preferred approach instead of exhaustive lists of permutated single values. Conclusion:The developed templates are to be used as entries in the Diagnostic Conclusion section of IHE APSR allowing for a structured data exchange so that automatic clinical decision support is maximized.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/176
10.17629/www.diagnosticpathology.eu-2016-8:176
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/176/315
Copyright (c) 2016 G. Haroske, F. Oemig
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/192
2018-06-19T08:58:51Z
dpath:OPE
History Of The European Conference Series On Digital Pathology: Memories And Perspectives
Kayser, Klaus
European Conference; Digital Pathology
The 13th European Congress on Digital Pathology is the most recent conference of a European Conference series that started in Heidelberg 26 years ago. It reflects to a continuous, unbroken exchange of technological and medical information. The digital world was still in its childhood at the date of the first conference. Technological research investigated in electronic communication and digital acquisition of coloured pictures. Frozen section services and its need for fast information transfer between different institutes and the surgical theatre dominated the application of technological development. Consecutively, all issues of telepathology were in focus at the start and the following conferences. The pioneers of that time tried to convince their colleagues of the promising perspectives and the increasing technological influence on pathology. It took several conferences in this series until the majority of or nearly all pathologists recognized the power of this new technology.  Retrospectively, some conferences remained at the scientific level of their preceding meetings, whereas others substantially promoted knowledge and application in research and routine pathology. At present, digital pathology is well implemented and mainly used for education and enhancement of molecular biology methods such as next generation sequencing, predictive diagnosis, or risk associated investigations. Implementation in routine diagnostic pathology (virtual slides, etc.) is on its way. In addition, digital pathology moves forward to explore still unknown areas in surgical pathology, and tissue – based diagnosis. These include considerations on morphology, function and order of structures, which can detect potentially endangered factors or repair of live threatening breakdowns, as well as biostatistics, data mining, or self recognition algorithms.Â
DiagnomX GmbH
2016-06-22
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/192
10.17629/www.diagnosticpathology.eu-2016-8:192
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/192/249
Copyright (c) 2016 K. Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/1
2018-06-19T09:07:53Z
dpath:EDI
Starting a new peer reviewed open access journal diagnosticpathology.eu
Kayser, Klaus
Electronic publication; open access; surgical pathology; virtual slides; acoustic information
This is an introduction editorial on behalf of the implementation of the peer reviewed open access journal diagnosticpathology.eu that covers all aspects in diagnostic pathology. The advantages, constraints, the present stage and expectations of open access publication are discussed, and details of the new journal are described.
DiagnomX GmbH
2015-02-20
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/1
10.17629/www.diagnosticpathology.eu-2015-1:1
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/1/1
Copyright (c) 2015 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/213
2018-06-19T09:00:47Z
dpath:EP
Features of an Expression of Smooth Muscle Actin by Muscle Cells of Arterioles and Venules of Ureter and Urinary Bladder of Newborns in Modeling Chronic Intrauterine Hypoxia
Gorianikova, I.
Sorokina, I.
Myroshnychenko, M.
Introduction/ Background
Chronic intrauterine hypoxia, accompanied numerous complications of pregnancy, is one of the damaging factor of the organism of fetus and newborn.
Aims
The purpose – to reveal the features of expression of smooth muscle actin by muscle cells of arterioles and venules of ureter and urinary bladder of newborns under the influence of experimental chronic intrauterine hypoxia.
Methods
An experiment was conducted on modeling high mountain hypoxia in rats of WAG line. Two groups were formed: I – newborns (n=11) born from 3 rats that were not subjected to high mountain hypoxia; II – newborns (n=10) born from 4 rats that throughout pregnancy were exposed to a daily high mountain hypoxia. The material of the study was the tissue of ureter and urinary bladder. It was used peroxidase reaction with the monoclonal antibodies to smooth muscle actin (DAKO, Denmark). The slides were studied in microscope «Olympus ВХ- 41». An experimental study was carried out in strict compliance with the requirements of the European convention (Strasbourg, 1986) on the housing, feeding and care of experimental animals, and their removal from the experiment. Mean values of indicators in groups were compared using a nonparametric U-criteria Mann-Whitney.
Results
In group I and II was observed expression of smooth muscle actin by muscle cells, forming muscle fibers
and including in the tunica media of arterioles and venules of ureter and urinary bladder, in a clear cytoplasmic staining in brown. In group I the mean values of indicators of thickness of muscle fibers in arterioles and venules of ureter were respectively (2,19±0,229)×10-6m and (1,38±0,189)×10-6m; in urinary bladder – (2,92±0,207)×10-6m and (2,11±0,160)×10-6m. In group II the mean values of indicators of thickness of muscle fibers in arterioles and venules of ureter were respectively (1,67±0,270)×10-6m and (0,88±0,107)×10-6m; in urinary bladder – (2,20±0,198)×10-6m and (1,49±0,239)×10-6m. Analyzing and comparing the obtained values, it was observed that in group I and II was determined significant predominance (р0,05) were absent. In group II in ureter and urinary bladder was a significant (р
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/213
10.17629/www.diagnosticpathology.eu-2016-8:213
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/213/367
Copyright (c) 2016 I. Gorianikova, I. Sorokina, M. Myroshnychenko
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/66
2018-06-19T09:01:16Z
dpath:RES
The detection of human papilloma virus 16 L1 capsid protein and p16 in cervical lesions
Uranbolor, Jugder
Erdenetsogt, Dongobat
Galtsog, Lodon
Sarantuya, Jav
Immunohistochemistry; Human papillomavirus; Cervical cancer; p16
BackgroundCervical cancer is the second most common type of cancer in women worldwide and also the second most common female malignancy in Mongolia. The association of p16 and hr-HPV in Asia and in more particular in Mongolia are still relatively unexplored. So we aimed to detect the immunohistochemistry expression of p16 and L1 protein of HPV16 and to investigate the combined expression of these markers in cervical lesions.MethodsA total of 96 cases were selected from the records of Pathology services, National Cancer center of Mongolia. There were 50 cases diagnosed as LSIL and 46 cases diagnosed as HSIL. The immunohistochemical staining with p16 and HPV 16 L1 were done on all cases.ResultsThe positive rate of HPV 16 L1 capsid protein was identified 74% in LSIL cases and 52% in HSIL cases.There were a significant difference for HPV16 in HSIL and LSIL groups.Immunohistochemistry of p16 staining shows 76% in LSIL cases and 72% in HSIL cases. There was not a statistically significant difference for p16 in HSIL and LSIL groups. A chi square test was used to analyze the result and the obtained p value was <0.05.ConclusionThe combination between hr-HPV and p16 is considered to be more useful, having a higher accuracy than hr-HPV or p16 alone. There is still critical need, to find other molecular surrogate markers, which can provide accurate information about which precursor lesions would progress toward cancer.Â
DiagnomX GmbH
2015-09-05
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/66
10.17629/www.diagnosticpathology.eu-2015-1:66
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/66/57
Copyright (c) 2015 Erdenetsogt Dungubat, J. Uranbolor, L. Galtsog, B. Jav, J. Sarantuya
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/229
2018-06-19T08:55:24Z
dpath:SY01
Classification of Degree of Differentiation of Colorectal Neoplasm by Changes in the Betti Number
Nakane, K.
Takiyama, A.
Introduction/ Background
The diagnosis of pathology provides important information for determining the treatment protocol,
but other than in developed countries, the number of pathologists is not sufficient. Even where the number is sufficient, they are often unevenly distributed, with most pathologists in large hospitals in metropolitan areas, and adequate services cannot be provided to all patients. For this reason, it is desirable to develop ways to allow for remote diagnosis or to develop automatic diagnostic systems. Digital diagnostic systems based on pattern-recognition techniques have been developed. Because the morphology of cancer tissue is quite complex, a library of all types of cancer morphology would be huge, it would require a high-performance computer system, and the costs in money and time would be very high. This makes it difficult to create an effective system.
Aims
Recently, a new method based on the homology theory for analyzing histological digital images has been developed. The method evaluates the Betti numbers in a unit area of an image of a colon to determine the region of interest (ROI). The Betti number is an important index for homology theory, and can be used to assess the degree of connectivity in tissue. This method, however, cannot distinguish between different types of tissue. When a tumor forms in the colon, because of the excessive growth of nuclei, the connections increase and become tight. The absolute value of b1 (the one dimensional Betti number) will be high, and the ratio of change will be small. When a tumor becomes more poorly differentiated, it frequently happens that the ties between the cells are weakened, and the intercellular areas are filled with impurities. Because of these impurities, the absolute value of b1 is very high. Its influence, however, will disappear immediately. Namely, b1 decreases very quickly, when we decrease the binarizing threshold. We calculate the decay ratio of the betti number, by changing the binarized thresholds. Our aim in this talk is that using this information, we will classify the degree of differentiation of colorectal neoplasm.
Methods
In the colon, cancerous regions show stronger color intensity when stained with hematoxylin. This stains blue, and so the distribution of blue in an image indicates the cancerous areas. Thus, for each image, we measured the peak of the blue distribution, and we will refer to it as the reference value. To determine the binarizing threshold, we multiplied the reference value by 0.55 to 0.72, in increments of 0.01. The binarization was carried out in gray scale using these values. We call this interval the reference interval. We may assume that there was no pathological information outside of the reference interval.
Results
The calculated results can be approximated by quadratic functions. The distribution of the coefficient on the squared term and the x-coordinates of the vertices are shown. We can see a characteristic distribution for each type of cancerous tissue. As the binarizing threshold decreases, the images gradually fade to white, and the structure of the tissue is lost. Under the proposed procedure, in areas where the connections in the tissue are tight and clear, b1 changes slowly. Conversely where the connections are vague, such as in a background area filled with impurities, it changes very quickly. The state of this change can be considered an expression of the strength of the connectivity, and it differs by type of cancerous tissue.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/229
10.17629/www.diagnosticpathology.eu-2016-8:229
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/229/384
Copyright (c) 2016 K. Nakane, A. Takiyama
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/104
2019-08-22T16:09:26Z
dpath:RES
Novel anti-human Axl monoclonal antibodies for improved patient biomarker studies
Ahmed, Lavina
Kiprijanov, Sergej M
nalwoga, Hawa
Wnuk-Lipinska, Katarzyna
Haugen, Hallvard
Lorens, James B
Akslen, Lars A
Micklem, David Robert
Monoclonal antibodies; cancer; EMT; diagnostic biomarkers; Axl; ELISA; IHC; Western blot
Background: Axl receptor tyrosine kinase has been associated with poor clinical outcome in a wide variety of malignancies including breast, lung, prostate, pancreatic, brain and myeloid cancers. Axl is up-regulated during tumour epithelial-to-mesenchymal transition (EMT) and is associated with metastasis, immune evasion and drug resistance.Methods: The aim of this study was to develop improved assays for detection of Axl protein in patient samples. We developed a panel of mouse monoclonal antibodies directed against the extracellular domain of human Axl, from mice immunized with a recombinant antigen comprising the extracellular domains of human Axl fused to human IgG1 Fc domain. Anti-Axl monoclonal antibodies (MAbs) were assessed for sensitivity, specificity and utility using surface plasmon resonance (SPR) analysis, sandwich enzyme-linked immunosorbent assay (ELISA), Western blot analysis and immunohistochemistry (IHC) staining.Results: One of the anti-human Axl MAb,1H12, performed particularly well, and SPR analysis confirmed both high affinity (50 pM) and high selectivity for Axl versus other Axl-family receptors. In IHC applications on selected human carcinomas and cancer cell line pellets, MAb 1H12 showed improved sensitivity and reduced background staining compared to other members of the MAb panel. A second MAb 5F11 showed very high affinity (5.8 pM) at a non-overlapping epitope and was selected as a partner for 1H12 in sandwich ELISA, producing a highly sensitive and specific assay.Conclusion: MAbs 1H12 and 5F11 represent new anti-human Axl monoclonal antibodies for improved patient biomarker studies.
DiagnomX GmbH
Research Council of Norway
2016-04-20
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/104
10.17629/www.diagnosticpathology.eu-2016-2:104
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/104/114
Copyright (c) 2016 Lavina Ahmed, Sergej M Kiprijanov, Hawa nalwoga, Katarzyna Wnuk-Lipinska, Hallvard Haugen, James B Lorens, Lars A Akslen, David Robert Micklem
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/254
2019-08-22T15:38:41Z
dpath:RES
Predatory Journals, Science Citation Index and Open Access Publications in Diagnostic Pathology
Kayser, Klaus
Borkenfeld, Stephan
Kayser, Gian
Background: Predatory behavior in open access peer reviewed scientific journals seems to be increasing. It is subject to serious discussions between editors, authors, and publishers. Herein we discuss some characteristics of electronic communication in science, the reasons for potential misuse, and present some entropy calculations.Theoretical considerations: Publication of research articles uses visual information transfer, and seldom acoustic communication. Advantages of open access electronic journals include prompt and worldwide distribution, free access, and several free re-use rights. Disadvantages might be seen in non congruent business models of authors and publishers, which include impact of financial issues on scientific quality and easy to perform, hard to detect manipulation of published data and their sources.Present stage: Citation Index (SI) and Journal Impact Factor (JIP) are the principal sources which are thought to guarantee the article’s quality and author’s prestige. Authors try to publish in and publishers try to offer journals with high SI and JIP. Independent review processes should serve to maintain the article’s quality. Reviewers are invited electronically in both conventional paper printed and electronically distributed journals. They are requested to act at their earliest convenience. Reviews are as all fast electronic information distribution exposed to become manipulated, in politics, commerce, and science as well.Proposal and perspectives:Electronic information exchange uses properties of virtual reality, which include the reversibility of time. They are scalable events and can be measured by an appropriate entropy concept. Authors can be considered information source that should be understood by the readers (receiver). The higher the information content the more precise is the reaction of the receiver. The readers’ reaction can be measured and be used to classify, modify, correct, or even erase the distributed information. The development of appropriate readers’ tools would improve the quality and originality of the article and journal. Conclusion: A readers’ oriented model would be an appropriate extension of quality assurance for open access journals and articles. Such a model could be based upon the entropy concept and be a reliable measure of research quality and impact on its future development.
DiagnomX GmbH
2017-12-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/254
10.17629/www.diagnosticpathology.eu-2017-3:254
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/254/550
Copyright (c) 2017 Klaus Kayser, Stephan Borkenfeld, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/127
2018-06-19T09:15:48Z
dpath:EP
Experiments In Extracting Digital Slides From Video
Della Mea, Vincenzo
Turetta, M.
Nobile, M.
Pilutti, David
Introduction/ BackgroundWhile digital pathology systems are becoming more and more affordable and thus diffused, for occasional, non diagnostic acquisitions (e.g., teaching) it might not be economically viable to buy a scanner. In addition to that, it is relatively common that videos from microscope are published for teaching purposes in particular in fields related to medical imaging [1]. Recently, a research group published a series of papers related to digital slide acquisition from non-automated microscopes [2]2 , [3]3. The developed technique allows to reconstruct a digital slide starting from a video flow acquired during slide examination. The proposed method seems interesting, and stimulated us in investigating further alternatives. In fact, the proposed process very closely resembles the creation of panoramas from multiple pictures through stitching, or the simulation of medium format photog- raphy through the Brenizer method [4] . AimsAim of the present work is to explore techniques for extracting digital slides from microscope video record- ings, possibly using already available and open source software.MethodsWe searched for panorama stitching software and found a number of packages, including a widely used open source software (Hugin) [5] . We concentrated on it and on a commercial product (AutoPano). We designed a two steps experiment:1)   For a first approach, we decided to use a screencast of a digital slide. This to reduce the possible sources of error, and also to have a gold standard to compare with.2)  At a second step, we recorded video from a microscope (Olympus Provis AX70) using a commercial camera (Sony Nex-6) on an easily replicable hardware setup (fig.1).We devised a sequence of steps to obtain digital slides as if they were panoramas recorded in video. This included pre-processing of the video source, and selection of parameters of the software for best reconstruction ResultsThe designed workflow include:record a video from the microscope while browsing a case, taking care in covering the whole sample in a continuous way.Transform the video in a sequence of images to feed the stitching software. This can be done with free software like ffmpeg and derivatives. It is not needed to have every frame of the video: the number is related to the speed of examination. In our experiment, 2-4 frames per second have been sufficient.With Hugin (or AutoPano), open all the images and set them as if they were captured with a teleobjective with very long focal length (e.g., 1000mm). This to minimize abherrations in reconstruction. Figure 1 shows a digital slide obtained with Hugin from digital microscope screencast; figure 2 shows a digital slide obtained from a real microscope. The former is much better, and this indicates a possible way for occasional scanning. Open issues include:the method should be validated by comparing with a gold standard, like a digital slide of the sample;if the focus position changes during the video, focusing should occur and further processing could be needed for applying also focus stacking to the operations.While looking at a slide at higher magnifications, it is difficult to ensure to visit the whole sample during visualization. From this point of view, the realtime implementation presented in [2] allows for continu- ously checking what it has been acquired.This work has been partially founded by the EU FP7 program within the Marie Curie Project “AIDPATHâ€, grant number 61247   Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/127
10.17629/www.diagnosticpathology.eu-2016-8:127
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/127/264
Copyright (c) 2016 V. della Mea, M. Turetta, M. Nobile, D. Pilutti
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/269
2019-08-22T14:50:39Z
dpath:the
Digital Image Content and Context Information in Tissue-based Diagnosis
Kayser, Klaus
Borkenfeld, Stephan
Kayser, Gian
Background and definitions: Image content information (ICI) comprises the information that an external observer can extract solely from the image itself, i.e., without additional notifications (labels, classification, etc.). Image analysis is the procedure to extract meaningful information from the image. It is an important issue in digital pathology and the prerequisite to implement algorithms of diagnosis assistance. Meaningful information (IMI) comprises the information which the observer can understand or which is transformed into an information related reaction. It corresponds to regions of interest (ROI). Pixel and gray value create all information of a digitized image. The spatial distribution of pixel gray values is called texture. Objects are externally defined pixel clusters; their spatial distribution forms a structure.Living organisms are limited spatially circumscribed systems which are included in external environment and possess an unstable inner volume. Development and limited stability of these open thermodynamic systems are guaranteed by their environment and additional not overlapping inner equivalent systems, which build the so - called hierarchically order of structures. Interaction between objects might alter appearance, development, appearance of new or disappearance of existing objects. The interactions are commonly called functions. They are equivalent to communication and based upon different ‘carriers’ such as electromagnetic signals, macromolecules, salt concentrations, etc.Detection and description of structures depend upon the observer time. The application of visible macromolecules which bind to boundaries of structures might detect and forecast changes of the boundaries, i.e. structures. The intensity of the visibility and its distribution reflect to the thermodynamic affinity. Detailed analysis of gray value intensities might allow an insight in thermodynamic properties of structures.Context is defined as information which can be derived from and added to object and structure related information, and, vice versa, might be applied to predefine the observer information capability which is needed to understand the ‘meaning’ of an image, or to select the most capable observer.Perspectives: The described algorithm is an appropriate tool to combine computerized image content information with its computerized ‘observer’ system. It will be able to measure, acquire, understand and to transfer image content information in an adequate reaction, i.e. diagnosis.
Tuberculosis
Fibrosis
DiagnomX GmbH
2018-12-21
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/269
10.17629/www.diagnosticpathology.eu-2018-4:269
Diagnostic Pathology; Vol 4 No 1 (2018): 2018
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/269/561
Copyright (c) 2018 Klaus Kayser, Stephan Borkenfeld, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/138
2018-06-19T09:28:00Z
dpath:SY01
Image Analysis Approach To Distinguish Lobular Structures In The Mammary Gland From Well-Differentiated Breast Cancer With Tubule Formation
Grote, Anne
Schaadt, N. S.
Feuerhake, F.
Introduction/ BackgroundAutomated detection of diagnostically relevant regions of interest (ROI) is one of the major challenges in medical image analysis. In digital pathology using whole slide images (WSI), the detection of certain biological structures is necessary, because the capacity for analysis of cells and subcellular structures at high resolution is limited by available processing time and computational power. For some applications it is also important to exclude irrelevant or misleading components of the image. One important challenge of this type is well differentiated (low-grade/G1) breast cancer.AimsWe aim at automatically distinguishing non-malignant lobular tissue from well-differentiated breast cancer to avoid erroneous evaluation of normal tissue in the detection of nuclear hormone receptor expression. A second goal of lobule detection is to exclude inflammation of non-malignant pre-existing structures from tumor immune cell scoring of breast cancer in oncoimmunology.MethodsTwo approaches for lobule detection were applied: The first includes modules of own image analysis algorithms developed specifically for lobule detection combined with elements of a commercially available software platform (Definiens Developer®), and the second is a software package optimized for use with a multispectral camera system (Inform, Perkin-Elmer ®). Breast cancer samples were stained for estrogen receptor (ER), progesterone receptor (PR) and the lymphocyte marker CD8. The first approach starts with a texture-based supervised classification to detect lobule candidate regions and uses a nuclear density image to refine the candidate regions. The second approach uses a supervised machine learning method whose features and algorithm are not disclosed to the user. Manual annotations of lobular tissue by expert pathologists were used for evaluation of results.ResultsThe accuracy of distinction between cancer areas and lobular structures decreased in cases with prominent glandular differentiation of the tumor. The major challenge was the separation of well-differentiated (G1) breast cancer with consistent hormone receptor expression from adjacent lobular areas. The second approach performed well on high-grade tumors and had advantages regarding speed and its convenient user interface. The modular first approach was superior on ER and PR images and successfully detected lobular areas even if the anatomical structure was disrupted by inflammation of infiltrating cancer cells. We conclude that modular approaches considering image context and allowing specific adjustments to the tissue of interest may be needed to overcome current limitations of automated ROI detection in clinical biopsy materials.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/138
10.17629/www.diagnosticpathology.eu-2016-8:138
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/138/292
Copyright (c) 2016 A. Grote, N. S. Schaadt, F. Feuerhake
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/155
2018-06-19T09:10:31Z
dpath:CAD
Automated Image Analysis Of Her2 Fish Enables New Definitions Of Genetic Heterogeneity In Breast Cancer Tissue
Radziuviene, G.
Rasmusson, Allan
Augulis, R.
Lesciute-Krilaviciene, D.
Laurinaviciene, A.
Clim, E.
Laurinavicius, Arvydas
Introduction/ BackgroundTherapy decisions for breast cancer rely on human epidermal growth factor receptor 2 gene (HER2) amplification testing. The HER2 status of tumors is primarily established by immunohistochemistry; borderline (2+) cases undergo further testing by fluorescence in situ hybridization (FISH). Current guidelines state that HER2 amplification is determined from manual counts of HER2 and CEP17 signals in 40 nuclei per case with an additional 20 nuclei in equivocal cases. The definitions are based on expert opinion rather than on objective statistical inference; they are complex, involving different quantities and cut-offs all at once (the signal counts and their ratio, proportion of cells amplified) and hard to follow. Automated image analysis (IA) extracts data from hundreds of nuclei and can aid HER2 testing in borderline cases.AimsWe therefore explored if objective, statistically-derived indicators of HER2 heterogeneity can be obtained from automated HER2 FISH IA data.Methods50 cases of female invasive ductal breast carcinoma with HER2 2+ immunohistochemistry status, evaluated by the standard manual FISH methodology, were subjected to IA. The IA, developed using StrataQuest (TissueGnostics,Austria), segmented and counted individual nuclei and HER2 and CEP17 signals. A range of 192 to 789 nuclei per tumor were evaluated by the IA. All segmented nuclei and FISH signals were inspected manually for quality assurance and accuracy estimates. Bimodality indicator (Ashman’s D) was computed for HER2 signal and HER2/CEP17 ratio in individual cells and included in factor analysis along with the data from manual and automated HER2 FISH analyses.ResultsNo significant bias was found between the automated and manually corrected HER2 FISH nuclei or signals, obtained by IA. However, the manual HER2, CEP17 counts and HER2/CEP17 ratio were significantly underestimated by the automated procedure due to differences in cell selection in the techniques. By formal criteria (Ashman’s D>2), 5 cases were classified as bimodal by HER2/CEP17 ratio and 23 cases by HER2 counts. Of those, 3 and 18 cases, respectively, were not amplified according to the cutoff of HER2/CEP17<2 by manual procedure. Factor analysis of the data set extracted 3 intrinsic factors of variation, representing amplification, “polysomyâ€, and bimodality. Importantly, the factor scores could be seen as “purified†indicators independent of well-known interactions between the absolute counts of HER2 and CEP17 signals per cell and their ratios. Therefore, the tumor cases may be independently characterized by the three vectors. Remarkably, the distribution of the tumors by the bimodality factor scores revealed a distinct peak of “highly bimodal†cases, suggestive of the possibility of robust stratification of the patients according to the bimodality indicators. We conclude that analysis of continuous HER2 FISH data obtained by IA enables new strategies for evidence-based stratification of heterogeneous breast tumors. In particular, indicators of bimodality of cell distribution according to their HER2 FISH signals may be useful in detection of heterogeneous cell populations, along with the currently used criteria based on cell proportions at a certain amplification cutoff. While clinical validity remains to be tested, we suggest that detection of bimodal distribution of cells can serve as robust, evidence-based stratification and decision support tool, highlighting potentially heterogeneous tumors.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/155
10.17629/www.diagnosticpathology.eu-2016-8:155
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/155/170
Copyright (c) 2016 G. Radziuviene, A. Rasmusson, R. Augulis, D. Lesciute-Krilaviciene, A. Laurinaviciene, E. Clim, A. Laurinavicius
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/171
2018-06-19T09:09:06Z
dpath:STD
A Review On International Guidelines For Digital Pathology
Garcia-Rojo, M.
Introduction/ BackgroundPathologists are looking at digital pathology not as much as an efficient telepathology solution but as an instrument to improve the quality and efficiency of their own daily clinical work beyond the use of the conventional microscope. The term digital pathology (DP) should also include interoperability and workflow considerations, and basic technical aspects of whole slide imaging (WSI), messaging, and standards should be also known by pathologists.AimsThe aim of this study is reviewing the technical features of WSI systems in existing guidelines available internationally.MethodsThe following guidelines and technical documents have been evaluated:College of American Pathologists (CAP), 2013: ValidationAmerican Telemedicine Association (ATA), 1999: TelepathologyDigital Pathology Association (DPA), 2011. First WSI guidelineFood and Drug Administration (FDA).Canadian Association of Pathologists (CAP-ACP).Centers for Medicare & Medicaid Services (CMS/ CLIA).Centers for Disease Control and Prevention (CDC/ CLIAC).Society of Toxicologic Pathology (STPath).European Commission (EU-EC).Spanish Society of Anatomic Pathology (SEAP-IAP).The Royal College of Pathologists (RCP).The Royal College of Pathologists of Australasia (RCPA).ResultsSince February 2015, a draft of Technical Performance Assessment of Digital Pathology Whole Slide Imaging Devices from FDA is available. Regarding display (monitor), a complete description of the display, graphics cards, and control software items to be considered are included (display technology [LED, LCD], color calibration, ambient light sensors,..) although there is no mention to refresh rate). In the College of American Pathologists (CAP) Digital Pathology Resource Guide, references to guidelines or position papers other than CAP guidelines are dispersed in other sections of this document. Hanna et al (2015) reviewed existing guidelines and position statements for digital pathology, with special attention to validation and telepathology. Evans et al (2014) made a comparison between American Telemedicine Association (ATA), Royal College of Pathologists (RCP) and Canadian telepathology guidelines. In summary we could find the following topics in the corresponding guidelines: System architecture was only mentioned in SEAP document. Components of DP system: ATA, DPA, FDA, SEAP, STPath. Badwith/Network: ACP, DPA, SEAP. Interoperability: ATA, ACP, CLIA, DPA, SEAP, STPath. Scanning speed: ACP, DPA, SEAP; Storage: ATA, DPA, RCP, SEAP. Image quality in WSI: ACP, DPA, RCP, SEAP; Image compression and processing: ATA, EU-EC, DPA, SEAP. Conclusions:Some basic technical features of a WSI systems that are of high interest to pathologists are scanning speed (e.g. 1-2 minutes 20x), autoloader capacity (100 slides), image quality (resolution 0.25-0.50 µ/ pixel) rescanning rate (<5%), image compression (<70%), monitor quality (30 inches 4-8 MPx),and viewing experience (refresh rate, network bandwith).In primary diagnosis, we need some new regulations also in European countries.Acknowledgment:This work has been supported by the AIDPATH project, an EU 7FP IAPP Marie Curie action, contract number 612471Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/171
10.17629/www.diagnosticpathology.eu-2016-8:171
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/171/298
Copyright (c) 2016 M. Garcia-Rojo
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/187
2018-06-19T09:09:45Z
dpath:EL
Virtual Patients And Serious Games In Medicine
Siregar, P.
Julen, N.
Introduction/ BackgroundSerious games (SGs) are immersive learning and training tools. They have gained a widespread interest worldwide and are gaining ground with respect to formal education. Most serious games follow a learn-by-doing pedagogic principle. One of the main advantages of this approach resides in the fact that people retain 90% of what they do as opposed to 10% of what they read [1]. It is also a very efficient means to transform theory into best practices and promote problem-solving competencies. SGs can be developed to diagnose virtual patients that incorporate real data. The educational goals should include: (i) how to make the most out of the patient history and the physical examination by notably acquiring a good knowledge of pathophysiology, (ii) request tests/ exams that are the most appropriate with the current differential diagnosis (iii) interpret the tests/exams results within a global patient view.AimsWe describe diagnostic concepts that can be incorporated in serious games dedicated to medicine. Diagnosis can be modeled as an iterated hypothetico-deductive loop (HDL): collect/elicit patient data, evaluate them, establish a differential diagnosis, repeat the HDL if needed. The initial steps of diagnosis consist of assessing the chief complaints and proceeding to a thorough history [2]. The differential diagnosis allows the physician to focalize his/her attention on specific body regions and anatomical systems during the physical examination leading to (perhaps) more specific hypotheses. When more than one hypothesis remains, diagnosis can be refined by requesting complementary exams leading to a new HDL. An IT approach to diagnosis can be built around the combination of expert heuristics[2], pathophysiology[3] and concepts burrowed from evidence-based medicine (EBM) [4][5], where decisions are based on weighted evidence. The generation of hypotheses during the initial steps is based on the prevalence of diseases that allow estimating prior probabilities. Post-test probabilities can then be established at the end of each HDL. Where appropriate, the choice of complementary exams will depend on two strategies: attempt to confirm the most probable hypotheses (given the current evidence) and attempt to refute potentially high-risk hypotheses. In short, this means selecting of exams that are specific (for confirmatory purpose) and/or sensitive (for refutation purpose). In Digital Pathology (DP), these considerations can help learners evaluate the cost of making false-positive and false-negative errors. For instance, a false-negative error in the context of a high-risk disease can be costly to the patient. Hence a global understanding of the patient case and a risk assessment of the competing hypotheses can help students in DP stratify the search of regions of interests (ROI) because they would know what image features they should attempt to confirm or refute first.ResultsWe are currently developing a technology platform dedicated to the realization of serious games in medicine. It incorporates generic reasoning modules that can combine expert heuristics, pathophysiology with concepts of EBM. Since annotated DP WSI can be integrated within the patient cases, such tools will contribute to illustrate (i) how applied sciences, medical devices and information technologies have become an integral part of modern medicine, and (ii) how each piece of information can contribute to an integrated approach to patient diagnosis and treatment.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/187
10.17629/www.diagnosticpathology.eu-2016-8:187
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/187/316
Copyright (c) 2016 P. Siregar, N. Julen
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/208
2019-08-22T16:03:15Z
dpath:RES
Cy-TEST - A new platform for training and testing in cytopathology
Lianas, Luca
Piras, Marco Enrico
Musu, Elodia
Podda, Simona
Frexia, Francesca
Ovcin, Emanuela
Bussolati, Giovanni
Zanetti, Gianluigi
elearning; telepathology; cytopathology; virtual microscopy
Introduction/ Background: Clinical training at the European level requires flexible ways to provide education across borders with the goal of a unified way to teach and assess quality. The Cy-TEST project focuses on Cytological Training at European Standard through Telepathology. The project (2014-1-IT01-KA202-002607) has been approved and funded in 2014 by EU within the ERASMUS+ Program. The project consortium is composed of 4 leading university Institutions (COREP and University of Turin, University of Padua, Imperial College of London, IPATIMUP/University of Porto and University of Graz) with technological development and support provided by CRS4. In addition, it benefits from the collaboration of International Organizations (EFCS, Eurocytology, OME) and is open to contributions from additional groups and Societies.Aims: Our aim was the establishment of a platform for the sharing of digital pathology images and of an auxiliary system that will use the latter platform for the distribution of cytologist training courses with an integrated virtual microscopy capability.Methods: The Cy-TEST platform is based on the integration between Moodle, an e-learning platform designed to create personalized learning environments, and OME OMERO, a well-known open source software for visualization, management and analysis of biological microscope images. The former is used to provide access to a database of questions produced by specialized trainers and the latter provides access to digital pathology images and related metadata. We chose to base our infrastructure upon Moodle because it is one of the top leading platform for online education with a large community of users across both academic and enterprise level, highly customizable and modular. OMERO was chosen because of its compatibility with a large number of image formats for digital pathology images, its handling of image metadata (i.e., TAGs and Regions of Interest) and its easily extensible web platform.Results: The web platform can be used with a wide range of devices, it is compatible with most of the image formats produced by digital slides scanners and it can scale to a wide student body. Teachers can create courses, populate the Question Bank and aggregate questions in quizzes, while students can take classes and tests. When creating questions, teachers can choose images previously loaded and annotated. We provide two new types of questions: multiple choice, focused on an image and its ROIs, and interactive, where students identify areas on the image by markers that will be automatically compared to instructor’s specified ROIs. The currently deployed system holds already a set of several hundreds of images classified by categories (e.g., tissue type and diseases) with associated ROIs identified by pathologists. The Cy-TEST platform provides a full technological solution for a more homogeneous training and testing of cytotechnicians and cytopathologists with uniform quality level assurance mechanism. The system could be easily extended to support the teaching of histopathological diagnosis. Moreover, the Cy-TEST platform paves the way to an e-QUATE test, thus providing an efficient and economical way to replicate the test at European scale (see Branca et al., 2000). The sustainability of the platform and the supported educational material (images, questions and evaluation algorithms) will be guaranteed by its integration in EFCS activities. We expect to distribute the Cy-TEST System for validation by October 2016, for further information contact infocytest@corep.it.
DiagnomX GmbH
CRS4
COREP
2016-08-29
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/208
10.17629/www.diagnosticpathology.eu-2016-2:208
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/208/347
Copyright (c) 2016 Luca Lianas, Marco Enrico Piras, Elodia Musu, Simona Podda, Francesca Frexia, Emanuela Ovcin, Giovanni Bussolati, Gianluigi Zanetti
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/57
2018-06-19T09:06:22Z
dpath:CAS
Metastatic embryonal rhabdomyosarcoma to the breast: a case report and review of the literature
Zioga, Christina
Destouni, Chariklia
breast, rhabdomyosarcoma, metastasis, fine needle aspiration, cytology
A 19-year-old fertile Caucasian female, with a medical history of embryonal rhabdomyosarcoma in the left upper extremity at the age of 17, presented with enlarged lymph node of left axilla. Fine needle aspiration (FNA) cytology of axillar lymph node revealed a metastatic malignant neoplasm, consistent with the primary embryonal rhabdomyosarcoma. Four months later, breast clinical examination revealed the presence of multiple hard and immobile masses located in both breasts. Ultrasound detected multiple opacity areas and ultrasound-guided FNA cytology was performed on two bilateral breast lumps. The final cytology diagnosis of FNA -using ThinPrep® technique- was “Positive morphologic and immunocytochemistry findings of metastatic malignant neoplasm of mesenchymal origin, consistent with patient’s history-embryonal rhabdomyosarcomaâ€. Today the patient is under first line chemotherapy and in good physical condition.
DiagnomX GmbH
2015-07-21
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/57
10.17629/www.diagnosticpathology.eu-2015-1:57
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/57/45
Copyright (c) 2015 Christina Zioga, Chariklia Destouni
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/224
2018-06-19T08:58:25Z
dpath:SY01
Micrometastasis Detection Guidance by Whole-Slide Image Texture Analysis in Colorectal Lymph Nodes
Venâncio, R.
Ben Cheikh, B.
Coron, A.
Saegusa-Beecroft, E.
Machi, J.
Bridal, L.
Racoceanu, D.
Mamou, J.
Introduction/ Background
Cancer is a disease that affects millions worldwide and accurate determination of whether lymph nodes (LNs) near the primary tumor contain metastatic foci is of critical importance for proper patient management. Histopathological evaluation is the only accepted method to make that determination. However, the current standard of care only examines a single central histological section per LN and yields an unacceptable false-negative rate.
Aims
To help pathologists in their examination we propose a method that extracts textural features from histopathological LN whole slide images (WSI) and then applies support vector machines (SVMs) to automatically identify regions suspicious for metastatic foci.
Methods
The database consisted of WSI from 44 LNs. Sections were stained with hematoxylin-eosin and examined at 20x (0.45μm resolution). Twenty-eight of the LNs were identified by an expert pathologist as positive for cancer (P), and the remaining sixteen were negative (N). This database was divided into two groups. Group 1 (15P and 5N) was used for training and Group 2 (13P and 11N) was used for testing the classification technique. For all analysis each WSI was divided into non-overlapping 1000 x 1000 pixel sub-images that will be referred to as high-power fields (HPFs). For each LN in Group 1, at least one WSI was annotated by a pathologist to identify rectangular, HPF-scale regions as locally cancerous or locally non-cancerous. From these annotated slides, 924 HPFs (462 P and 462 N) were obtained. For each of these HPFs, statistical features based on gray-level co-occurrence matrices [1] and Law’s texture energy measures [2, 3] were extracted from 9 derived images [4]. The extracted features were submitted to a sequential forward selection (SFS) method [5] to select few non-redundant features providing best class separation (cancerous vs. non-cancerous region). Combinations of the selected features were tested on the 924 HPFs using k-fold cross-validation to find those that produced the best results and consequently to train our SVM-based classifier. In Group 2, WSI were not annotated for cancerous and non-cancerous zones on a HPF scale. Each LN, however, had been labeled by a pathologist as positive or negative for cancer. For each WSI, each section was divided into contiguous HPFs, and those which mainly contain fatty tissue, background, and tears were automatically excluded. Each selected HPFs was classified as cancerous or non-cancerous using the previously trained classifier to obtain the total number of cancer-classified per LN. A receiver operating characteristics (ROC) curve was traced by changing the discriminator threshold (T) used to label the LN as P for cancer as a function of the total number of cancer-classified HPFs.
Results
During training, 5 Laws features were selected by SFS. Highly satisfactory k-fold cross-validation with a F-score of 0.996 ± 0.005 was obtained using only 2 statistical features computed at different scales. The ROC curve obtained by applying the SVM-classifier to the test set is shown in the next figure. Two valuable operating points can be identified which both guaranteed no false-negative. At T=11 we got 2 false-positives and an optimal F-score of 0.917, and with a more conservative approach, T=1, we got 7 false-positives and a F-score of 0.759. The top-left part of the slide displayed in next figure would have been proposed to the pathologist as the most suspicious region of the cancerous LN.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/224
10.17629/www.diagnosticpathology.eu-2016-8:224
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/224/379
Copyright (c) 2016 R. Venâncio, B. Ben Cheikh, A. Coron, E. Saegusa-Beecroft, J. Machi, L. Bridal, D. Racoceanu, J. Mamou
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/94
2018-06-19T09:04:46Z
dpath:HYP
Is there an association between date of birth and date of death? A statistical investigation on exit and transcendence into the eternal world
Fatu, Constatin
Moscu, Mihaela
Vascu, Bogdan
Fatu, Ana Maria
association date of birth and death; geneticaly programmed death; civil tomb; military tomb
The idea of this study came out long time ago, in relation to some personal unfortunate events. I have extended my research on 10000 funerary inscriptions and documents from civil and military tombs to find out if the relation between the date of birth and the date of death  is significantly correlated . Our findings point out that in about 75% cases the date of death is up to 2 months before or after the date of birth. This suggests a genetic determinism of death moment.
DiagnomX GmbH
Constantin Fatu, Department of Anatomy and Embriology, Apollonia University, Iasi, Romania
2016-01-18
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/94
10.17629/www.diagnosticpathology.eu-2016-2:94
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/94/101
Copyright (c) 2016 Ana Maria C. Fatu, Constantin I. Fatu, Mihaela G. Moscu, Ion C. Fatu, Bogdan M. Vascu
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/248
2019-08-22T15:52:52Z
dpath:RES
Cognitive Algorithms and digitized Tissue – based Diagnosis
Görtler, Jürgen
Kayser, Klaus
Borkenfeld, Stephan
Carvalho, Rita
Kayser, Gian
Aims: To analyze the nature and impact of cognitive algorithms and programming on digitized tissue – based diagnosis.Definitions: Digitized tissue – based diagnosis includes all computerized tissue investigations that contribute to the most appropriate description and forecast of the actual patient’s disease [1]. Cognitive algorithms are programs that encompass machine learning, reasoning, and human – computer interaction [2].Theoretical considerations: Digitized blood data, objective clinical findings, microscopic, gross, radiological images and gene alterations are analyzed by specialized image analysis methods, and transferred in numbers and vectors. These are analyzed by statistical procedures. They include higher order statistics such as multivariate analysis, neural networks and ‘black box’ strategies, for example ‘deep learning’ or ‘Watson’ approaches. These algorithms can be applied at different cognitive ‘levels’, to reach a digital decision for different procedures which should assist the patient’s health condition. These levels can be grouped in self learning, self promoting, self targeting, and self exploring algorithms. Each of them requires a memory and neighbourhood condition. Self targeting and exploring algorithms are circumscribed mechanisms with singularities and repair procedures. They develop self recognition. Consecutives: Medical doctors including pathologists are commonly not trained to understand the basic principles and workflow of applied or potential future procedures. At present, basic medical data only serve for simple cognitive algorithms. Most of the investigations focus on ‘deep learning’ procedures. The applied learning and decision algorithms might be modified and themselves be used for ‘next order cognitive algorithms’. Such systems will develop their own strategies, and become independent from potential human interactions. The basic strategy of such IT systems is described herein.Perspectives: Medical doctors including pathologists should be aware about the abilities to enhance their work by supporting tools. In some case the users may not be able to fully understand these tools. Furthermore, these tools will probably become self learning, and, therefore, seem to propose the daily workflow probably without any medical control or even interaction.
DiagnomX GmbH
2017-07-28
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
application/xml
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/248
10.17629/www.diagnosticpathology.eu-2017-3:248
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/248/537
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/248/538
Copyright (c) 2017 Jürgen Görtler
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/122
2018-06-19T09:14:11Z
dpath:TP
Provincial Telepathology Networks And Their Connection Into National/Central Telepathology Network In China: A Result Analysis From 2012 To 2015
Zhou, Chen
Jiao, Y.
Zhang, Z.
Chen, J.
Introduction/ BackgroundIn recent years, telepathology has played an increasingly important role in pathology consultation/second opinion. SinceChinaimplemented a national/central telepathology network for cancer diagnosis in 2011, many provinces have also planned and implemented their own provincial or local telepathology networks.AimsWe here reported the provincial telepathology network and their operation from 2012 to 2015. We also reported their connection to national/central network.MethodsAll available provincial and local telepathology networks inChinawere surveyed. Only those provincial or local telepathology networks meet following criteria were included: (1) Network uses whole slide images and internet based platform technology; (2) Network sponsored or owned by provincial or local pathology quality control center; (3) Network currently functioning.ResultsFrom 2011 to Dec 2015, 6 provincial telepathology networks have been implemented. Xinjiang provincial network was set up in 2011 and connected to 40 local hospitals; Shandong provincial network (www.pathol- ogy.telemedicine.net.cn) was established in 2012 and connected to 50 local hospitals; Hainan provincial network (59.50.108.88) was set up in 2013 and connected to all 50 local hospitals in the province; Guangxi provincial network (www.gx.chinapathology.cn) was set up in 2013 and connected to 28 hospitals; Shenzhen city network (www.szcenter.cn) was set up in 2013 and connected to 15 local hospitals; Fujian provincial network (www.fj.mpathology.cn) was connected to 107 local hospitals. By 2015, 5 out of the 6 provincial networks have connected to national/central network. From 2012 to 2015, both national/central network and provincial networks provided pathology consultation for a total of 78,264 patients. Our survey indicated that in recent years multiple provincial telepathology networks have been set up in China. Through both national/central and provincial networks, telepathology consultation has played an important role in reducing diagnostic errors inChina.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/122
10.17629/www.diagnosticpathology.eu-2016-8:122
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/122/255
Copyright (c) 2016 C. Zhou, Y. Jiao, Z. Zhang, J. Chen
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/133
2018-06-19T09:14:47Z
dpath:EP
Accuracy Of Whole Slide Imaging Stack Alignment In Consecutive Sections Of The Carotid Artery
Lucas, Marit
Jansen, I.
de Boer, O.
van Leeuwen, T.
de Bruin, D.
Marquering, H.
Introduction/ BackgroundAtherosclerosis is a chronic inflammatory disease of middle-sized and large arteries, characterized by the accumulation of inflammatory cells, especially mac- rophages [1] . A detailed visualization of the presence and distribution of macrophages in the atherosclerotic plaque contributes to a better understanding of the pathogenesis of atherosclerosis and the onset of acute coronary syndromes after atherosclerotic plaque rup- ture. Three-dimensional (3D) reconstruction of histology sections has the potential to improve both the detection of lesions as well as understanding in plaque growth and destabilization.AimsThe objective of this study is to implement a image marker independent 3D histology reconstruction method in order to visualize the arteriosclerotic vessel and evaluate its accuracy.MethodsA dataset comprising 48 consecutive cross-sections with a slice thickness of 10µm of a formalin-fixed paraf- fin-embedded (FFPE) carotid artery was used. The slideswere double stained with monoclonal antibodies and were scanned with anOlympusdotSlide scanner with a 10x objective leading to 0.65 micron pixel size. In these images, the smooth muscle cells and macrophages were visualized in blue and red, respectively. Rigid, rigid & affine, and rigid & affine & b-spline (non-rigid) automatic stack alignment was performed using elastix, an open-source toolbox for alignment of images [2]. As a consequence of the image deformation in non-rigid approaches, the diagnostic accuracy might be hindered. Therefore a small bending energy, i.e., sum of the spatial second-order derivatives of the transformation, was al- lowed. In order to increase processing speed, the stack alignment was performed on downsampled data. An automatically determined mask of the vessel was used for pair-wise reconstruction of the vessel with re- spect to the middle slide that was chosen as a reference section. Accuracy was visually assessed using a surface plot of the lumen of the vessel. In addition, the Dice similarity coefficient, which is a measure of spatial image overlap, of consecutive pairs of slides was calculated for the different stack alignment approaches.ResultsVisual assessment of the surface plot of the vessels’ lu- men after pair-wise stack alignment, showed a relatively smooth surface of the lumen. This was the case for the rigid (i.e. translation and rotation), rigid & affine, and rigid & affine & b-spline approaches. The Dice similarity coefficient of the registered masks increased with each additional alignment step. Slides alignment using rigid, rigid & affine and rigid & affine & b-spline approaches resulted in average Dice similarity coefficient of 0.85, 0.87, and 0.98, respectively. A more accurate result of the alignment comes at the cost of an increase in computation time by roughly a factor of two in each additional alignment step.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/133
10.17629/www.diagnosticpathology.eu-2016-8:133
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/133/271
Copyright (c) 2016 M. Lucas, I. Jansen, O. de Boer, T. van Leeuwen, D. de Bruin, H. Marquering
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/283
2021-03-12T16:03:17Z
dpath:RES
VHL expression level in the pathological tissue is significantly associated with clinical outcomes of platinum-based chemotherapy in non-small cell lung cancer patients. (withdrawn 03/11/2021)
Cao, yejun
Wang, Lingwei
Zhang, Qiying
Han, Yang
Ma, Liang
Liu, Jie
Wang, Jinyi
Sun, Zhengliang
Zhao, Tian
Chen, Guohan
Hong, Xuan
Objective To investigate the association between expression level of VHL in pathological tissue and outcomes of platinum-based chemotherapy in non-small cell lung cancer (NSCLC) patients. Methods The pathological samples of NSCLC patients were obtained for immunohistochemical staining to evaluate the expression level of VHL. Furthermore, their clinical data were collected and prognosis was traced by phone. The correlation between gene expression level and the hematotoxicity was evaluated by chi-square test. The influence of VHL expression level on the risk of hematotoxicity was tested by logistic regression model. The survival curve was plotted by Kaplan-Meier method and the survival rate between the two groups was compared by log-rank test. Results A total of 110 NSCLC patients were enrolled in this study, the median follow-up time of these patients was 27.5 months. In the whole group, 31 patients had died by the last date of follow-up to get their survival information (Nov.10,2020), with a median survival time of 24.3 months. Though immunohistochemical analysis,we found that 59 patients(53.6%) had weak expression level of VHL or lack of expression in their tumor tissues,while 51 patients(46.4%) presented moderate or high expression. We found that the patients with weak expression of VHL in their carcinoma tissue or lack of expression had more opportunities to occur neutropenia after platinum-based chemotherapy(OR=0.264,95%CI=0.085-0.818,P-value=0.021).And the expression level of VHL was correlated with OS(Logrank test:P-value= 0.007,HR= 4.219,95%CI: 1.75-10.174, P-value=0.001), while not related with DFS(Logrank test:P-value=0.256,HR= 1.334,95%CI:0.642-2.769, P-value=0.440). Conclusion The expression level of VHL gene in pathological tissue is related with Granulocytosis and leukocytotoxicity after platinum-based chemotherapy in NSCLC patients. It can be used as a biomarker to predict the risk of neutropenia and the prognosis of NSCLC patients.
DiagnomX GmbH
2021-02-20
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/283
10.17629/www.diagnosticpathology.eu-2020-6:283
Diagnostic Pathology; Vol 6 No 1 (2020): Vol 6 No 1
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/283/572
Copyright (c) 2021 yejun Cao, Lingwei Wang, Qiying Zhang, Yang Han, Liang Ma, Jie Liu, Jinyi Wang, Zhengliang Sun, Tian Zhao, Guohan Chen, Xuan Hong
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/150
2018-06-19T09:28:24Z
dpath:VM
Portable Viewers For Whole Slide Images
Alfaro, Luis
Introduction/ BackgroundWhole slide images are the basis of actual Digital Pathology. We have not yet solved the problem of lack of standardization in image formats. Many different kinds of image formats coexist. Most of the time we use free viewers for local reviewing and complex servers for remote access. There is a tendency to integrate whole slide images inside hospital information environment with the rest of medical records. However this organization led to a loss of the physical management of the pathology images. We moved from the glass slides into a link in a server, and digital microscopy is really virtual microscopy.AimsWith the aim of recovering the physical file archive for whole slide images to facilitate universal sharing of digital pathology images we evaluated the possibility of employing portable viewers from whole slide images. Technical difficulties have reduced the use of this type of viewers but they have the enormous advantage of the easiness of use and universal access without any installation, and display from any platform even from DVD. Open portable viewer are available and panoramic image photography generates a software technology that can be applied to Digital Pathology.MethodsFour different source of whole slide images were used from four scanners: a Roche iScan Coreo, a 3D-histech Mirax Midi, a Leica SCN400 and a Dako ACIS III, getting .jp2, .mrxs, .scn and .tiff files. Aperio Image Scope viewer was used to read and convert files into three kinds of testing format tiff, jp2 and flat jpg files. A commercial Zeiss Java based software was used as portable viewer for tiff files. No direct jp2 portable viewer could be found available so flat jpg files were used instead to evaluate three other portable viewers: Zoomify, Deep Zoom and HD View. Zoomify has its own file converter from a single jpg into a image folder containing hundreds or thousands of small fragmented jpf files to reproduce the pyramidal file organization of whole slide images. Microsoft Deep Zoom Composer was used to generate the specific type of jpg fragmented pyramidal files and both hdmake command line software and Microsoft Image Composite Editor (ICE) was employ for HD View (HDV) files.ResultsAll four tested solutions can be used as portable viewers and keep good image quality and easiness of use and distribution, independent of servers and software installation. However previous work of conversion is necessary. The use of flat jpg files as source with its known file size limit of 65.000 pixels was overcame with ICE that works as stitcher software from different files. HDV works with zip files facilitating the use of a folder with a high number of small files. These solutions have for the future another standardization issue. They are using as visualizations technology Java, Flash and Silverlight. It seems that HTML5 will be soon substitutive standard, and probably has better security built but among its limitations is a bad solution as a local and portable active content viewer like whole slide images need.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/150
10.17629/www.diagnosticpathology.eu-2016-8:150
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/150/165
Copyright (c) 2016 L. Alfaro
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/166
2018-06-19T09:08:24Z
dpath:IMT
Hematoxylin Counterstain To Simplify Whole Slide Scanning Of Immunofluorescence Stains
Isola, J.
Tolonen, T.
Tolonen, P.
Ylinen, O.
Introduction/ BackgroundWhole slide scanning of immunofluorescence (IF) stained slides is a well-recognized need, because fluorescence signal fading makes slides non-archivable. Technically scanning of IF has remained difficult, because tissue finding and autofocus operations are slow and prone to errors under epifluorescence illumination.AimsTo simplify and to make IF scans more reliable, we started to look for counterstains that are compatible with IF and that can be scanned under brightfield illumination first.MethodsOf the many alternative counterstains tested, light hematoxylin (H) proved the best counterstain for IF (with or without DAPI). Hematoxylin staining allowed the scanner (OIT Turboscanner) to perform rapid and accurate tissue finding and to define autofocus points, yet it did not increase background autofluorescence or decrease true fluorescence signal during subsequent scanning of IF under epifluorescence illumination. By using Cy2 (green) and Cy3 (orange) as secondary antibody fluorochromes (Jackson Immunotech), we were able to use standard xylene-based DPX mounting medium without observing significant fluorescence signal fading.ResultsAs a result, IF scans of H counterstained slides could not be distinguished from those stained without hematoxylin counterstaining. As a bonus, the two scans (IF and H) could be viewed on the viewer screen side-by-side, or by gradually blending the two layers with each other. Both viewing modes were found useful in diagnostic dermatopathology when analyzing e.g. blistering skin lesions. A brightfield-IF scanning combination was also found useful in double immunostains, where cellular co-localization makes use of two precipitating (chromogenic) markers unreliable. The peroxidase IHC-hematoxylin-IF stain was exemplified with Ki-67 and pan-cytokeratin in breast cancer samples. The brightfield WSI of Ki-67 with H counterstain is an easily evaluable chromogenic DAB stain, but the image analysis software (ImmunoRatio2, embedded in the WSI viewer) utilizes the hidden pan-cytokeratin IF to create a cancer mask to exclude counting of non-epithelial stromal and lymphoid cells in the Ki-67 labeling index counting. Together these results demonstrate that a minor modification in the staining protocol (using hematoxylin instead of or in parallel to DAPI as counterstain) provides a significant help for whole slide scanning of immunofluorescence stains. Some scanners may need to be re-programmed to allow scanning of brightfield and epifluorescence automatically in sequence.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/166
10.17629/www.diagnosticpathology.eu-2016-8:166
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/166/289
Copyright (c) 2016 J. Isola, T. Tolonen, O. Ylinen
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/182
2018-06-19T09:09:45Z
dpath:EL
The Impact Of Introducing Virtual Slides As A Replacement For Powerpoint Presentations In The Students’ Microscopy Labs
Vaduva, Adrian
Cornea, R.
Cornianu, M.
Mihai, I.
Muresan, A.
Vita, O.
Derban, M.
Jurescu, A.
Gheju, A.
Taban, S.
Lazureanu, C.
Duta, C.
Lazar, F.
Dema, A.
Introduction/ BackgroundThe medical school students in Timisoara, Romania have been studying pathology slides in microscopy labs according to a protocol which uses classical PowerrPoint presentations as guides for understanding the microscopic features of diseases, followed by individual examination of the glass slides under the microscope.AimsWe aimed to assess the impact of replacing those presentations with virtual slides (VS).MethodsIn the middle of the semester, for the benign tumors microscopy lab, which is presented over the course of 2 weeks, we used 3 VS, while the other 3 slides were presented in the classical PowerPoint manner. All attending students from the 3rd year of the Medical School of the University of Medicine and Pharmacy “Victor Babes†Timisoara were asked to fill out an anonymous questionnaire at the end of the lab, in which they graded the difficulty in identifying lesions, chose the best/least understood lesion and pointed out the best manner of presentation.Results431 valid questionnaires were collected. 52.9% of the students indicated one of the 3 VS as the best understood lesion, while 59.62% chose a different VS as a least understood one. One VS was also the top best (113/332 votes) while another the least understood (34/126 votes) lesion. 74.01% students agreed that VS helped them understand the microscopic criteria better, while 74.71% would like VS to be used in the labs to come.Conclusion: VS were appreciated by the students as a novelty and a more impressing way of studying pathology slides, but did not dramatically improve the easiness with which they identify and understand the lesions. Work supported by the project „Studiu multicentric privind utilizarea abordului robotic în corelarea scăderii nivelului de adipokine circulante din obezitate cu riscul apariÅ£iei cancerului pelvin < ROBOCAPE >†- ID 1846 / Cod SMIS 48478 - POSCCEÂ
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/182
10.17629/www.diagnosticpathology.eu-2016-8:182
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/182/309
Copyright (c) 2016 A. Vaduva, R. Cornea, M. Cornianu, I. Mihai, A. Muresan, O. Vita, M. Derban, A. Jurescu, A. Gheju, S. Taban, C. Lazureanu, C. Duta, F. Lazar, A. Dema
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/198
2018-06-19T09:06:43Z
dpath:EP
Patch-Based Nonlinear Image Registration For Gigapixel Whole Slide Images
Lotz, J.
Olesch, J.
Weiss, N.
Lotz, J.
Breuhahn, K.
Hahn, H.
Modersitzki, J.
Introduction/ BackgroundImage Registration of whole slide histology images allows the fusion of fine-grained information –  like different immunohistochemical stains – from neighboring tissue slides. Traditionally, pathologists fuse this information by looking subsequently at one slide at a time. If the slides are digitized and accurately aligned at cell-level, automatic analysis can be used to ease the pathologist’s work. However, the size of those images exceeds the memory capacity of regular computers, preventing the application of established image registration methods at a high magnification.AimsAn accurate and automatic alignment helps the pathologist to analyze the combination of different antibodies without memorizing multiple slides. For some applications, cell-level accuracy is needed. This also enables automatic image analysis to take advantage of multislide information.MethodsWe extend available registration methods by using image data at fine spatial resolution. However, this data is not simultaneously globally available due to the computer’s memory restrictions.Typical approaches either reduce the amount of data to be processed by downsampling or partition the data into smaller chunks to be processed separately. We combine the patch based approach with an elastic deformation model to obtain a global registration result. Our method first registers the complete images on a low resolution with a nonlinear deformation model and later refines this result on patches by using a second nonlinear registration on each patch. The deformation information on the individual patches can be contradictory and needs to be combined into one global model. As an extension to our previous work, the global solution is computed by minimizing an energy function that preserves the patch-wise deformation and establishes global smoothness. The NGF distance measure is used to handle multi-stain images.ResultsThe method will be applied to whole slide image pairs. The alignment of corresponding structures will be measured by comparing manual segmentations from neighboring slides. First results show an improvement of the registration accuracy compared to the low-resolution nonlinear registration.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/198
10.17629/www.diagnosticpathology.eu-2016-8:198
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/198/279
Copyright (c) 2016 J. Lotz, J. Olesch, N. Weiss, J. Lotz, K. Breuhahn, H. Hahn, J. Modersitzki
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/10
2018-06-19T09:07:29Z
dpath:CAS
Cryptosporidiosis in an Immunocompetent Individual An unusual case with brief review of the literature
Jin, Bo
Yashpal, Anveil
Deol, Nisha
AbuRashed, Ahmed
Saleh, Husain
cryptosporidiosis, immunocompetent, chronic diarrhea
Cryptosporidiosis infection involves most commonly the small intestine but can occur in any part of the gastrointestinal (GI) tract. Typical infection by this parasitic organism occurs in immunocompromised individuals. However, rare cryptosporidiosis in immunocompetent individuals has been reported. Herein, we describe a case of cryptosporidiosis in an 85-year old woman who has hypertensive heart disease and diabetes, but is otherwise immunocompetent. This patient had protracted chronic diarrhea, however, medical workup failed to identify the etiology of this diarrhea.Awareness of the possibility that cryptosporidiosis can involve immunocompetent individuals should be kept in mind among healthcare professionals to avoid misdiagnosis or lengthy delay in identifying the cause of the diarrhea or other GI illness. In particular, obtaining biopsy of the small or large intestines by the examining gastroenterologists in spite of normal endoscopy is very important to establish the diagnosis.  Â
DiagnomX GmbH
2015-05-26
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/10
10.17629/www.diagnosticpathology.eu-2015-1:10
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/10/16
Copyright (c) 2015 Bo Jin, Anveil Yashpal, Nisha Deol, Ahmed AbuRashed
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/219
2018-06-19T08:59:26Z
dpath:EP
Assessment of Microvascular Density in the Neuroendocrine Tumors of the Pancreas: a Correlation with Multidetector Computed Tomography (MDCT) Features and Tumor Grade
Glotov, A.
Belousova, E.
Kalinin, D.
Introduction/ Background
The biologic course of pancreatic neuroendocrine tumors (NET) can be accurately predicted on the basis of pathology parameters which, unfortunately, cannot be fully assessed until the entire tumor has been resected. When obvious landmarks of malignancy (metastases, vascular invasion) are lacking, tumour size is the only reliable preoperative parameter used to differentiate between presumably benign and malignant pancreatic NETs. It is generally accepted that pancreatic NETs exceeding 2 cm in their diameter may have borderline pathology or even malignancy. Anyway, up to 10% of tumors with diameter less than 2 cm are although malignant. That is why there is need in studies focusing on additional imaging characteristics, such as contrast-enhanced MDCT, useful for the aggressiveness assessment.
Aims
To determine whether it is possible to predict pancreatic NET Grade and microvascular density (MVD) according to contrast-enhanced MDCT findings.
Methods
A retrospective study was conducted and 70 patients with pancreatic NETs were retrieved from the institutional archives. Twenty eight of them had met the including criteria (a - patients underwent surgery in our Institution and b - patients underwent preoperative dynamic abdominal CT within 30 days prior surgery) and comprised the study population. Thus, research included 15 patients with functioning and non-functioning pancreatic NETs Grade 1 and 13 of patients with Grade 2 (according to the WHO classification of 2010). Radiology All preoperative CT examinations were performed by a 256-slice CT scanner. Dynamic CT images, including non-enhanced, arterial, portal venous and delay phase images, were obtained for all patients. For contrast-enhanced CT, 90–120 mL of high concentration contrast mediaiomeprol 400 (Iomeron 400; Bracco Imaging SpA, Milan, Italy). CT images were reconstructed with a section thickness of 1-2 mm.
Pathology
For identification of vessels, regardless lymphatic or venous, immunohistochemistry with CD34 (clone
QBEnd/10, CellMarque) was performed on formalin-fixed paraffin-embedded (FFPE) tumor blocks.
Image analysis
Density of vessels was defined on 3 fields at x 200 (~ 1,8 mm2). The choice of fields of vision was carried out among sites with visually greatest density of vessels (“hot spotsâ€). Determined total number of the pixels belonging to vessels by the Color Threshold tool (ImageJ) and divided this number into total of pixels in the image.
Results
The median of density of vessels at patients with NET Grade 1 made 8% ± 2% whereas in group of patients with NET Grade 2 this indicator made 5 ± 4%. The difference was statistically significant (p
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/219
10.17629/www.diagnosticpathology.eu-2016-8:219
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/219/374
Copyright (c) 2016 A. Glotov, E. Belousova, D. Kalinin
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/91
2018-06-19T09:01:44Z
dpath:DIA
How do I diagnose Cystic Ameloblastoma
Mrachacz, Andreas
Kayser, Klaus
Kühnel, Thomas
Pappa, Spiridula
Schmidt, Frank
Cystic ameloblastoma; Dental cyst; Inflammation; Maxilla; Excision
This 59 year old woman presented with teeth pain. Brown red material measuring 6 * 4 * 3 mm of soft consistence was excised from the region 16
DiagnomX GmbH
2015-12-10
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/91
10.17629/www.diagnosticpathology.eu-2015-1:91
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/91/72
Copyright (c) 2015 Andreas Mrachacz, Klaus Kayser, Thomas Kühnel, Spiridula Pappa, Frank Schmidt
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/236
2018-06-19T08:55:24Z
dpath:EDI
Diagnosticpathology.eu ; Experiences 2016 – Perspectives 2017
Kayser, Klaus
www.diagnosticpathology.eu, citation index, open source journal, communication network, virtual slide, automated measurement, environmental hazards.
The peer reviewed open access journal diagnosticpathology.eu is embedded in a financially completely independent medical communication network of nodes which serve for different duties.
The nodes include the services of the unique Virtual International Pathology Institute (VIPI, www.diagnomx.eu/vipi), an automated image measuring system (EAMUS), an anatomy training course, and a collection of sixty rare and common lung diseases.
An atlas of ‘Natural and Synthetic Mineral Fibers affecting Man’ (including fine granulate) has been added in 2016 as well as all articles of the former ‘Electronic Journal of Pathology and Histology’, which was the first solely electronically published peer reviewed medical journal to our knowledge.
The announced collection of more than 120 rare cases including virtual slides and the original publications is in preparation, as well the atlas of ‘all known lung diseases’, a data base that covers approximately 860 different lung diseases, including available clinical, endoscopic, radiological, pathological, genetic and occupational data. These projects have left the start phase and will probably be ready in 2017.
The journal has published more than 120 original articles and the proceedings of the 13th European Congress on Digital Pathology, held in Berlin, Germany, May 25 – 28, 2016. Its specific publication tools ‘publish beside the microscope’ and to submit data for ‘interactive publication’ have been used in 10 (2) cases. Both tools are unique, and cannot be found elsewhere. The preparation of virtual slides (submission of glass slides) is mandatory for publication of suitable articles.
The journal’s name diagnostic pathology seems to be attractive for some publishing companies that try to copy some issues of the real journal on diagnostic pathology (www.diagnosticpathology.eu).
DiagnomX GmbH
2016-12-21
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/236
10.17629/www.diagnosticpathology.eu-2016-2:236
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/236/391
Copyright (c) 2016 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/117
2018-06-19T08:58:51Z
dpath:SY01
Impact Of Tissue Sampling On Accuracy Of Ki67 Immunohistochemistry Evaluation In Breast Cancer
Besusparis, Justinas
Plancoulaine, B.
Rasmusson, Allan
Green, A. R.
Augulis, R.
Ellis, I. O.
Laurinaviciene, A.
Herlin, P.
Laurinavicius, Arvydas
Introduction/ BackgroundGene expression studies have identified molecular subtypes of breast cancer with implications to chemotherapy recommendations. For distinction of these types a combination of hormone receptors and proliferative activity of tumor cells, estimated by Ki67 labeling index from immunohistochemistry (IHC) is used. Clinical studies are frequently based on IHC performed on tissue microarrays (TMA) with variable tissue sampling. This raises the need for evidence-based sampling criteria for individual studies. We present a novel tissue sampling simulation model and demonstrate its application on Ki67 assessment in breast cancer tissue taking into account its intra-tumoral heterogeneity.AimsThe aim is, using a novel method for easy virtual TMA simulation, to determine the optimal tissue sampling requirements in the context of variable intra-tissue heterogeneity level of Ki67 immunohistochemistry in breast cancer.MethodsWhole slide images (WSI) of 297 primary breast tumors immunohistochemically stained for Ki67 were subjected to digital image analysis (DIA). Percentage of invasive tumor cells stained for Ki67 were computed for hexagonal tiles superimposed on the WSI. From this, intra-tumoral Ki67 heterogeneity indicators (Haralick’s entropy values) were extracted and used to dichotomize the tumors into homogeneous and  heterogeneous populations. Simulations with random selection of hexagons, equivalent to 0.75 mm circular diameter, were performed. The tissue sampling requirements were investigated in relation to tumor heterogeneity using linear regression and extended error analysis.ResultsThe sampling requirements were dependent on the heterogeneity of the biomarker expression. To achieve a coefficient error of 10%, 5-6 cores were needed for homogeneous cases, while 11-12 cores for heterogeneous cases. In mixed tumor population, 8 TMA cores were required. Similarly, to achieve the same accuracy, approximately 4,000 nuclei must be counted when the intra-tumor heterogeneity is mixed/unknown. Tumors at the lower scale of proliferative activity would require larger sampling (10-12 TMA cores, or 5,000 nuclei) to achieve the same error measurement results as for highly proliferative tumors. Our data show that optimal tissue sampling for IHC biomarker evaluation is dependent on the heterogeneity of the tissue under study and needs to be determined on a per-use basis. We propose a method that can be applied to determine the TMA sampling strategy for specific biomarkers, tissues and study targets. In addition, our findings highlight the importance of high-capacity computer-based IHC measurement techniques to improve accuracy of the testing.
DiagnomX GmbH
2016-06-22
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/117
10.17629/www.diagnosticpathology.eu-2016-8:117
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/117/250
Copyright (c) 2016 J. Besusparis, B. Plancoulaine, A. Rasmusson, A. R. Green, I. O. Ellis, A. Laurinaviciene, P. Herlin, A. Laurinavicius
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/262
2018-11-26T16:07:14Z
dpath:REV
State of PD-L1 and PD-1 screening and therapy in NSCLC
Bruehl, Frido
Csanadi, Agnes
Neeff, Hannes
Rawluk, Justyna
Kayser, MD, Gian
Lung cancer is still the leading cause of death among all malignancies worldwide. The development of targeted therapies against driver mutations such as EGFR, ALK1, ROS1 and BRAF have led to a significant improvement in patient progression free survival and to a benefit in quality of life of patients suffering from advanced and metastasized non-small cell lung cancer. But since these genetic aberrations are found only in a small subset of lung cancer more globally directed therapeutic approaches are needed to address the therapeutic dilemma of this highly diverse disease. For a long time, it is known that lung cancer is a so called immunogenic disease, i. e. it often evokes a host immune response. Likewise, lung cancers are also developing mechanisms to escape these anti-cancerous immune reactions. One immunogenic axis is that of PD1 and PD-L1. In investigation of this activation-deactivation chain involving lymphocytes, tumor cells but also stromal fibroblasts and macrophages new humanized antibodies have been developed and approved for the treatment of non-small cell lung cancer (NSCLC). Clinical trials have shown effectiveness of these agents, but a valid and reproducible predictive marker has not been found so far. Here we review the current literature on the PD1/PD-L1 axis in NSCLC, its biological function on histological subtype. Together with meta-analytic data performed for this review and results from our own investigations we also give a comprehensive outlook on future developments considering predictive testing and therapeutic options.
DiagnomX GmbH
2018-04-11
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/262
10.17629/www.diagnosticpathology.eu-2018-4:262
Diagnostic Pathology; Vol 4 No 1 (2018): 2018
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/262/556
Copyright (c) 2018 Frido Bruehl, Agnes Csanadi, Hannes Neeff, Justyna Rawluk, Gian Kayser, MD
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/276
2020-01-02T16:27:11Z
dpath:EDI
Artificial Intelligence (AI) in cloud integrated, open access pathology publications: perspectives on 2020.
Kayser, Klaus
Goal: To describe, maintain and further develop the communication network of medical sciences www.diagnosticpathology.eu that publishes electronically submitted peer reviewed medical articles and fully takes advantage of its electronic environment, and to give the reader the opportunity to view digitized whole slide images (virtual slides, VS), to measure image objects, and to annotate images and text.Background: The unique open access, peer reviewed journal www.diagnosticpathology.eu is embedded in a communication environment of different cloud components. The components include several distributed servers and databank systems such as access to article integrated VS, data storage, or scientific data banks (atlas of fine granulate and natural and synthetic fiber hazards). Implementation specificities: Theoretical considerations on specific substantial differences between the physical real world and its virtual transformations guide the implementation. The differences include, for example, the minimum number of mandatory space dimensions, of their essential (ir)-reversibility of objects, structures, and functions as well as the relationship of image features to the observation time.The implemented system focuses on communication issues in tissue – based science only. Its volunteers allow disregard any predominantly financial impact such as financial profit. Artificial intelligence (AI) is used to maintain its sustainability, connectivity, distribution, measurement and discussion of medical images, especially microscopic slides. 2019 Data: The journal and its concurrent operation of interactive communication demonstrate the advantage of AI in open access publication. VS are ready to be screened and annotated by any reader worldwide. QR codes provide DOI registration and upload of oral presentations by the auditorium. Interactive publication permits the release of a distinct continuous article chain. Annotations of VS images can be transferred in public or private databanks. The reader is invited to check his impression of marker scores by own automated measurements.Perspectives: Applications of AI in tissue – based diagnosis, communication and implementation are not limited to deep learning, quality assurance or so-called diagnosis assistants. AI is on the way to significantly modify medical diagnostics and treatment. These modifications will, in addition, modify our understanding of disease and life. www.diagnosticpathology.eu is one of the pathfinders and pioneers in this unavoidable process.Keywords: Artificial Intelligence, Open Access Journal, Virtual Slide, Deep Learning, Tissue – based Diagnosis.
Virtual Slides:
Tuberculosis Fibrosis
The exemplarily included virtual slides and AVI Videos are published in http://dx.doi.org/10.17629/www.diagnosticpathology.eu-2018-4:269
DiagnomX GmbH
2019-12-31
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/276
10.17629/www.diagnosticpathology.eu-2019-5:276
Diagnostic Pathology; Vol 5 No 1 (2019): Vol. 5 No. 1 2019
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/276/567
Copyright (c) 2019 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/145
2018-06-19T09:27:28Z
dpath:SY01
Fractal Behavior Of Gleason And Srigley Grading Systems
Serbanescu, M.S.
Plesea, R.M.
Pop, O.T.
Bungardean, C.
Plesea, I.E.
Introduction/ BackgroundProstate cancer remains one of the major malignancies of modern society. The need of grading this malignancy is still in dispute. Two major grading systems have emerged and are world-wide adapted: Gleason grading system [1] and Srigley grading system [2]. Both systems use optical subjective descriptions of different architec- tural growth patterns of prostate adenocarcinoma. The fractal dimension (FD) is used in the medical field as an objective feature for describing a given image rather than showing a precise value for a known fractal. The FD can be an objective measurement for different patterns description. AimsThe aim of our study is to assess the fractal behavior of images labeled according to Gleason and Srigley grading systems both in terms of in-class and inter-class variation. Methods299 Gömöri stained microscopic digital images of prostate adenocarcinoma were labeled independently according to Gleason and Srigley patterns. Each image was firstly transformed to grayscale then a maximum cropped square of the image was resized to a standard 256x256 pixel image. For the resulted images the fractal dimension was approximated with two different algorithms: a standard box-counting algorithm (applied to the binary image obtained with Roberts’s method for edge detection) and a novel algorithm that is applied to the grayscale version of the  image  consisting  in the ratio between image’s volume and area (R-VA) at different scales [3]. In-class variation was assessed as the average standard deviation (SD).Lower SDmeans better discrimination. For the inter-class variation assessment each class was compared with all other classes using a two-tail, Student’s t-test. The resulted value was defined as the ratio between the statistically different means and the total number of comparisons. The maximum possible value for Gleason grading system was 28, be- cause there were no images labeled as Gleason pattern 1, while for the Srigley grading system the maximum possible value was 6. ResultsIn-class variation was 0.045 using the box-counting algorithm and 0.048 using the R-VA algorithm for Gleason grading system and 0.161 using the box-counting algorithm and 0.178 using the R-VA algorithm for Srigley grading system. Inter-class variation was, for Gleason grading system 13/28 using the box-counting algorithm and 20/28 using the R-VA algorithm while for the Srigley grading system was 3/6 using the box-counting algorithm and 5/6 using the R-VA algorithm respectively. Srigley grading system seems to perform better than Gleason’s on inter-class variation, but has lower performance on in-class variation. Nevertheless, we must note that there is a large difference between the two systems regarding the number of classes. The FD computed with the R-VA algorithm has better discrimination results than the one computed with the box-counting algorithm in both grading systems, thus proving once again the R-VA’s performance [3].
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/145
10.17629/www.diagnosticpathology.eu-2016-8:145
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/145/323
Copyright (c) 2016 M.S. Serbanescu, R.M. Plesea, O.T. Pop, C. Bungardean, I.E. Plesea
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/161
2018-06-19T09:10:30Z
dpath:DA
Semi-Automatic Classification Of Histopathological Images: Dealing With Inter-Slide Variations
Gadermayr, Michael
Strauch, M.
Unger, J.
Boor, P.
Klinkhammer, B.M.
Djudjaj, S.
Merhof, D.
Introduction/ BackgroundThe large size and high resolution of histopathological whole slide images renders their manual annotation time-consuming and costly. State-of-the-art computer-based segmentation approaches are generally able to classify tissue reliably, but strong inter-slide variations between training and evaluation data can cause significant decreases in classification accuracy.AimsIn this study, we focus on alpha-SMA stainings of the mouse kidney, and in particular on the classification of glomerular vs. non-glomerular regions. Even though all slides had been recorded using a common staining protocol, inter-slide variations could be observed. We investigate the impact of these variations as well as methods of resolution.MethodsWe propose an interactive, semi-automatic tissue classification approach [1] which adapts a pre-trained classification model to the new image on which classification should be performed. Image patches for which the class (glomerular/non-glomerular) is uncertain are automatically selected and presented to the user to determine the class label. The user interaction step is repeated several times to iteratively adjust the model to the characteristics of the new image. For image representation and classification, well known methods from the literature are utilized. Specifically, we combine Local Binary Patters with the support vector classifier.ResultsIn case of 50 available labelled sample patches of a certain whole slide image, the overall classification rate increased from 92 % to 98 % through including the interactive labelling step. Even with only 20 labelled patches, accuracy already increased to 97 %. Without a pre-trained model, if training is performed on target domain data only, 88 % (20 labelled samples) and 95 % (50 labelled samples) accuracy, respectively, were obtained. If enough target domain data was available (about 20 images), the amount of source domain data was of minor relevance. The difference in outcome between a source domain training data set containing 100 patches from one whole slide image and a set containing 700 patches from seven images was lower than 1 %. Contrarily, without target domain data, the difference in accuracy was 10 % (82 % compared to 92 %) between these two settings. Execution runtime between two interaction steps is significantly below one second (0.23 s), which is an important usability criterion.It proved to be beneficial to select specific target domain data in an active learning sense based on the currently available trained model. While experimental evaluation provided strong empirical evidence for increased classification performance with the proposed method, the additional manual effort can be kept at a low level. The labelling of e.g. 20 images per slide is surely less time consuming than the validation of a complete whole slide image processed with a fully automatic, but less reliable, segmentation approach. Finally, it should be highlighted that the proposed interaction protocol could easily be adapted to other histopathological classification or segmentation tasks, also for implementation in a clinical system.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/161
10.17629/www.diagnosticpathology.eu-2016-8:161
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/161/284
Copyright (c) 2016 M. Gadermayr, M. Strauch, J. Unger, P. Boor, B.M. Klinkhammer, S. Djudjaj, D. Merhof
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/177
2018-06-19T09:09:06Z
dpath:CWI
Choosing And Implementing The Correct Whole Slide Imaging System
Branders, Peter
Tousseyn, T.
Weynand, B.
Introduction/ BackgroundThe whole slide imaging (WSI) market has developed enormously in the recent years. This evolution has made the selection and the implementation of digital pathology more complicated. Based on a validation process, we developed recommendations that need to be taken into account when implementing whole slide imaging. In addition to selecting the right hardware, one should also focus on laboratory organization, integration, training and handling.AimsThe aim is to integrate WSI as efficiently as possible in a standardized process. This should lead to a user friendly workflow for pathologists and must ensure the quality of the diagnosis.MethodsWe organized on-site demonstrations to test several available WSI systems with a fixed set of histology slides. We evaluated scanning quality, measured the scanning time, the amount of data produced and made a simulation of a routine workflow. We developed a to-be workflow beginning with the scanning process until the final diagnosis of the pathologist. The workflow focused on the integration of the system into the laboratory information system. We standardized the technical laboratory processes to increase the quality of the slides and the efficiency of WSI. The standardization included good labeling, adequate quality, standardized location and correct number of sections on the slide. We introduced a continuous workflow to reduce batch size and to decrease the turn-around-time. The pathologists were only allowed to work with WSI after training in order to manipulate the images as efficiently as possible. Finally we validated the system according to CAP guidelines for WSI for diagnostic purpose in pathology.ResultsIt is very important to determine what the purpose of WSI implementation in the lab is. The different systems show large variations between them and not every set up will fit in the specific workflow of each lab. The workflow simulation gave us an idea of the scanning turn-around-time and made it possible to estimate the amount of scanners that would be necessary in daily routine. Another focus point is the total integration of WSI to find a synergy between the hardware, workflow and the way the system can be integrated into the IT infrastructure of the lab. Beside the bidirectional communication with the laboratory information system, data storage organization and its influence on the lab’s productivity is also very important. Organizing the laboratory with a standardized continuous workflow will reduce the amount of data, increase speed and lower the amount of rescans. To prevent that WSI is used inefficiently, it is crucial to train the pathologists before they start using it. A lack of training will lead to a dislike of WSI due to poor knowledge of the available applications. The pathologists are indicating that it’s crucial to have the correct hardware to manipulate the image in order to ensure diagnostic speed and to lower the threshold towards WSI. We may conclude that choosing and implementing the correct WSI solution needs a systematic approach to succeed on the long term. Defining and optimizing the workflow before implementing whole slide imaging is crucial. Hardware, workflow and IT infrastructure should match to ensure productivity. Training of the pathologists is decisive in order to ensure efficient use.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/177
10.17629/www.diagnosticpathology.eu-2016-8:177
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/177/304
Copyright (c) 2016 P. Branders, T. Tousseyn, B. Weynand
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/193
2018-06-19T09:06:44Z
dpath:EP
Computer-assisted quantification of caix membrane immunoreaction destined for the clear cells in renal carcinoma. A pilot study.
Slodkowska, J.
Markiewicz, T.
Wdowiak, M.
Mlot, B.
Kozlowski, W.
Introduction/ BackgroundCarbonic Anhydrase IX [CAIX] has been considered as a candidate prognostic factor in clear-cell renal carcinoma [CCRC], however the supporting evidence is conflicting. CAIX is strongly induced by hypoxia via HIV-1α, and in CCRC via mutations to the VHL gene. CAIX expression could be identify as an immunohistochemical predictor of CCRC patients outcome but the published studies related to the patients prognosis have based on the diverse quantification protocols of CAIX expression (TMAs vs. whole tissue section; semiquantitative vs. computerised image analysis; with/without intensity scoring; with various software). The available commercial image analysis tools are mainly for general purpose e.g. software for breast carcinoma HER2 membrane immunoreaction has been used in various tumour tissue studies. However the cytological images of CCRC and breast carcinoma show essential differences related to the nuclei (size, outlines, intracellular location) and nuclear/cytoplasmic proportion which could influence the measurement credibility in maladjusted algorithm.AimsThe aim of our study was to evaluate an algorithm for quantification of the membranous CAIX expression specifically dedicated to CCRC (“snake variantâ€) in comparative analysis to applied HER2 breast cancer algorithm for CCRC.MethodsIn the quantitative analysis of the specimen, the image processing follows: recognition of the cell nuclei; segmentation of the immunoreactive cell membranes; the assignment of the membrane segments to an individual cell. The last step is challenging for analysis due to frequent discontinuities in membranous immunoreaction, great variability of cellular counters and intracellular nuclei location. Because the classical watershed method for the individual cell separation is insufficient, the snake active contour method was applied, starting from each nucleus outline. The built gradient image allowed to select the most adequate parameters in the snake adaptation process. The recognized snake represents the membrane associated with the particular cell. The material includes records of 39 patients with the histopathologically verified diagnosis of CCRC who had nephrectomy (between 2009-2011) and were treated with tyrosine kinases agents (the Clinic of Oncology registry). 74% (29 out 39) of patients presented stage I - T1 N0; 20,5% - stage III and 5,4% stage TII. The formalin-fixed tissue sections of the resected CCRCs (the Pathology Department registry) were immunostained for CAIX protein using CAIX antibody (clone NB100-417) (Antibodies-online GmbH) with EnVisionTM (DAKO) according to the manufacture recommendations. The representative digital images were selected from each Whole Slide Image (scanned with Aperio, under 20x) and were assessed automatically by 3 independent observers using two algorithms: “snake variant†and “breast HER2â€. The extend of staining (percentage) was scored in the 10% intervals of CAIX positive carcinomatous cells and the intensity of immunoreaction was evaluated in 3 grade scale (1-3).ResultsThe obtained results have been under investigation for the intra- and inter-observer accuracy as well as for the comparative data analysis of both types of algorithm. The statistical analysis has been incorporated. This approach explores a new possibility of the computerised quantitative estimation of the membrane CAIX immunoreaction destined
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/193
10.17629/www.diagnosticpathology.eu-2016-8:193
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/193/274
Copyright (c) 2016 J. Slodkowska, T. Markiewicz, M. Wdowiak, B. Mlot, W. Kozlowski
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/7
2018-06-19T09:07:53Z
dpath:CAS
Mucinous tubular and spindle cell carcinoma of the kidney: case report with literature review
Oliveira, Rui Caetano
Silva, Edgar Tavares
Abrantes, Carlos
Rodrigues, Pedro
Marinho, Carol
Sousa, Vitor
Simoes, Pedro
Castro, Ligia Prado e
Spindle cell carcinoma; kidney cancer; papillary renal cell carcinoma; incidence; immunohistochemistry
Mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney is a rare renal cancer type, recently recognized by the World Health Organization (WHO) in 2004, with indolent behavior. We present a case of a 50-year-old female that revealed a renal mass on an abdominal echography, incidentally discovered during a hepatic hemangioma follow-up. The patient underwent partial nephrectomy, and after pathological evaluation the final diagnosis of MTSCC was made. MSTCC is a special renal cancer type, with low degree of malignancy and a favorable prognosis. Surgical resection is the treatment of choice. It’s important to be aware of this entity in order to differentiate MTSCC with renal cancers of less favorable prognosis and higher degree of malignancy like papillary renal cell carcinoma.Â
DiagnomX GmbH
2015-03-22
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/7
10.17629/www.diagnosticpathology.eu-2015-1:7
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/7/3
Copyright (c) 2015 Rui Caetano Oliveira
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/214
2018-06-19T10:20:43Z
dpath:EP
Apoptotic Activity of Cells of Thymus and Spleen in Children Born To Women Who Led an Unhealthy Lifestyle
Gorianikova, I.
Sorokina, I.
Myroshnychenko, M.
Introduction/ Background The health of children largely depends on the health of parents and their lifestyle.
Aims The purpose – to identify the apoptotic activity of cells of thymus and spleen in children born to women who led unhealthy lifestyle.
Methods The material of the study was the tissue of thymus and spleen of children born to women who led a sedentary lifestyle, smoked, drank alcohol and ate foods containing tartrazine. Investigated material was divided into three groups: I – cases of stillbirth (n=14); II – cases of autopsy of children who died before the age of 6 months (n=38); III – cases of autopsy of children who died at the age from 6 months to 1 year of life (n=15). The cells in apoptotic state were detected using monoclonal antibodies to CD 95 in the fluorescent microscope «Axioscop-40». Immunohistochemical investigation was performed using the indirect Koons method in modification of M. Brosman (1979). Mean values of indicators in groups were compared using a nonparametric U-criteria Mann-Whitney.
Results In thymus of children was observed a significant (p=0,000345) increasing the number of cells in apoptotic state in group II (35,61±0,701) in comparison with the group I (31,29±0,794) and in group III (42,13±1,073) in comparison with the group II (p=0,000014). In spleen was found a significant (p=0,010395) increasing the number of cells expressing receptor for CD 95 in group II (19,89±1,055) in comparison with group I (14,50±1,550) and in group III (26,73±1,469) in comparison with group II (p=0,001693).
Conclusion: Unhealthy mother lifestyle (sedentary lifestyle, smoking, drinking alcohol and eating foods containing tartrazine) leads to increasing apoptotic activity in organs of immune system (thymus and spleen) of children with the increasing of their age.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/214
10.17629/www.diagnosticpathology.eu-2016-8:214
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/214/369
Copyright (c) 2016 I. Gorianikova, I. Sorokina, M. Myroshnychenko
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/80
2018-06-19T09:01:16Z
dpath:REV
Quo vadis universitas?
Guski, Hans
University formation, driving forces, structural defaults, the guild concept, university reformation, successful and failed reforms, the Bologna process, bachelor and master degree courses, excellence cluster, elite universities, university ranking, caus
The article considers the advantages and disadvantages of the European universities that can be explained only by the analysis of their history. In contrast to the conventional theories, the economic enforcement was the driving cause for university formation in the Middle Ages. The guild concept created by Siegfried Bär 15 years ago explains the historical imperative, but also the construction faults of the universities resulting from their specific features essentially the principles of self-autonomy and cooptation. The faults of university organization are the main reasons why nearly all university reforms failed. There does not exist any convincing proof that the introduction of new organization models such as bachelor and master degree courses or excellence clusters are of more efficiency in teaching and research. The international university ranking did not change in recent years; the top ten universities are still located in the USA and Great Britain. The majority of German universities range between the middle and the end of the ranking list. It is demonstrated that the main causes of this discrepancy are the delay of academic qualification, the lack of competition, the dependency of the public policy, and the insufficient financial support. Progress in university research and teaching can be obtained only if these problems can be solved.Â
DiagnomX GmbH
2015-10-14
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/80
10.17629/www.diagnosticpathology.eu-2015-1:80
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/80/59
Copyright (c) 2015 Hans Guski
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/230
2018-06-19T08:55:24Z
dpath:SY01
Deep Convolutional Neural Networks for Histological Image Analysis in Gastric Carcinoma Whole Slide Images
Sharma, H.
Zerbe, N.
Klempert, I.
Hellwich, O.
Hufnagl, P.
Introduction/ Background
In this paper, histopathological whole slide images of gastric carcinoma are analyzed using deep learning
methods. A convolutional neural network architecture is proposed for two classification applications in H&E stained tissue images, namely, cancer classification based on immunohistochemistry (IHC) into classes Her2/neu+ tumor, Her2/neu- tumor and non-tumor, and necrosis detection based on existence of necrosis into classes necrotic and non-necrotic. The studies in [1] and [2] explored computer-aided classification using graphbased methods and necrosis detection by textural approach respectively, which are extended using deep convolutional neural networks. Performance is quantitatively compared with established handcrafted image features, namely Haralick GLCM, Gabor filter-banks, LBP histograms, Gray histograms, RGB histograms and HSV histograms followed by classification by random forests, another well-known machine learning algorithm.
Aims
Convolutional neural networks (CNN) have recently gained tremendous attention in general image analysis [3-5]. There has also been an emergence of deep learning in digital histopathology for diverse
classification and detection problems [6-8]. The prime motivation behind this work is that no previous study has explored deep learning for the specified goals in gastric cancer WSI. Automated cancer classification can assist pathologists in computer-aided diagnosis in H&E stained WSI without the requirement of IHC staining, thereby reducing preparation and inspection times, and decreasing inter- and intra-observer variability. Necrosis detection can play an important role in prognosis, as larger necrotic areas indicate a smaller chance of survival and vice-versa. Moreover, most deep learning studies have used smaller image sizes mainly due to memory restrictions of GPU, however, we consider larger regions in order to preserve context i.e. neighborhood information and tissue architecture at higher magnification. Further, this method is independent of nuclei segmentation, hence its performance is not limited by segmentation performance as in [1] (evaluation details in [9]).
Methods
Firstly, standard data augmentation techniques are applied on the available gastric cancer WSI dataset and
thousands of images of size 512x512 are generated. Different CNN architectures are empirically studied to observe the behavior of variation in model characteristics (network depth, layer properties, training parameters, etc.) by training them from scratch on a representative subset of whole data for cancer classification. One of these is the Imagenet model [4], however it doesn’t perform desirably on the representative dataset. The self-designed CNN architecture with best classification rates is selected. Later, the proposed CNN is also applied for necrosis detection. Performance is compared with state of the art methods using handcrafted features and random forests. For evaluation, randomized three-fold stratified shuffle split and leave-one-patient-out cross validations are used.
Results
Conclusion: A self-designed CNN architecture is proposed for image analysis (cancer classification based on IHC and necrosis detection) in H&E stained WSI of gastric cancer. Quantitative evaluation shows that deep learning methods mostly compare favorably to state of the art methods, especially for necrosis detection. In future the aim is to expand the current WSI dataset and to improve the CNN architecture for optimal performance.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/230
10.17629/www.diagnosticpathology.eu-2016-8:230
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/230/385
Copyright (c) 2016 H. Sharma, N. Zerbe, I. Klempert, O. Hellwich, P. Hufnagl
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/106
2019-08-22T16:06:42Z
dpath:RES
How to analyze Structure and Function in Tissue – based Diagnosis?
Kayser, Klaus
Borkenfeld, Stephan
Carvalho, Rita
Djenouni, Amina
Kayser, Gian
Digital pathology; structure, function; galectin-7; structural entropy; cellular heterogeneity
Background: Tissue – based diagnosis (morphological analysis of human tissue) judges, measures and interprets morphologic images which have been acquired from human tissue. It translates the findings into a diagnosis or description of biological functions. What are its principle algorithms and theoretical background?Theory:Pathologists are used to distinguish between structure and function. Biological structures are ordered clusters of material (genes, nuclei, cells, organs, etc.), which remain constant during the period of detection and observation. They are commonly embedded or appear in circumscribed spaces. These spaces are clearly separated from their environment (background). Functions are forces that act on structures. They modify their appearance, create and delete structures and their spatial relationship. The recognition of both structures and functions is dependent upon the observation time: Material that remains unchanged within the observation period is called structure, its changes between a series of observations a function.Derivatives: Biological structures and functions should be interpreted in relation to the observation time. Functions can be considered structural gradients of time or of observation periods.Implementation: The analysis of conventional stained histological slides reflects to a short non changeable observation time, which in reality cannot be repeated at different times on the same tissue. Acquired digital images such as virtual slides (VS) offer the opportunity of simulating different observation times if object features are analyzed that reflect structural changes at different times. The measurement of immunohistochemal intensity levels performed on the same structure can be considered a time series of the binding or antigen – antibody process. The obtained frame of these measurements can be mapped on chemical significant descriptors such as Shannon’s and structural entropy, and their entropy flows.Material and Methods: Histological glass slides displaying with kidneys of 39 chicken embryos were incubated with AP labelled galectin-3. In addition, 20 control cases were analyzed. One snapshot per case was digitalized and the staining intensity was measured in relation to a series of segmentation grey levels (0 – 255). The data were mapped on the principal measures Shannon’s and structural entropy as well as on the entropy flow derived from texture analysis.Results: The mapped functions of entropies display with significant changes between the galectin-3 positive images and their negative control counterparts. The data indicate that the binding capacities of galectin-3 hold a significant function during the development of foetal chicken kidneys.Conclusions: Laboratory techniques that simulate time-related series of measurements can be used to describe and interpret biological functions in living organisms at the cellular level.
DiagnomX GmbH
2016-04-21
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/106
10.17629/www.diagnosticpathology.eu-2016-2:106
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/106/117
Copyright (c) 2016 Klaus Kayser, Stephan Borkenfeld, Rita Carvalho, Amina Djenouni, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/256
2019-08-22T15:36:31Z
dpath:EDI
www.diagnosticpathology.eu: Reflections of 2017 – Perspectives on 2018
Kayser, Klaus
The peer reviewed open access journal www.diagnosticpathology.eu remains still the only financially autonomous, solely science and medicine obliged journal. It is embedded in a medical communication network of different service nodes.The nodes include the unique Virtual International Pathology Institute (VIPI, www.diagnomx.eu/vipi), an automated image measuring system (EAMUS), a lexicon of air borne hazards such as natural and synthetic mineral fibers, fine granulate and air pollutants (Natural and Synthetic Mineral Fibers affecting Man), an anatomy training course, and a collection of sixty rare and common lung diseases. It offers access to the articles of the first solely electronically distributed journal of pathology (Electronic Journal of Pathology and Histology)In 2017 we focused on the implementation of a new open journal system (OJS) release. We had to correct several inborn errors prior to the final usage. Therefore, the announced collection of virtual slides in concordance with the original publications remained still in its start phase. The journal’s ‘outfit’ has been adjusted to the modern styles in use.The number of submitted articles declined remarkably, and the journal experienced hard competition in 2017. The main reasons are a missing Scientific Citation Index (SCI) and its listing in journal databanks such as pubmed. Entropy calculations of the journal’s scientific impact and value are in the range of well known pathology journals such as the conventional paper printed ‘The Pathology Journal’.The implemented specific publication tools ‘publish beside the microscope’ and the submission of contributions for ‘interactive publication’ have been successfully tested but only rarely been used. We still expect attractive and scientifically high standard publications in 2018.
Keywords: www.diagnosticpathology.eu, open source journal, communication network, virtual slide, automated measurement, predatory journal.
DiagnomX GmbH
2017-12-17
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/256
10.17629/www.diagnosticpathology.eu-2017-3:256
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/256/551
Copyright (c) 2017 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/128
2018-06-19T09:14:47Z
dpath:EP
Virtual Microscopy New, Old, Out, Or Just A Part Of Education
Klempert, Iris
Jöhrens, K.
Introduction/ BackgroundMore than six years ago – accompanying the start of the new study program “Modellstudiengang†– we began a virtual microscopy program for our students. This started with slides to accompany the course to use during the lesson and for review of the slides at home (or in the library). But we wanted to go further.How far have we come? AimsOur aim was to provide our students with more benefi- cial information and to increase the amount of material available - in the form of slides and accompanying exercises.A secondary goal was streamlining the education of our students (fewer slides to manage and better opportuni- ties for students to prepare for lessons). MethodsThe slides were scanned using NanoZoomer 2.0-HT slide scanner.The virtual slides were made available to students using Slidebox system (version 4.4.3.) in three different ways:We provided annotated slides with healthy (physio- logical) and diseased (pathological) samples to ac- company the entire course. Some of the slides were for use during lessons, others as supplementary material.The virtual slides were integrated into a new style of lecture (“blended learningâ€) mixing learning opportu- nities from case reports, including clinical information; radiological images; and virtual slides. To review acquired knowledge memory-quizzes were used.We complement the cases seen in the practical course “Autopsy – How, why, to what end?†with histology. Thus students are able to have a complete overview of the case from clinical history, to macroscopic findings and their correlation with the microscopic findings, to the final report. ResultsUsually the students were suprised, when they first come in contact with the virtual microscopy. But the Initial suprise yields to experimentation and getting used to it. Virtual microscopy is not only just a part, but an import- ant part of our education.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/128
10.17629/www.diagnosticpathology.eu-2016-8:128
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/128/266
Copyright (c) 2016 I. Klempert, K. Jöhrens
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/271
2019-08-22T16:45:27Z
dpath:EDI
www.diagnosticpathology.eu: 2018 Reflections – Perspectives 2019
Kayser, Klaus
Basics: The peer reviewed open access journal www.diagnosticpathology.eu remains the only peer reviewed scientific journal that publishes virtual slides. Several innovative procedures have been implemented too which can only be performed and distributed in an electronic environment. These include for example annotations of text and images, and visual / acoustic display of animations. www.diagnosticpathology.eu is a non - profit oriented and financially autonomous journal. It is supported by volunteers and only obliged to science and medicine. These features permit a flexible and fast implementation of recently developed publication tools. It is part of a scientific communication network and consists of different service nodes which act in a cloud.Compartments: The nodes include the closed PHP forum Virtual International Pathology Institute (VIPI, www.diagnomx.eu/vipi ), an automated image measuring system (EAMUS), a lexicon of air borne hazards such as natural and synthetic mineral fibers, fine granulate and air pollutants (Natural and Synthetic Mineral Fibers affecting Man), an anatomy training course, and a collection of sixty rare and common lung diseases. All articles of the worldwide first solely electronically distributed journal of pathology (Electronic Journal of Pathology and Histology) are herein accessible without any fee for the readers.Short report of 2018: In focus have been the implement of virtual slides (VS) and the publication of articles which address theoretical and practical issues of digital pathology. A ‘general pathologist’ might not be familiar with these issues; however, they are already waiting at the horizon. These include discussions on a ‘potential replacement’ of a diagnostic pathologist by an autonomous computerized diagnosis system as well as basic principles of scientific communication and ‘work distribution’.The guidelines of digital pathology presented by the Professional Association of German Pathologists have been included as well. VS are included in the articles in close collaboration with smartinmedia GmbH & Co KG www.smartinmedia.com using the image visualization and annotation system www.easyzoom.com.Five characteristic examples of virtual slides are included in this editorial. They exemplarily demonstrate completely digitized routine glass slides of a rare case (pulmonary Morbus Castleman, hyaline vascular type, HE stain, DAB antibody immune histochemical stains, CD3, CD20, CD21, Factor VIII). The reader might check the image quality, navigate, and annotate the VS. The details of VS image evaluation are described in detail in the appendix I.All published articles are now open for text annotations by the author and / or reader too, either in a private section or in an environment open for all readers. The details of adequate annotation by the open access system www.hypothes.is are described in appendix II.Oral presentations have been equipped with a bar code and provided with a DOI reference. We consider them a bridge between the ‘classic review performance’ and a potential new publication performance which neglects reviews. It will hold on or to delete the article after a certain time dependent on specific ‘article hold on’ measurements (which might include conventional rewire statements too). The number of published articles remained limit, and stayed at the low level of publications in 2017. The main reasons have been mentioned in 2017 already and include a missing Scientific Citation Index and listing in journal data banks such as PubMed. Both issues primarily focus on financial issues (the higher the SCI the more expensive is the publication fee). They are of limited scientific value and do not really promote innovative ideas or experiments to our opinion.
DiagnomX GmbH
2018-12-23
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/271
10.17629/www.diagnosticpathology.eu-2018-4:271
Diagnostic Pathology; Vol 4 No 1 (2018): 2018
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/271/562
Copyright (c) 2018 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/139
2018-06-19T09:27:59Z
dpath:SY01
Automated Ki67 Hotspot Detection For Breast Cancer Biopsies
Pilutti, David
Pegolo, E.
La Marra, F.
Della Mea, Vincenzo
Di Loreto, C.
Introduction/ BackgroundThe quantification of immunohistochemical Ki67 and the detection of active areas of tumor cell proliferation (hotspots) have a critical importance in the prognosis and treatment planning for breast cancer.AimsIn this work an automated and robust method for the detection of hotspot areas in breast cancer biopsies is proposed with the aim of supporting the pathologists by highlighting hotspot areas.MethodsThe proposed method has been tested on one Ki67 stained image from Openslide [1] acquired at 40x with an Hamamatsu scanner and on 5 Ki67 stained images of breast cancer biopsies acquired at 40x with AperioCS. Each input image is divided in tiles, whose colors are deconvolved using the method of Ruifrok [2] to estimate the presence of Ki67. Tiles with an estimated Diaminobenzidine (DAB) positivity of more than 5% are considered as potential hotspots. Â Neighbouring positive tiles are merged to form a final hotspot area. The three hotspot areas with higher DAB positivity are also highlighted in the output. The hotspot areas are then written in an XML file which is read by a medical image viewer such as Aperio ImageScope. The proposed method has been implemented in Java using the BioFormats open source library [3].ResultsThe color deconvolution of each tile has been performed by applying the standard Hematoxylin/Diaminobenzidine (H/DAB) deconvolution matrix provided in Fiji [4]. The tests have been performed at different zoom levels resulting in similar, coherent outputs of hotspot areas. The resulting hotspot areas have been validated by visual comparison with the hotspot areas determined by experts, showing a significant superimposition as shown in Fig. 1. The proposed method has been compared with the ASH method [5] for the image acquired with Hamamatsu scanner, producing similar results in comparable time.In conclusion, a new fully automated method for the detection of Ki67 hotspot areas in breast cancer biopsies has been proposed to support the pathologist by highlighting different hotspot areas. It is able to process different medical images formats, making it more interoperable. The time performance is comparable with existing methods such as ASH [5]. The proposed method at low magnification such as 1x, 2x, and 4x produced varying results influenced by the size that each tile assumes at such magnification levels. Further extension of the proposed method will also include the MIB-1 estimation within the hotspot areas as well as extensive testing and validation. This work is partially founded by the EU FP7 program, grant number 612471.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/139
10.17629/www.diagnosticpathology.eu-2016-8:139
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/139/293
Copyright (c) 2016 D. Pilutti, E. Pegolo, F. La Marra, V. Della Mea, C. Di Loreto
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/156
2018-06-19T09:10:31Z
dpath:CAD
Long-Term Application Of Automated Ki67 Quantification In Routine Breast Cancer Diagnostics
Wienert, Stephan
Klauschen, F.
Loibl, S.
von Minckwitz, G.
Denkert, C.
Introduction/ BackgroundThe measurement of cell proliferation via Ki67 immunohistochemistry is an important part of tumor diagnostics leading to treatment decisions. The assessment according to the current guidelines is very time consuming which likely leads to counting only few cells or making the analysis completely estimated in many cases. Here, automated image analysis promises a standardized, time-saving and reproducible assessment.AimsWe prior developed a computerized method that allows for an automated scoring of Ki67. This approach was validated with a study cohort of more than 1000 patients and showed a very high significance in both overall and disease free survival. The aim of this study was to test the capability of this method for the application in the daily routine diagnostics with the concomitant time pressure and huge variability in the patient material and staining results.MethodsThe developed computer algorithm and software was applied in daily routine breast cancer diagnostics under real conditions over more than one year. More than 100 cases have been analyzed.ResultsThe retrospective analysis showed that the method was capable of accurately processing most of the images. Problems occurred when the counter staining was too weak which made it even difficult to conventionally assess those images. A user interaction was required in some cases to exclude falsely counted non-tumor cells.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/156
10.17629/www.diagnosticpathology.eu-2016-8:156
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/156/171
Copyright (c) 2016 S. Wienert, F. Klauschen, S. Loibl, G. von Minckwitz, C. Denkert
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/172
2018-06-19T09:09:06Z
dpath:STD
Optimal Image Data Compression For Whole Slide Images
Isola, J.
Introduction/ BackgroundWhole slide scanning is rapidly entering routine pathology laboratories. Modern scanners enable digitization of tens or even hundreds of thousands slides each year. If all WSI images are stored permanently, hundreds of terabytes image files need to be stored. It is essential to use image storage methods that preserve the scan image quality, but also keep storage costs in a reasonable level.AimsToday all WSIs are stored with lossy compression methods using a variety of different file formats. At the practical level it is important to find an image file format, which results in small-sized image files but retaining image quality as “visually losslessâ€.MethodsIn this study we compared file formats ofHamamatsu, Aperio, and 3D-Histech scanners to standard JPEG2000 and to JPEG2000 specially optimized for brightfield histology WSIs. As for image quality readout we used standardized resolution charts, and evaluation by three pathologists who ranked the images by their visual quality, when displayed on a 4K computer monitor.ResultsDifferences in WSI file sizes of scanned images deemed “visually lossless†were significant. If we set Hamamatsu Nanozoomer .NDPI file size (using its default “jpeg80 qualityâ€) as 100%, the size of a “visually lossless†JPEG2000 file was only 15-20% of that. Comparisons to Aperio and 3D-Histech files (.svs and .mrxs at their default settings) yielded similar results. A further optimization of JPEG2000 was done by treating empty slide area as uniform white-grey surface, which could be maximally compressed. Using this algorithm, JPEG2000 file sizes were only half, or even smaller, of original JPEG2000. Variation was due to the proportion of empty slide area on the scan. We anticipate that wavelet-based image compression methods, such as JPEG2000, have a significant advantage in saving storage costs of scanned whole slide image. In routine pathology laboratories applying WSI technology widely to their histology material, absolute cost savings can be substantial.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/172
10.17629/www.diagnosticpathology.eu-2016-8:172
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/172/299
Copyright (c) 2016 J. Isola
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/188
2018-06-19T09:07:02Z
dpath:MIP
Semi-Automatic Quantification Of mRNA Expression In Whole-Slide Tissue Images
Meas-Yedid, Vannary
Fuica, O.
Boukerroucha, M.
El Guendi, S.
Dallongeville, S.
Olivo-Marin, J.-C.
Josse, C.
Marée, R.
Introduction/ BackgroundFor complex diseases, commercially available anti- bodies directed again specific protein sometimes lack the specificity required for clinical purpose. Therefore, novel techniques have been proposed recently to better assess the expression status of molecules at the mRNA level, e.g. by in situ hybridization. With such a technique, single-molecule signals can then be quantified on a cell-by-cell basis in whole tissue slides. However, highly heterogeneous expression of mRNA is often observed at the tissue level, requiring the development of accurate and reproducible quantification methods.AimsIn this work, our aim is to propose and evaluate a methodology for the quantification of mRNA expression in digital slides to help biomedical researchers to analyze their large-scale imaging data. In particular, we will work on a dataset of breast cancer tissue samples and evaluate the accuracy of such a methodology to quantify Breast cancer susceptibility gene 1 (BRCA1) mRNA expression levels. BRCA1 is a tumor suppressor gene associated with the triple negative breast cancer (TNBC) subtype. An accurate technique to determine BRCA1 protein tumoral expression status in TNBC would allow for informed decision and choosing adapted treatments.MethodsData: To design and evaluate our methodology, we use the data from [1]. In that study, the BRCA1 mRNA expression was assessed by in situ hybridization using RNAscope technology [2] (ACD-Bioke) for formalin-fixed, paraffin-embedded tissue samples. 88 glass slides were scanned (Hamamatsu, 40X, 0.23µm/pixel) and transferred on a Cytomine server (http://www.cytomine.be/) [3]. These slides correspond to 62 tumours (TNBC subtype). Using Cytomine web manual annotation tools, a total of more than 200 regions of interest were manually drawn by an expert in these whole-slide images. Then, independent assessment was performed by two observers in these ROI: they manually draw point annotations corresponding to tens of thousands of BRCA1 mRNA expression signals.Algorithms: We have developed the Icytomine plugin to communicate between Icy and Cytomine. It allows the importation of the subtumor images at a desired resolution and the expert annotations from Cytomine and the exportation of detection results from Icy software (http://icy.bioimageanalysis.org) [4]. In order to quantify mRNA signals, we combined several image processing routines in the Icy. Our workflow is composed of three steps: 1) color deconvolution [5] to extract the dark brown staining, 2) detection of spots based on undecimated wavelet transform [6], 3) post-processing to remove artifacts based on size, shape and color features. This transform is fast and ideal for representing isotropic objects. We will use a colocalisation coefficient to quantify the concordance between the experts. For a purpose of automation, we use scripts and protocols of Icy.ResultsAn illustration of our results is given in Figure Our ongoing large-scale empirical study stresses the need for more confident ground-truths hence more robust algorithms. Interestingly, our current strategy detects accurately spot locations. We believe it will help us to create a larger ground-truth dataset using expert proofreading. We will report at the conference our best quantitative results. Overall, we believe that our approach will speedup in a confident way the quantification of mRNA signals in whole-slide tissue samples. Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/188
10.17629/www.diagnosticpathology.eu-2016-8:188
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/188/317
Copyright (c) 2016 V. Meas-Yedid, O. Fuica, M. Boukerroucha, S. El Guendi, S. Dallongeville, J.-C. Olivo-Marin, C. Josse, R. Marée
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/212
2018-06-19T09:02:14Z
dpath:SY01
Significance of Morphometric Analysis of HPV-Induced Cervical Dysplasia
Djurdjevic, B. Vukomanovic
Introduction/ Background Genomic integration of high-risk human papilloma virus in the nucleus of cervical epithelial mucosal cells leads to epithelial dysplasia.Aims The aim of this study was to establish the significance of morphometric analysis of the nuclear area in the assessment of the degree of cervical dysplasia.Methods This study included 85 women with primary, previously untreated lesions, and colposcopic findings indicating dysplasia, in whom a cytological test by Papanicolaou method was interpreted according to the Bethesda criteria as low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL), and atypical squamous cells of undetermined significance (ASCUS). We performed human papiloma virus (HPV) typing by PCR for evidence of viruses’ types 16, 18, 31, 33. After biopsy of the cervical mucosa, we performed hematoxylin-eosin (H-E) and morphometric analysis of tissue samples. Morphometric analysis was performed on H&E stained slides at 400 x magnification. We analyzed four representative fields of dysplasia; 70 nuclei were photographed, using a digital optical microscope (Nikon Coolscope, Japan) and the morphometric computer program. The control group consisted of 10 women without dysplasia and without a verified infection of cervical high-risk HPV.Results A high statistical correlation between the degree of dysplasia and the area of nuclei at different degrees of cervical dysplasia (p = 0.000). The high-grade cervical dysplasia had a more than 2-fold higher level of ranking in comparison to low-grade dysplasia, and a more than 10-fold higher ranking than the control group without cervical dysplasia. Our results suggest that the use the morphometric analysis is useful in the assessment of cervical epithelial dysplasia.
DiagnomX GmbH
2016-08-31
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/212
10.17629/www.diagnosticpathology.eu-2016-8:212
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/212/353
Copyright (c) 2016 B. Vukomanovic Djurdjevic
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/61
2018-06-19T09:06:21Z
dpath:REV
A review of graph-based methods for image analysis in digital histopathology
Sharma, Harshita
Zerbe, Norman
Lohmann, Sebastian
Kayser, Klaus
Hellwich, Olaf
Hufnagl, Peter
Digital histopathology, graph-based methods, whole slide images, medical image analysis, image understanding, tissue architecture, spatial arrangement
Digital image analysis of histological datasets is a currently expanding field of research. With different stains, magnifications and types of tissues, histological images are inherently complex in nature and contain a wide variety of visual information. Several image analysis techniques are being explored in this direction. However, graph-based methods are gaining most popularity, as these methods can describe tissue architecture and provide adequate numeric information for subsequent computer-based analysis. Graphs have the ability to represent spatial arrangements and neighborhood relationships of different tissue components, which are essential characteristics observed visually by pathologists during investigation of specimens. In this paper, we present a comprehensive review of the graph-based methods explored so far in digital histopathology. We also discuss the current limitations and suggest future directions in graph-based tissue image analysis.
DiagnomX GmbH
German Academic Exchange Service (DAAD)
2015-08-15
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/61
10.17629/www.diagnosticpathology.eu-2015-1:61
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/61/53
Copyright (c) 2015 Harshita Sharma, Norman Zerbe, Sebastian Lohmann, Klaus Kayser, Olaf Hellwich, Peter Hufnagl
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/225
2018-06-19T08:58:25Z
dpath:QAM
Image Quality – Requirements For Clinical and Research Applications
Zerbe, N.
Heim, D.
Wetzel, T.
Domhardt, M.
Wienert, S.
Alekseychuk, A.
Schlüns, K.
Hufnagl, P.
Introduction/ Background
The digitalization of slides and subsequent utilization of whole slide images has a highly visible penetration within digital pathology workflows. Not only research applications moving towards daily use, but also clinical pathology applies digital images increasingly. The use of virtual microscopy, with all of their advantages and benefits, requires additional efforts to assure sufficient image quality [1]. This consist of multiple aspects to be fulfilled, such as sharpness, tissue completeness, color fastness primary and additional secondary properties like existence of artifacts, compression, availability of digitalization metadata and others.
Aims
Scanning devices use multiple different technologies such as brightfield, laser or confocal. Moreover, they partly divide into patch and line scanning concepts. But not only hardware is constantly changing due to upgrades or further developments but also software algorithms, e.g. focus and stitching, are modified. This requires a standardized measurement algorithms and procedures to assure an appropriate quality for relevant aspects, depending on dedicated use cases.
Methods
Each dedicated requirement towards image quality has to be investigated separately, due to the fact that they differ in their origin. Distortions may be introduced through slide preparation, calibration of scanning device or even scanner software parameter. Therefore, we developed multiple algorithms and software tools to calculate a quality measure for each aspect automatically. Recently we are focusing on image sharpness [2], color fastness [3, 4] and completeness of tissue. Sharpness is measured by a no-reference focus algorithm per slide. Color fastness is calculated based on CIEDE2000 [5] for a reference IT8.7/1 color target mounted onto a glass slide per scanner. Completeness is automatically analyzed based on registration and comparison of whole slide overview image and preview camera data. Secondary quality parameters were not part of this investigation.
Results
We established a standard operation procedure to automatically apply slide based tests directly after digitalization. This enables scanning personal to execute quality inspection at a glance and schedule insufficient whole slide images for a rescan. Moreover, we made some of these tools available as a web-based service including a based web-frontend with user management. This enables everyone within the digital pathology community to validate their slides, scanning devices and scanning parameter.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/225
10.17629/www.diagnosticpathology.eu-2016-8:225
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/225/380
Copyright (c) 2016 N. Zerbe, D. Heim, T. Wetzel, M. Domhardt, S. Wienert, A. Alekseychuk, K. Schlüns, P. Hufnagl
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/101
2018-06-19T09:04:46Z
dpath:DIA
How do I diagnose Primary neuroendocrine tumor of the breast
Fónyad, László
Piros, László
Arató, Gabriella
Keyword - Diagnosis: Primary neuroendocrine tumor of the breast Keyword - differential diagnosis: Metastatic neuroendocrine tumor Keyword - side findings: Keyword - organ: breast Keyword - methods: Immunohystochemistry
Primary neuroendocrine tumor of the breast is a rare condition. Although 20-30% of primary breast cancers show neuroendocrine differentiation to some degree, according to the WHO classification, at least 50% of the tumor cells have to be positive with at least one neuroendocrine immunohistochemical marker to establish a diagnosis of neuroendocrine tumor of the breast while clinically excluding other primary sites and a metastatic nature. Due to the low prevalence of this disease our understanding of its development, prognosis and effective therapy is limited. Up to date there are 125 cases reported in the English and non-English literature, now including our own case as well. We report a case of a 75 years old female. The patient presented with a 2 cm large mobile nodule in the upper outer quadrant of the left breast. Lumpectomy was performed based on fine needle aspiration cytology with a positive result showing malignant proliferation. Examination of the surgical specimens revealed neuroendocrine differentiation in approximately 90% of the tumor cells. Immunohistochemical studies and additional imaging studies revealed no other primary.
DiagnomX GmbH
2016-02-04
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/101
10.17629/www.diagnosticpathology.eu-2016-2:101
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/101/103
Copyright (c) 2016 Gabriella Arat
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/249
2019-08-22T15:52:02Z
dpath:RES
Evaluation of a confocal WSI scanner for FISH slide imaging and image analysis
Fu, Xiujun
Lennerz, Jochen K.
Onozato, Maristela
Iafrate, Anthony
Yagi, Yukako
Background: Technological advances contribute to the maturation of digital pathology in clinical and research applications. However, there are only few reports on fluorescence scanning especially on confocal fluorescence imaging technology in digital pathology, which has superior depth resolution compared to wide-field fluorescence imaging. Here, we explored the features of a confocal WSI scanner for typical diagnostic and research imaging applications of fluorescence in situ hybridization (FISH) assay.Methods: Multi-layer stacking (Z-stack) which stores all image information from each layer, and extended focus which stores the optimal image information from all scanned layers, featured in the Pannoramic Confocal scanner (3DHISTECH Ltd., Budapest, Hungary) were employed in digitizing 14 FISH slides (ALK, EGFR, and multi-gene). The slides were scanned with a 40× water immersion objective producing a final image with pixel resolution of 0.1625 µm/pixel. Z-stack and extended focus were used for N=6, 13, and 26 multiple layers scanning at 1, 0.4, and 0.2 µm depth intervals respectively. Single-layer scanning was also done for comparison. Scanning time and resultant file size were recorded. The CaseViewer from 3DHISTECH was used to visualize images and export the annotated regions, and the exported images were further analyzed in Imaris (Bitplane, Zurich, Switzerland) for 3-dimensional reconstruction, nuclear segmentation, and the quantification and co-localization analysis of dots inside nuclei. Quantification data from Imaris were imported into Excel for statistic analysis.Results: Confocal fluorescence scanning of FISH slides enabled sharper image than wide-field scanning, although it required longer scanning time and larger file storage. More intra-nuclear dots were quantified from multi-layer Z-stack images than single-layer images, and the Z-stack increased scanning time and image file size. Furthermore, there were a reduced in the number of dots and an increased in the number of co-localized dots in extended-focus images compared to Z-stack. Dots in multiple channels were quantified and analyzed automatically, which supports clinical diagnosis of gene amplification, deletion, and translocation. Three-dimensional reconstruction of Z-stack produced precise measurement of spatial distance, which supports molecular research.Conclusion: Confocal provides sharper image than wide-field for FISH slide scanning. Extended focus reduces file size and storage, but could cause inaccurate analysis due to misinterpretation of overlapping information. Z-stack scanning provides high volume image information for spatial analysis. We foresee confocal multi-layer scanning as a digital pathology application tool for FISH imaging in both clinical and research in future.
DiagnomX GmbH
2017-08-07
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
application/xml
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/249
10.17629/www.diagnosticpathology.eu-2017-3:249
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/249/541
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/249/542
Copyright (c) 2017 Xiujun Fu
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/123
2018-06-19T09:14:11Z
dpath:TP
Mucinous Neoplasms Of The Appendix And Peritoneum: Virtual Microscopy For Histomorphologic Assessment And Interobserver Diagnostic Reproducibility
Villa, I.
Villeneuve, L.
Carr, N. J.
Isaac, S.
Glehen, O.
Capovilla, M.
Chevallier, A.
Croce, S.
Kaci, R.
Lang-Averous, G.
Laverriere, M.-H.
Leroux-Broussier, A.
Mery, E.
Poizat, F.
Valmary-Degano, S.
Verriele-Beurrier, V.
Gilly, F.-N.
Bibeau, F.
Dartigues, P.
Introduction/ BackgroundAmong gastrointestinal (GI) tumours, pseudomyxoma peritonei (PMP) from appendiceal origin has unique clinical and morphologic features. Due to the relative paucity of patients and the absence of therapeutic consensus, evaluation and refinement of the morphologic criteria used for assessment of the disease are still difficult. As a result, a uniformly accepted classification is still lacking. In collaboration with NJ Carr, who initiated the conference consensus process, in Basingstoke, and on behalf of the French group RENA-PATH, 11 experienced GI pathologists agreed to participate to a virtual workshop, in order to assess inter-observer variability in PMP diagnosis and staging.AimsThe goal of the study was to evaluate, for appendiceal and peritoneal mucinous neoplasms, the degree of concordance in the identification of diagnostic histological criteria by experienced pathologists, and to assess the degree of inter-individual variation in the application of WHO classification (2010) and TNM staging system (7th  edition).MethodsA single section stained with hematoxylin and eosin from 9 resected cases of mucinous neoplasms was selected by members of RENA-PATH. All digitalized at a maximum resolution (X40) using an HAMMAMATSU scanner system, to ensure that all participants evaluate exactly the same tumour areas; 1 to 16 questions were prepared for each case. On Teleslide web platform, interactive services provided by TRIBVN. All submitted cases were then reviewed by a panel of 11 pathologists with specific expertise and interest in PMP. Data were analyzed using SAS program.ResultsWhole slide set evaluated by all participants; no abstention or “unknown diagnosis†for any submitted case. Agreement for classification, WHO 2010:Appendiceal mucinous neoplasms: LAMN 83 %; mucinous adenocarcinoma 92%.Peritonei mucinous carcinoma: Low grade 91.7%; high grade 91.7%.Disagreement on the concept of High Grade AMN defined by low power architecture of LAMN + high grade cytology.Agreement for using pTNM classification (82%) in PMP.Pushing Invasion (PI) and dissection by acellular mucin (DAM) in appendix wall are not reproducible criteria and need to be better defined.Criteria need to be redefined to use HAMN according to a majority of participants.The identification of signet ring cells is not reproducible; the lesion needs to be better defined.Invasion of organs and pattern of invasion (broatfront invasion / classic by irregular glands or single cells with desmoplasia) are not reproducible criteria.Improvement in staging assessment is needed Conclusion: Although histopathological features of peritoneal disease are significant prognostic factors requiring pathologists to classify mucinous carcinoma peritonei (pseudomyxoma peritonei), reproducibility in interpretation must be improved. This international collaborative project allows pathologists worldwide to share their expertise and knowledge through a dedicated interactive workshop session. It is expected an improvement in the management of mucinous neoplasms of the appendix and peritoneum.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/123
10.17629/www.diagnosticpathology.eu-2016-8:123
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/123/258
Copyright (c) 2016 I. Villa, L. Villeneuve, N. J. Carr, S. Osaac, O. Glehen, M. Capovilla
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/134
2018-06-19T09:14:46Z
dpath:EP
Automated Quantification Of Proliferation With Automated Hot-Spot Selection In Phosphohistone H3/Mart1 Dual-Stained Melanomas
Nielsen, P. S.
Riber-Hansen, R.
Schmidt, H.
Steiniche, T.
Introduction/ BackgroundStaging of melanoma includes quantification of a pro- liferation index, i.e., presumed melanocytic mitoses of H&E stains are counted manually in hot spots. Yet, its reproducibility and prognostic impact increases by im- munohistochemical dual staining for phosphohistone H3 (PHH3) and MART1, which also may enable fully automated quantification by image analysis. AimsTo ensure manageable workloads and repeatable measurements in modern pathology, the study aimed to present an automated quantification of proliferation with automated hot-spot selection in PHH3/MART1- stained melanomas.MethodsFormalin-fixed, paraffin-embedded tissue from 153 consecutive stage I/II melanoma patients was immuno- histochemically dual-stained for PHH3 and MART1, and whole slide images were captured. An algorithm that automatically detects the number of PHH3/MART1-pos- itive cells was developed using commercial software. In preprocessing, the intensity band of the HSI color model and color deconvolution including a standard deviation filter highlighted PHH3 positivity. Threshold- ing functions classified the image into brown PHH3, red MART1, and blue hematoxylin. Finally, postprocessing al- gorithms pinpointed PHH3/MART1-positive cells based on size, MART1 surrounding, color intensity, and nuclearirregularity. Based on the labels of image analysis, a hot spot was automatically selected by a processing step where circles that detect PHH3/MART1-positive cells produce a heat map according to their cluster. The number of PHH3/MART1-positive cells was counted both automatically and manually in the global tumor area and in a manually and automatically selected hot spot, i.e., a fixed 1-mm2 square.ResultsThe mean difference between manual and automated global counts was 2.9 cells/mm2 (P = 0.0071) and 0.23 cells per hot spot (P = 0.96) for automated counts in manually and automatically selected hot spots. In 77% of cases, manual and automated hot spots overlapped. Fully manual hot-spot counts yielded the highest prog- nostic performance with an adjusted hazard ratio of 5.5 (95% CI, 1.3–24, P = 0.024) as opposed to 1.3 (95% CI,0.61–2.9, P = 0.47) for automated counts with automated hot spots. In conclusion, the automated index and auto- mated hot-spot selection were highly correlated to their manual counterpart, but altogether their prognostic impact was noticeably reduced. Because correct rec- ognition of only one PHH3/MART1-positive cell seems important, extremely high sensitivity and specificity of the algorithm is required for prognostic purposes. The automated analysis may thus still aid and improve the pathologists’ detection of mitoses in melanoma and possibly be useful in other malignancies and future research studies.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/134
10.17629/www.diagnosticpathology.eu-2016-8:134
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/134/272
Copyright (c) 2016 P. S. Nielsen, R. Riber-Hansen, H. Schmidt, T. Steiniche
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/284
2022-04-08T14:52:45Z
dpath:CAS
Pituicytoma- Case Report Of A Rare Sellar/ Suprasellar Mass
Mani, Sandeep
Lakshmanan, Archana
Subramanyan, Annapurneswari
Background: Pituicytoma is a rare primary tumor of the sellar and suprasellar region, arising from the pituicytes which are specialized glial cells in the neurohyphophysis and infundibulum.
Objective: Radiological features being non- specific, histopathological examination and immunohistochemistry will help us in arriving at the correct diagnosis.
Material and methods: We report a case of pituicytoma in a 48 year old woman arising in the sellar/suprasellar region.
Results: Histopathological examination of the lesion showed elongate bipolar spindle cells arranged in fascicular and storiform pattern. The neoplastic cells were diffusely positive for TTF-1, S-100, vimentin, variably positive for GFAP, negative for synaptophysin and Ki-67 index was less than one percentage.
Conclusion: Pituicytomas are rare tumors of the sellar and suprasellar region and its diagnosis is typically based on histopathological examination with a varied immunohistochemical profiles but with consistent TTF-1 positivity.
DiagnomX GmbH
2022-03-31
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/284
10.17629/www.diagnosticpathology.eu-2022-7:284
Diagnostic Pathology; Vol 7 No 1 (2022): Vol 7 No 1
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/284/575
Copyright (c) 2022 SANDEEP MANI
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/151
2018-06-19T09:28:24Z
dpath:VM
Cytomine: An Open-Source Software For Collaborative Analysis Of Whole-Slide Images
Marée, R.
Rollus, L.
Stévens, B.
Hoyoux, R.
Louppe, G.
Vandaele, R.
Begon, J.-M.
Kainz, P.
Geurts, P.
Wehenkel, L.
Introduction/ BackgroundMajor software for whole-slide image analysis and digital pathology are proprietary / closed-source which is not in line with current trends in open science and reproducible research. While some open-source software libraries exist for digital pathology (e.g. OpenSlide or NDPITools for reading and converting slide formats), to the best of our knowledge no open-source software exists that combines remote visualization, collaborative and semantic annotation, and semi-automated analysis of digital slides.AimsOur Cytomine project started in 2010 to build a rich web environment for multi-gigapixel imaging data. This tool has been designed with the following objectives in mind: provide remote and collaborative principles, rely on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way (using user-defined ontologies), efficiently support high-resolution multi-gigapixel images (incl. major scanner image formats), and provide mechanisms to readily proofread and share image quantifications produced by any image recognition algorithms. By emphasizing collaborative principles, our aim with Cytomine is to accelerate scientific progress and to significantly promote image data accessibility and reusability. We want to break common practices in this domain where imaging datasets, quantification results, and associated knowledge are still often stored and analyzed within the restricted circle of a specific laboratory.MethodsSince the start of our project, we collaborated with biomedical researchers, pathologists, and computer scientists to shape the software and meet user and researcher needs. During development, we combined recent web, database, software development, and machine learning methodologies using open-source libraries. We also adopted modern practices (such as continuous integration and code quality testing) to build an industrial-grade software. In order to enable software extensibility and interoperability, we used a RESTful architecture so that e.g. other computer scientists can import/export data with their own algorithms and share their quantification results.ResultsThe Cytomine software (http://www.cytomine.be/) has been released under an open-source licence since January 2016. In terms of code, Cytomine is composed of roughly 70K lines of code decomposed into its four main modules: Cytomine-Core (web server and database), Cytomine-WebUI (web user interface), Cytomine-IMS (image server), and Cytomine-DataMining (image recognition algorithms). Cytomine has now been used on various bio(medical) imaging datasets that involved various types of images and experts in different collaborative operating modes to perform various quantification tasks (in renal pathology, toxicology, developmental studies, lung and breast cancer research,...). By providing detailed documentation, installation instructions and source code, we hope that Cytomine will be used and extended for many purposes in digital pathology. Overall, we believe Cytomine is an important new tool of broad interest to foster active communication and distributed collaboration between pathologists, life scientists, computer scientists, teachers and students working with digital slides.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/151
10.17629/www.diagnosticpathology.eu-2016-8:151
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/151/166
Copyright (c) 2016 R. Marée, L. Rollus, B. Stévens, R. Hoyoux, G. Louppe, R. Vandaele, J.-M. Begon, P. Kainz, P. Geurts, L. Wehenkel
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/167
2018-06-19T09:08:24Z
dpath:IMT
Microanatomical Analysis And Quantification Of Plasma Cell Niche Interactions In The Bone Marrow
Hauser-Hankeln, A.
Zehentmeier, S.
Cseresnyes, Z.
Holzwarth, K.
Stefanowski, J.
Reismann, D.
Niesner, R.
Radbruch, A.
IntroductionLong-lived plasma cells (PCs), responsible for the production of long-term antibody titers, have been shown to survive in the bone marrow for months to years in the absence of antigen. They are supported by a special microenvironment, the PC survival niche. Various cell types have been reported to contribute to this niche by providing survival factors, e.g. CXCL12-producing reticular stromal cells. Additionally, hematopoietic cells have been shown to mediate PC survival in vivo, amongst them megakaryocytes and eosinophils, but the spatiotemporal dynamics of the various niche components in the tissue remain elusive.AimsThe aim of our work is to analyze the cellular and molecular composition of plasma cell survival niches in the bone marrow in situ.MethodsIn order to unambiguously quantify the localization of PCs, we are analyzing bone marrow cryosections and whole mounts for PCs, stromal cells, vasculature and accessory niche cells. Additionally, we have developed a computer modeling approach which allows us to distinguish random co-localization from non-random cell positioning.Using these approaches, we have previously shown that PCs directly contact reticular stromal cells in a non-random fashion, while 30% of PCs are found in 10 µm vicinity to eosinophils, which represent only transient contributors to the niche. We have now analyzed PC localization in relation to mineralized bone, bone marrow vasculature and hematopoietic cell types in 3 dimensions and found that PC niches are situated at large distance to sinusoids.ResultsSemi-automated 3D analyses of whole mounts allow for a comprehensive and unbiased quantification of PC localization and their possible interactions with accessory niche cells in the bone marrow. We show that the survival niche for long-lived PCs is located distant from sinusoidal blood vessels, in contrast to what has been reported for the hematopoietic stem cell niche. We are now testing ways to mobilize PCs from their niches, which should result in shifted PC localization - from vessel-distant to peri-sinusoidal spaces. We are further exploring ways to perform multiplexed histological analysis using multi-epitope ligand cartography (MELC) in the bone marrow in order to further characterize the plasma cell niche.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/167
10.17629/www.diagnosticpathology.eu-2016-8:167
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/167/324
Copyright (c) 2016 A. Hauser-Hankeln, S. Zehentmeier, Z. Cseresnyes, K. Holzwarth, J. Stefanowski, D. Reismann, R. Niesner, A. Radbruch
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/183
2018-06-19T09:09:45Z
dpath:EL
Development Of An Android Based Interactive Guide For The Berliner Medizinhistorisches Museum Der Charité
Klempert, Iris
Arndt, T.
Schnalke, T.
Hufnagl, P.
Zerbe, Norman
Introduction/ BackgroundPathology is the science of diseases that ranges from macroscopic to histologic, and of course molecular changes. To offer a holistic education we wanted to involve portable electronic devices to combine information on diseases with microscopic changes and formalin fixed organs (macroscopic preparation).AimsAt the time of compilation of this application there was no alternative, useful solution that offers the possibility of extensions towards virtual microscopy. Moreover, other solutions always use fixed databases or do not provide tools for content updates. Hence, it was required to create an appropriate system. Additional aimed feature are high performance, data-caching and the opinion to use the app in offline mode without a network connection. By the reason of the large amount of smartphone and tablet computer that runs the Android operating system and cheaper devices this platform was used.MethodsWe combined our virtual microscope „AndroScope“ [1] with a new developed user-interface of the „Berliner Medizinhistorisches Museum“(BMM) for android based mobile devices such as smartphone and tablet computer. As content we used images of the exhibition samples, information on the corresponding organ and disease, as well as the epidemiology data and whole slide images for visualization of histological changes. Linkage of digital content and samples is realized using QR-codes to assure valid and user-friendly recognition. We have also evaluated other technologies such as NFC, Bluetooth, WiFi or GPS to ensure that the QR-Code solution is the best opinion [2]. The application offers an online mode with full functionality and an offline mode with limited access to images as well as to the virtual microscope. The application main database is stored local on the android device and online update capabilities were added.ResultsThe “BMM Guide†is available for all visitors of the museum on lendable devices or for students (professional audience) using their personal devices and installing the application manually via the web-access eduroam. The guide is connected to the internet. It is designed to easily expand, update or transfer the content catalogue data. At the moment there is a connection between the exhibit and text-, image-, video- or virtual microscope content via QR-Code. The offline mode is limited to the connection between text content and the exhibit. We also implemented a multi-language support for English and German. The application has information like room plans, opening times and latest news of the museum. The museum guide is an easy handable, selfexplaining blended learning tool that can be embedded in the general education. .This guide for the exhibitions of the Berliner Medizinhistorisches Museum opens a new branch for self-study of students. Nevertheless he still has a potential to be integrated in curricular lectures in the future.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/183
10.17629/www.diagnosticpathology.eu-2016-8:183
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/183/310
Copyright (c) 2016 I. Klempert, T. Arndt, T. Schnalke, P. Hufnagl, N. Zerbe
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/199
2018-06-19T09:06:43Z
dpath:TP
Towards Efficient Collaborative Digital Pathology: A Pioneer Initiative Of The FlexMIm Project
Racoceanu, D.
Ameisen, D.
Veillard, A.
Ben Cheikh, B.
Attieh, E.
Brezillon, P.
Yunès, J.-B.
Temerson, J.-M.
Toubiana, L.
Verger, V.
Pomerol, J.-F.
Klossa, J.
Lallemand, F.
Constant, P.
Capron, F.
Guettier, C.
Phan, N.
Bertheau, P.
Introduction/ BackgroundThe development of digital resources for pathologists is a long process before truly validated algorithms can be used in daily practice.AimsIn addition to developing new tools for helping Whole Slide Image (WSI) analysis by pathologists, the cooperative research project FlexMIm aims at setting up a shared platform allowing further technological improvements to be tested and evaluated online by a community of pathologists.MethodsThe FlexMIm consortium includes 27 pathology laboratories in the Paris area (coordinated by Assistance Publique-Hôpitaux de Paris), research laboratories from University Pierre et Marie Curie (UPMC Univ Paris 06) and University Paris Diderot, as well as 3 companies: TRIBVN, PERTIMM and Orange (project coordinator). Based on a cloud architecture, the project embeds a dedicated WSI database and visualisation support. Groups of partners developed dedicated algorithms. These algorithms have been tested separately, then integrated into the online platform. A large test and validation protocol, involving operational versions of these algorithms, is on-going among the 27 pathology laboratories participating to this project.ResultsOne algorithm was built for blur detection in WSI in order to improve the quality of the workflow. Other quantitative algorithms were built for immunohistochemical counts such as Ki67, for mitosis detection from H&E (Hematoxylin – Eosin) stained WSI and for supporting the detection of Regions of Interest (ROI) for dysplasia screening in inflammatory bowel diseases (IBD). A series of algorithms (as gland detections in IBD) are at the proof of concept stage. Dedicated semantics and research engine are included in the platform, supporting the ROI collaborative annotations in WSI. The ontology used is generated by an operational contextual graph produced and validated for IBD diagnosis, consolidated by a semantic template linked to the annotations of IBD WSI. Another collaborative tool on the platform allows the online implementation of ontologies, with creation and edition of concepts. A full IBD diagnostic ontology is already available and a prostate cancer diagnostic ontology is underway. A major point of this platform is that all participating pathologists can finally evaluate online all the resources developed during the project. Anonymised WSI uploaded by each pathologist can be annotated by all other pathologists. These WSI can then be analysed by all the algorithms and tools available in the platform. Pathologists can eventually fill evaluation forms that are analyzed by the project steering committee. Beside online resources, another goal of FlexMIm was to implement tools for faster WSI communication through networks especially in low bandwidth environments. The pathologists used a test bed in order to evaluate several compression algorithms on several visualisation devices (laptop, tablets), eventually leading to a “smart transportation†algorithm that can be activated in case of non-optimal network. Within 3 years, FlexMIm partners have thus built a platform which now integrates a whole set of algorithms to foster digital pathology adoption by a large cluster of Pathology laboratories.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/199
10.17629/www.diagnosticpathology.eu-2016-8:199
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/199/256
Copyright (c) 2016 D. Racoceanu, D. Ameisen, A. Veillard, B. Ben Cheikh, E. Attieh, P. Brezillon, J.-B. Yunès, J.-M. Temerson, L. Toubiana, V. Verger, J.-F. Pomerol, J. Klossa, F. Lallemand, P. Constant, F. Capron, C. Guettier, N. Phan, P. Bertheau
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/14
2018-06-19T09:07:28Z
dpath:RES
Texture and object related image analysis in microscopic images
Kayser, Klaus
Borkenfeld, Stephan
Djenouni, Amina
Kayser, Gian
Tissue-based diagnosis; content image analysis; MST entropy; Immunohistochemistry; Glycohistochemistry; Segmentation
Background
Tissue based diagnosis or surgical diagnostic pathology undergoes significant changes and focuses on image content analysis in our days. Herein we describe and discuss new approaches of content image analysis and compare their applications, benefits and constraints.
Theory
Any useful microscopic image contains information that can be evaluated and transferred into a tissue-based diagnosis. A correctly derived diagnosis depends upon the image information and the pathologist’s knowledge, i.e. his ability to recognize and transfer the image content information into clinical application. Thus, image information is related to external “disease†information and “pure†image content information. Application of external image information requires a separation of objects from the background, or segmentation procedures. “Pure†image information is solely pixel based. It can be analyzed using different approaches, such as entropy measure, construction of image primitives and their spatial distribution, or image similarity operations. Our approach uses entropy calculations dependent upon all possible gray value thresholds in combination with syntactic analysis of pixel based image primitives.
Implementation
Virtual slides underwent the evaluation of regions of interest (ROI) as described previously. ROIs were interactively controlled and subject for application of developed image analysis procedures. The “classic method†of object recognition and syntactic structure analysis is applied too. Trials were performed on antie Her2_new stained, DAB visualized, and glycohistochemically stained, AP visualized slides. The images were measured at magnifications, which correspond to x20, and x40 objectives.
Results
The algorithm displayed only weak changes of the evaluated gray level based structural entropy (GL-MST)-entropy in the selected ROIs in contrast to the whole image. In addition, significant differences could be obtained when the measures were associated to the clinical impact (diagnosis, fetal developing stage).Conclusions: Images textures and pixel primitives can serve for evaluating “pure†image content information. They do not require segmentation and additional external information for measurement. Interpretation of the measures, i.e. external information can be implemented at a later stage. The described algorithm is probably applicable for image analysis of different fields such as histology, forests, traffic, or can serve for objective image quality evaluation.
DiagnomX GmbH
2015-05-26
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
text/html
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/14
10.17629/www.diagnosticpathology.eu-2015-1:14
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/14/17
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/14/535
Copyright (c) 2015 Klaus Kayser, Stephan Borkenfeld, Amina Djenouni, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/220
2018-06-19T08:59:53Z
dpath:SY01
Analysis of Color Standardization Methods for the Automatic Quantification of IHQ Stain in Breast TMA
Fernandez-Carrobles, M. M.
Deniz, O.
Bueno, G.
Introduction/ BackgroundIHC biomarkers in breast TMA samples are used daily in pathology departments. This generates large amounts of information, which requires careful analysis [1]. Automatic methods to evaluate positive staining have been investigated since they may save time and reduce errors in the diagnosis that are due to subjective evaluation.AimsThe aim of this work is to develop a density tool able to automatically quantify the positive brown IHC stain in breast TMA. One of the problems when dealing with stained samples is color variation and distortion [2]. This is due to several factors such as the fixation process, the amount of stain or the digitalization process. One solution to the color variation problem is to apply standardization of reagents and procedures in histological practice. However, stains fade over time and therefore, it is not possible to achieve complete standardization with the current technology. In this paper, different methods for stain normalization have been analyzed and compared in density quantification.MethodsThe methods implemented for stain normalization are based on the use of color distribution by means of dominant color descriptor, scalable and color structure descriptor. These algorithms adjust the color values of an image on a pixel-by-pixel basis so as to match the color distribution of the source image to that of a target image. Then, two main processes were performed to estimate TMA density: a) evaluation of total cylinder area and b) quantification of IHC stained area. For the 1st process, the algorithm distinguishes between normal, broken or distorted cylinders. The 2nd process deals with the evaluation of the positive brown pixels inside the cylinder. The segmentation is based on Lab thersholding together with binary thresholding applied to the H, S and B channels of the HSV and RGB color models. Finally, the tool segments all the positive areas and quantifies the brown density areas.ResultsA dataset of 879 TMA images were used to evaluate the methods. TMAs were prepared with an automatic tissue arrayer (Arraymold tool) composed of 50 holes/TMA with a cylinder diameter of 2mm. Slides were stained using different IHC stains, that is, CD1A, CD4, CD8, CD21, CD57, CD68, CD83, CD123, CK19, OXP3, LAMp3 and S100. The acquisition of the digital TMA images was done with Aperio ScanScope XT scanner at 40x (0.25 µm/ pixel). Afterwards, each cylinder image was individually extracted [3]. The use of color standardization makes the segmentation robust and free of parameter setting. Furthermore, the standardization process is able to reduce noise and facilitate the density quantification. The results were compared to manual density quantification by expert pathologists. The tests carried out provided up to 98% agreement when color standardization was applied against 90% without color standardization. The biggest error comes from FOXP3 samples.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/220
10.17629/www.diagnosticpathology.eu-2016-8:220
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/220/375
Copyright (c) 2016 M. M. Fernandez-Carrobles, O. Deniz, G. Bueno
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/92
2018-06-19T09:01:44Z
dpath:DIA
How do I diagnose Odontoma
Mrachacz, Andreas
Kayser, Klaus
Kühnel, Thomas
Pappa, Spiridula
Schmidt, Frank
Odontoma, complex type; Paradontosis, calcification; Posterior maxilla; Exctraction
This 17 year old man of Turkish descent developed a solid somewhat painful mass at the region 37. X-rays displayed with a solid bony density measuring 4 * 5 * 4 mm. The lesion was extracted. Histological examination revealed a solid non structured circumscribed cementum mass with a small central bony area and some surrounding fibrous fibers. Postoperative course was unsuspicious.
DiagnomX GmbH
2015-12-10
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/92
10.17629/www.diagnosticpathology.eu-2015-1:92
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/92/73
Copyright (c) 2015 Andreas Mrachacz, Klaus Kayser, Thomas Kühnel, Spiridula Pappa, Frank Schmidt
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/238
2019-08-22T16:00:09Z
dpath:RES
Morphometric study of facial wrinkles and aesthetic skin as dermaroller treatment combined with platelet rich plasma (PRP)
Oyunsaikhan, Surmaajav
Amarsaikhan, Bazar
Batbayar, Badral
Dungubat, Erdenetsogt
dermaroller, platlet rich plasma, PRP, wrinkle, skin aging
Background: Facial wrinkles are a multifactorial, complex process that negatively affects individuals’ appearance, consequently their quality of life. The treatment for these wrinkles varies with the degree of severity. This prospective study aimed to evaluate the clinical effect of pure dermaroller and dermaroller combined with platelet rich plasma therapy (PRP dermaroller), to treat facial wrinkles, and to quantitatively evaluate histological changes of the skin that occur in the two different cohorts.Methods and materials: Twenty healthy women aged 43-48 years with scores ranging between 2 and 4 on the baseline facial fine wrinkle grading scale were enrolled in the this clinical study. Nineteen of the patients were treated with a pure dermaroller on the one half of face, and with a dermaroller that included a platelet rich plasma on the other half of the face. Three treatments, each in a 4 weeks interval were performed. Standard photographs and skin biopsies were obtained from the treatment area at baseline and 8 weeks after the final session. Comparisons of the treatments were analyzed using clinical and histological findings.Results: The degree of baseline facial fine wrinkle grading scale after treatment revealed statistically significant effects of the PRP dermaroller treatment side compared to the side of pure dermaroller treatment. At 8 weeks after the final session, the wrinkling grade on the PRP dermaroller side and the pure dermaroller side showed significant differences (p<0.05). Microscopic evaluation of haematoxylin eosin and Masson’s trichrome stained sections revealed significant differences in dermal fibers, epidermal thickness, papillas and skin glands.Conclusion: Significant changes were noted between treatments of facial wrinkles with pure dermaroller and PRP dermaroller. Dermaroller combined with platelet rich plasma is a promising novel method of facial rejuvenation.
DiagnomX GmbH
2017-02-09
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/238
10.17629/www.diagnosticpathology.eu-2017-3:238
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/238/392
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/238/545
Copyright (c) 2017 Erdenetsogt Dungubat
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/118
2018-06-19T09:14:11Z
dpath:SY01
Morphometric Analysis In Benign, Atypical And Invasive Breast Lesions And Its Correlation With Histological Diagnosis, Tumour Grading And Her2 Overexpression
Gahlaut, Renu
Arora, B.
Introduction/ BackgroundComputer image analysis has become an important tool in the pathology laboratory for quantitative morphometric analysis, which has several advantages over conventional visual assessment: Objectivity, reproducibility and the ability to detect changes not immediately apparent to naked eyes. The nuclear and cytoplasmic alterations during the development of various breast lesions are the cornerstone for typing and grading of these lesions, including carcinomas. The current study was aimed at analyzing the morphometric parameters like mean nuclear area, mean cytoplasmic area, nuclear:cytoplasmic ratio in various breast lesions including benign, atypical and malignant cases, with and without lymph node metastasis. AimsThe purpose of this study was to compare the morphometric parameters of various breast lesions on formalin fixed paraffin embedded (FFPE) tissue sections with conventional histological diagnosis, tumour grading and HER2 overexpression. MethodsA total of 100 cases were selectively obtained from archival paraffin blocks. 75 cases were of breast tissues from wide local excision/mastectomy or excision biopsy specimens along with 25 cases of positive lymph nodes with metastatic deposits from infiltrating ductal carcinoma. FFPE sections were stained with conventional methods of haematoxylin and eosin (H&E) and examined for histological diagnosis. The sections with representative breast lesions were stained immunohistochemically to determine HER2 status. Morphometric analysis was performed on H&E sections. ResultsThe current study showed that ‘p’ value was highly significant (p<0.001) for nuclear area and N:C ratio among different categories. The cytoplasmic area was found significant (p<0.001) in discrimination of benign from malignant lesions but not atypical from malignant lesions, indicating that cytoplasmic area alone is not a very reliable parameter.Conclusion: The morphometric evaluation of breast lesions has proved to be a useful technique in tumour pathology and a valuable adjunct to histomorphology in rapid and accurate diagnosis of different breast lesions. As nuclear changes precede morphological changes, nuclear morphometry can prove beneficial in diagnosing the malignant changes, both at the earliest and with accuracy.In our study we found that mean nuclear diameter and N:C ratio were higher in grade III tumors than grade I and grade II tumours. The difference was statistically significant. The malignant lesions with strong HER2 expression (3+) had higher mean nuclear area as compare to HER2 negative/ borderline (2+) tumours. Thus, the correlation between histological diagnosis, tumour grading and morphometric nuclear parameters, in combination with HER2 overexpression, can improve the evaluation of the patient’s prognosis, and possibly predict response to therapy.Computer assisted nuclear morphometry can also be used in objective grading and standardizing grading performance between different laboratories. Hence nuclear morphometrical analysis will bring a factor of objectivity and help in quantification of the nuclear atypia and limit the subjective variability in grading of breast cancers.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/118
10.17629/www.diagnosticpathology.eu-2016-8:118
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/118/251
Copyright (c) 2016 R. Gahlaut, B. Arora
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/263
2019-08-22T14:52:41Z
dpath:REV
Whole body plastination, intra-organ heterogeneity, and tissue based diagnosis – a survey
von Hagens, Gunther
Kayser, Gian
Borkenfeld, Stephan
Kayser, Klaus
Background: The corpse is the final structural relict of life. Its detailed analysis, the autopsy formed the basis and contributed significantly to our understanding of location, function and interaction of organs in man. Today, autopsies are performed rarely. They have been replaced by radiological in vivo visualization techniques and the analysis of organ excisions and biopsies. Which attributes do whole body preservations possess in this context?Techniques of Whole Body Analysis: In vivo imaging transfers the appearance of body organs and cellular structures in virtual images. The patient’s exposure to X-rays, fundamental particles (electrons, positrons, etc.), strong magnetic fields (nuclear resonance), or ultra sounds release the corresponding signals. The obtained images are interpreted in search for local abnormalities such as cancer, acute and chronic infections, inborn errors, hypertrophy or atrophy.Autopsies require the removal and visual inspection of organs shortly after the victim’s death. In addition, tissue probes of suspicious lesions are fixed and microscopically analyzed. The search for gene or protein abnormalities are added dependent upon the clinical history and gross findings.The whole body plastination is performed in separated steps which include fixation, anatomical dissection, forced polymer impregnation, positioning and curing. Organs and other tissue structures can be taken out of the body and separately demonstrated, or aligned and fixed within the body. Additional tissue examinations are possible at this stage, which is followed by hardening and fixation of the still flexible body. Fixation is done with heat, light or gas. Results and Interpretation: Tissue conservation is a prerequisite to analyze and investigate in diagnosis and forecast of disease occurrence and behaviour. In history, autopsies have opened the door to localize the position and to understand the functions of organs. Today, they have been replaced by tissue banking and in vivo examinations in a wide range, especially when local lesions of organs are under investigation. Analysis of blood and serum is the main technique to search for organ dysfunction. Whole body plastination is an appropriate technique to investigate and demonstrate healthy appearance of organs, intra-organ heterogeneity, connection to and communication with neighbouring or distant organs as well as localization and distribution of organ lesions, and the associated functional impact.Perspectives: Modern societies try to inform their citizens by numerous investigations of the public health status and to improve the health condition as well as to minimize the development of behaviour associated diseases such as smoking and lung cancer, or overweight and infarction. Well performed body conservation supports these efforts. In addition, it can be considered an innovative technique to understand, diagnose, and even treat dysfunction of intra-body communication at the physical and even mental level.
DiagnomX GmbH
2018-04-13
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/263
10.17629/www.diagnosticpathology.eu-2018-4:263
Diagnostic Pathology; Vol 4 No 1 (2018): 2018
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/263/557
Copyright (c) 2018 Gunther von Hagens, Gian Kayser, Stephan Borkenfeld, Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/277
2020-02-26T13:29:28Z
dpath:TP
Development of Telepathology in Europe – in commemoration of Professor Etienne Martin
Kayser, Klaus
Implementation of telepathology in Europe started in the late 1980th and was actively promoted by an international European team of well - known pathologists. They formed a group of innovative colleagues, informed each other of their research goals and organized a series of European Telepathology Scientific Conferences which lasts until today.In their early days their main interest focussed on remote and straight forward frozen section services followed by consultation activities, and less often by image quantification and analysis.Now-a-days most members of the group were retired, others passed away.Therefore, it seems indicated to retrospectively analyse some early activities of telecommunication in pathology, to validate the results and specific conditions, and to commemorate the involved actors.One of the main players was Professor Etienne David Martin, Paris, who passed away recently.Herein, we describe the predominant incidents, factors and actions of the pathologists who implemented and directed the present stage of telepathology, including image analysis and diagnosis assistance.
DiagnomX GmbH
2020-02-23
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Text
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/277
10.17629/www.diagnosticpathology.eu-2020-6:277
Diagnostic Pathology; Vol 6 No 1 (2020): Vol 6 No 1
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/277/568
Copyright (c) 2020 Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/146
2018-06-19T09:27:28Z
dpath:DIM
Biobank Semantic Information Management With The Health Intelligence Platform
Seebode, Christian
Ort, M.
González Ãlvarez, S.
Regenbrecht, C.R.A.
Introduction/ BackgroundTraditionally Biobanks were mostly used as repositories of cells and tissues. They are addressing scientific questions mainly for retrospective trials where stored tissues and cells can be used. This paradigm has been changing lately. Biobanks can play a different and more prominent role in the scientific process. In fact, the information contained in biobanks can fuel the scientific reasoning itself more than just accompanying it with management of specimens and data. Information management for biobanks should integrate all kinds of information from various sources including clinical records and documents to support flexible retrieval and analytics based on that information. One of the key concepts to support this is to treat the sample like the patient or donor. Selecting a sample for a research trial may be done based on real-time data from the clinical processes. This closes the loop and opens the iron curtain between clinical processes and clinical research. It is a key requirement for supporting research for precision medicine allowing for dynamic decisions and trial designs. Another important aspect is collaboration and sharing of important information preserving data security and patient safety. Informed consent should be dynamically integrated into the scientific process and support patient/donor literacy for the scientific question.AimsMore precisely we define requirements for biobank management systems to be:Collaboration and global sharing of data;Support for Scientific workflows and knowledge management;Association of genotype and phenotype data and Integration of patient records;Integration with registries and standards integration;Support for informed consent. MethodsWe present a biobank architecture based on our product ‘Health Intelligence Platform (HIP)’ that supports these requirements. We describe a way to support scientific reasoning directly with HIP and integrate sample management in a way that it contributes to scientific reasoning and outcome. The NLP semantic information extraction together with information extraction from (semi)structured sources provide a necessary integration to support the link between sample and clinical information. The semantic convergence model of HIP supports semantic queries based on an integrated semantic information base. Selecting samples or running analytics based on this information is possible in real time. The flexible knowledge management supports quick adaption of the knowledge base. Researchers are able to adapt the ontologies by visual interaction with the data sources and semantic tagging. The semantic workbench supports roundtrip engineering of ontologies and conflict resolution. We will present an evaluation framework that compares traditional biobank processes with HIP biobank management. We present the integration capabilities and provide an outlook to allow patient participation in research to address upcoming issues in precision medicine. Conclusion:Biobank management with HIP supports biobank management by providing tools and services for horizontal (across stakeholders, workflows and collaborations) and vertical (across institutions and disciplines) semantic integration of data into one common data model. HIP biobank management supports semantic retrieval of sample data and associated scientific and patient centered information. The HIP Core is used already and is used to identify patients for clinical trials based on information from clinical records and documents.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/146
10.17629/www.diagnosticpathology.eu-2016-8:146
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/146/260
Copyright (c) 2016 C. Seebode, M. Ort, S. González Ãlvarez, C.R.A. Regenbrecht
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/162
2018-06-19T09:10:30Z
dpath:DA
Estimating Liver Steatosis: Can Artificial Neural Network And Image Analysis Improve The Accuracy
Capar, A.
Türkmen, I.
Akhan, A.
Saka, B.
Cakir, A.
Ramadan, S.
Dogusoy, G.B.
Introduction/ BackgroundLiver steatosis is very important in transplantation pathology as it directly influences the graft dysfunction. Pretransplant donor biopsy materials are evaluated by the pathologists, and degree of steatosis, especially large droplet steatosis (LDS) which is described as lipid droplets with a diameter of at least 15 micron, is estimated under light microscope. But when doing so, there can be great intra- and inter-observer variability. In order to overcome this problem several automated systems and image analysis methods are used.AimsThe most challenging issue for automated steatosis image analysis is to distinguish real oil droplets from sinusoidal regions. Although some morphometric features are employed to make this discrimination, whole feature space could not be represented for a fatty liver cell. In this study we have contributed a new approach, which tries to solve this discrimination issue with an artificial learning system.MethodsTen consecutive hematoxylin and eosin (HE) stained, formalin fixed paraffin embedded donor liver biopsies, reported by 2 pathologist, were evaluated by a third pathologist and steatosis percentage was given as total and LDS by using the percentage of area occupied by lipid droplets to total biopsy area. Automated image analysis was performed on about 200 photographs taken to represent the whole biopsy at X20 magnification by Zeiss Axio Scope.A1 microscope using Kameram™ software and established as percentage of LDS to total biopsy area. Segmented positive (oil) and negative (non- oil) components are labeled by an expert pathologist and after some preprocesses they are fed to an Artificial Neural Network for training. We have used about 1000 droplets for training and 1500 droplets for performance evaluation. The proposed scheme is utilized to calculate liver fat ratio on digital images and the results are compared with expert’s opinions.ResultsThere was great variation among pathologists and when compared to the automated analysis and pathologists were prone to overestimate the steatosis (Table 1). As this overestimation can lead to nonuse of the donor liver, the accurate assessment of the steatosis is critical. Since the biopsy is the gold standard for the assessment of steatosis, methodology of this examination should be as objective as possible. Our results show that automated assessment of liver steatosis is very useful in order not to loose donor livers, by overestimation. Automated image analysis used before were based on morphometric features of liver droplet regions, and usePatient IDSystem TDSSystem LDSExpert 1-2 TDSExpert 1-2 LDSExpert 3 TDSExpert 3 LDS18.85.53025251526.52.615103553862520353046.13.713815554.31.910825565.128325 78.24.320153520811.89.6302045259117.425153525Table 1: The total droplet steatosis (TDS) and large droplet steatosis (LDS) percentages estimated by the pathologists and calculated by the softwareof this Artificial Neural Network for training to discriminate sinusoidal areas from lipid areas reached a high accuracy. In this study, we proposed a new approach to discriminate lipid areas from sinusoids without using morphometric features, which needs be confirmed in a large cohort. The performance can be improved by employing some different pattern classification techniques such as Support Vector Machines as a future study.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/162
10.17629/www.diagnosticpathology.eu-2016-8:162
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/162/285
Copyright (c) 2016 A. Capar, I. Türkmen, A. Akhan, B. Saka, A. Cakir, S. Ramadan, G.B. Dogusoy
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/178
2018-06-19T09:09:45Z
dpath:CWI
The Effects Of Digital Workflow Support And Workflow Control For The Performance Of Routine Pathology
Haroske, Gunter
Mörz, M.
Introduction/ BackgroundAlthough the scanning technology for microscopic slides has been known for more than 15 years, its practical use in daily routine is still on the very beginning. Fast and reliable scanners enabled their increasing use in teaching, but not yet in consultation and primary diagnostics. So far the scanning is not handled as a process in the pathology laboratory by most of the pathology systems, leading to an interrupted workflow with delays and additional expenses. The requirement profiles for slide scanners can only be formulated with respect to their workflow integration.AimsThe effects of different degrees of workflow digitalization have been studied as to analyze the sources of possible benefits of digital pathology as well as to identify the bottlenecks and inconsistencies in the workflow control in a routine pathology laboratory. The adherence to existing IHE Technical Frameworks has been evaluated, too.MethodsPerformance statistics of routine pathology were evaluated in different phases of digital workflow control over more than 10 years in a medium-sized institute of pathology.Three phases were defined:Uncontrolled, but digitally supported workflow with digital dictation, digital macrophotography, digital microphotograpy at few pathology Workstations, and a “classic†pathology software system;Digital workflow control including digital dictation and digital photography;In a pilot study at the end of the evaluation period the additional benefits of slide scanning were estimated.ResultsIn the period between 2006 and 2015 a decrease of turnaround-time of roughly 40% was seen. Alone the effects of a (sub)total digital workflow control contributed about half of that effect. The implementation of slide-scanning did not add further acceleration so far, but enabled some additional functionality for improving quantitative reporting. This was achieved without an explicit commitment of the pathology software to standards in workflow control and with still leaving a few laboratory processes out of the control. Milestones and key elements of workflow management are reported in detail. Conclusion:All processes both in the laboratory and in the diagnostics have to be checked (and changed, if necessary) for being fit in a streamlined pathology workflow. The implementation of scanners into the routine diagnostics will enforce those essential developments leading to increased productivity and quality.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/178
10.17629/www.diagnosticpathology.eu-2016-8:178
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/178/305
Copyright (c) 2016 G. Haroske, M. Mörz
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/194
2018-06-19T09:06:44Z
dpath:EP
Correlations Between Interstitial Stromal Fibrillary Network And Disease Progression In Hepatitis C
Plesea, I.E.
Uscatu, C.D.
Serbanescu, M.S.
Indries, M.
Plesea, R.M.
Introduction/ BackgroundSince the virus description in the 80s [1] , [2], the infection with hepatitis virus C (HVC) became a real health problem because 50-80% of acute HVC infections evolve to chronic hepatitis, from which 4–20% of patients develop liver cirrhosis within 20 years and, finally, the risk of developing HCC of patients with liver cirrhosis is 1–5% per year [3]. The principal stage of pathological processes is the interstitial space and mainly the portal areas. Fibrillary network, one of the important components of the interstitial space, undergoes dramatic and highly variable changes, fibrosis representing one of the elements of the morphologic triad of the pathologic conflict within the liver parenchyma.AimsThe aim of the study is to assess quantitatively the liver fibrosis on biopsy fragments of patients with virus C hepatitis (VCH) and to compare it with the fibrosis score described qualitatively in METAVIR system.MethodsThe studied material was represented by liver biopsies from 87 patients with VCH. Tissue fragments were processed following classical histological techniques (formalin fixation and paraffin embedment) and serial sections were stained, for each case, with Hematoxylin Eosin and Mason Trichrome. Tissue fragments images were acquired with a dedicated optical system, using   the X10 objective and the portal and periportal areas were acquired using X20 objective. The fibrosis was firstly assessed using METAVIR qualitative score for fibrosis (MV-F1, MV-F2 and MV-F3). There were no cases with no fibrosis or with cirrhosis. The quantitative parameters determined were: total area of examined hepatic parenchyma, portal spaces area, total area of fibrosis and area of portal fibrosis. The quantitative parameters calculated were: the percentage of the total parenchymal area represented by fibrosis (TF/TA-HP), the percentage of the parenchymal area represented by the portal spaces (PS-A/TA-HP), the percentage of the portal spaces represented by the portal fibrosis (PS-F/PS-A). The measurements were made with two dedicated software programs, after preceding software calibration. For numerical parameters minimum (MIN), maximum (MAX) mean (AV) values and standard deviation (STDEV) were calculated. For comparison with METAVIR fibrosis score grades, the values of quantitative parameters calculated were stratified in classes. For statistical analysis of the correlation between the quantitative and qualitative assessment of fibrosis, t-test (2-sample, unequal variance), One-Way ANOVA test and χ2 test were used.ResultsTF/TA-HP and PS-A/TA-HP correlated with the METAVIR degrees of fibrosis (Figure 1). Both correlations were statistically validated at very high significance level. (Figure 2). In turn, PS-F/PS-A didn’t correlate with the METAVIR degrees of fibrosis, as statistical tests revealed (Figures 1 and 2).So, in VCH, one of the main morphological aspects is the constant enlargement of portal spaces but with a reduced extension of the destructive and reparatory processes towards the lobule center. Collagen fibers production is not an accelerated process, being in a relative equilibrium with the reactive inflammatory cellular population as demonstrated by the relatively constant percentage of the portal spaces represented by the fibrillary structures.Figure 1. Figure 2.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/194
10.17629/www.diagnosticpathology.eu-2016-8:194
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/194/275
Copyright (c) 2016 I.E. Plesea, C.D. Uscatu, M.S. Serbanescu, M. Indries, R.M. Plesea
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/3
2018-06-19T09:07:53Z
dpath:RES
Specificities of Electronic Publication in Medicine
Borkenfeld, Stephan
Kayser, Klaus
Open access publication; citation index; faked data; publication manufactories; globalization diagnostic pathology;
BackgroundElectronic Media are considered to be a useful tool to distribute scientific information in medicine. Starting in this century all main publishers use electronic information transfer and distribution, either solely by electronic media or in combination with conventional paper printing.TheoryInformation distribution and communication require a sender (author), a transport medium (visual or acoustic signals, telephone, radio, TV, printed journals), and a receiver (hearer, reader). Information distribution in science and medicine should permit an objective and non-biased understanding of the transferred information by the receiver (doctor). These actions should be repeatable in time and space. This aim is in contrast to emotional, business-oriented, or political information transfer that commonly wants to direct the receiver in a certain surge or emotion.ImplementationScientific, peer reviewed open access journals have been established since the beginning of this century. After a period of hesitation and resistance which lasted for about 10 years, now-a-days nearly all big publishing companies offer open access journals in their product line. Most of them still hold on paper printed journals in addition, others offer hybrid journals, i.e., paper printed information display contemporary with electronic distribution. The electronic structures differ from classic structures (different, subject oriented domains) to articles of different focus that are fully integrated in only one individual domain. The advantages and disadvantages of the different structures are discussed in detail.Conclusions and perspectivesInformation distribution and communication is one important issue of life. The progress of technology does not stop at the doors of research and practice in medicine. To the contrary, it promotes both, understanding, interpretation and innovation of research, and the practical application. These facilitations of promotion are accompanied by ease of falsification and faked data. Business models of open access publication open doors of temptations to undercut science by anticipated profit. Previously serious publishers are already spoiled, and the scientific community should be aware that global investors are already misusing modern communication in science and research for their profit interest.
DiagnomX GmbH
2015-03-31
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/3
10.17629/www.diagnosticpathology.eu-2015-1:3
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/3/5
Copyright (c) 2015 Stephan Borkenfeld
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/215
2018-06-19T08:59:26Z
dpath:EP
Correlation Analysis of the Feto-Placental Parameters Et Intrauterine Growth Retardation
Gorianikova, I.
Kononenko, O.
Zinchenko, O.
Antonova, O.
Introduction/ Background
A number of studies suggest that some disproportions and retardations in feto-placental growth may lead to various pathologies in adults.
Aims
The aim of the present work was to identify alterations in correlations between placental and fetal parameters in cases of intrauterine growth restriction (IUGR) at 20-25 weeks of gestation (wg).
Methods
18 cases with IUGR and high placenta/fetal weight index (PFI) have been compared with 20 controls in cases of induced abortions for socio-economic reasons at 20-25 wg. Recorded data included weights of placenta (PW) and fetus (FW), fetus length (FL), head (Ch), chest (Cch), abdominal (Ca) circumferences, fetal kidneys (KW), liver (LW) and heart (HW), as well as some indices(FPI, FW/FL, LW/PW, HW/PW, KW/PW). The correlation analysis of the morphometric data was performed.
Results
IUGR group had smaller parameters of FW, FL, Cch, Ch, and Ca. All IUGR cases had decreased LW; W and HW. PW was unchanged at 20-22 wg and increased at 23-25 wg, compared with controls. The negative correlation has been found between PW and LW/PW, FPI and LW at 20-22 wg, and between W and HW/PW at 23-25 wg. The longer gestation the more new positive strong correlations have been discovered within the IUGR group (between FPI and HW, KW, LW, KW/PW).
Conclusions: the study suggests that the increase in the number and the intensity of correlations between morphometric parameters might represent a discrepancy between the fetal and placental growth at 20-25 wg and alterations in fetal organ adaptation mechanisms, which may result in future pathologies.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/215
10.17629/www.diagnosticpathology.eu-2016-8:215
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/215/370
Copyright (c) 2016 I. Gorianikova, O. Kononenko, O. Zinchenko, O. Antonova
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/86
2018-06-19T09:01:16Z
dpath:CAS
Amelanotic metastasing melanoma mimicking lung cancer
Xhemalaj, Daniela Flamur
Caushi, Fatmir
Ulazzi, Linda
Rinaldi, Rosa
Lanza, Giovanni
Hafizi, Hasan
Alimehmeti, Mehdi
Pumo, Gisela
Hasa, Asela
Malignant Melanoma, Lung metastasis, Immunohistochemistry, Lobectomy.
Lung is one of the most common site of metastasis in patients with malignant melanoma. We report a 64 year old man, who was submitted to our hospital. He complained of increasing intensity of shortage of breath, cough, and loss of weight within the last weeks. Serum analysis was normal. X-ray and CT images displayed a circumscribed density in the lower left lung, suspicious for lung cancer. Bronchoscopy and biopsy indicated a non differentiated malignancy which could not be further classified. Excision of the lower left lobe and of mediastinal lymph nodes was performed. The post surgical definite histological diagnosis revealed an amelanocytic epithelioid melanoma (positive for HMB-45, S-100). Pathologists, pulmonologists and thoracic surgeons should be aware of different cell types of intrapulmonary malignancies although primary lung cancer contributes to the outstanding majority of large and solid lung lesions.
DiagnomX GmbH
Giovanni Lanza, University of Ferrara, Department of Pathology
2015-10-30
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/86
10.17629/www.diagnosticpathology.eu-2015-1:86
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/86/60
Copyright (c) 2015 Daniela Xhemalaj, Fatmir Caushi, Linda Ulazzi, Rosa Rinaldi, Giovanni Lanza, Hasan Hafizi, Mehdi Alimehmeti, Gisela Pumo, Asela Hasa
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/211
2018-06-19T08:55:24Z
dpath:EL
Open Access Publication in Pathology – Advantages, Constraints and new Tools
Carvalho, Rita
Borkenfeld, Stephan
Kayser, Klaus
Open Access Publication, Pathology, Virtual Slides, review forum, automated measurements.
BackgroundOpen access journals are financed by authors (i.e. research grants), rather than by readers or subscribers. This business model allows a world – wide uncontrolled distribution of medical information and scientific knowledge. The financial of shifting the finance and the opportunities for misuse raise significant concerns regarding non – scientific impact and article content integrity. Herein we report and discuss ideas and experiences of open access publication focusing on diagnostic pathology.Material and MethodsOur experiences are drawn from an electronic communication network in pathology that includes the open access online journal diagnosticpathology.eu. The network includes a) the journal www.diagnosticpathology.eu, b) the Virtual International Pathology Institute (www.diagnomx.eu/vipi), c) several scholar atlases (a selection of common and rare lung diseases (Digital Lung Pathology), an atlas of fine granulate & natural and synthetic mineral fibers, a virtual slide atlas (in preparation)). The journal offers the opportunity to publish case reports “beside the microscope†and to submit data for “interactive publicationâ€. Both tools are unique, and cannot be found elsewhere. For publication of suitable articles, we demand the submission of glass slides, which will become completely digitized (virtual slides, VS).Results and ExperiencesThe journal is online since March 2015, and the only completely financially independent open access journal in medicine. We have published several case reports under the headline “How do I diagnose…?†The presented form offers a guide through the article and permits a complete publication “besides the microscopeâ€, commonly in less than one hour. Automated links to reference search items are included as well as virtual slides. The strict publication format permits fast submission of unique or interesting cases, and, in addition, the implementation of the publication into a case – related open and flexible image date bank.ConclusionsThe mandatory inclusion of virtual slides is a unique quality control. The journal diagnosticpathology.eu is embedded in a cloud that will consist of an archive of published cases with virtual slides, an express review forum with a corresponding duty plan, an automated measurement system of histological slides, and open access atlases such as hazards of natural and artificial fibers (fine granulate) and a collection of all known pulmonary diseases. Diagnosis assistants and image databanks customized according to the needs of an individual user (reader, author, consultant, automated measurements, etc.) will be available in the near future too.
DiagnomX GmbH
2016-10-10
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/211
10.17629/www.diagnosticpathology.eu-2016-2:211
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/211/386
Copyright (c) 2016 Rita Carvalho
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/107
2018-06-19T09:03:24Z
dpath:DIA
How do I diagnose Extramedullary Hematopoiesis
Carvalho, Rita
Mafra, Manuela
Extramedullary hematopoiesis; Extramedullary myeloid sarcoma; : Posterior mediastinum, para-vertebral mass; CD34, CD117, TdT
Extramedullary hematopoiesis occurs in bone marrow disorders and is most commonly seen in thalassemia and myelofibrosis. We present a case of a 58 year-old male, with a history of thalassemia, which presented with a para-vertebral mass composed of hematopoietic tissue. When considering the differential diagnosis, a primary concern was an extramedullary proliferation of neoplastic hematopoietic elements, like extramedullary myeloid sarcoma. Neoplastic extramedullary proliferations can consist of triline age marrow elements and closely mimic the appearance of benign extramedullary hematopoiesis. The morphologic appearance may be a diagnostic clue, but cannot be completely relied upon.
DiagnomX GmbH
2016-04-29
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/107
10.17629/www.diagnosticpathology.eu-2016-2:107
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/107/127
Copyright (c) 2016 Rita Carvalho, Manuela Mafra
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/253
2019-08-22T15:37:30Z
dpath:RES
Cytology consultations with associated image quality evaluation – experiences of the Virtual International Pathology Institute (VIPI)
Kayser, Gian
Borkenfeld, Stephan
Ayad, Essam
Djenouni, Armina
Mariamidze, Armaz
Mkhitaryan, Armen
Kayser, Klaus
Background: The virtual international Pathology Institute (VIPI, www.diagnomx.eu/vipi) is the only image consultation forum that is organized in close organization to a conventional institute of pathology. Its approximately 160 experts in pathology and cytology consult and diagnose difficult cases on the basis of a convent weekly duty plan. Herein we report the consultation results of a specific series of cytology specimens, and discuss potential application in routine virtual cytology.Material and Methods: Still images of fine needle aspirations sent for consultation to VIPI were evaluated by five members of VIPI. A total of forty and seven cases was analyzed, and scored in four classes (benign, probably benign, probably malignant, and malignant). In addition, the consultants evaluated and graded their impression of colour, focus and general image quality in 10 classes (10 = very good <> 1 = not acceptable). Automated measurements of objective image quality, calculation of the regions of interest (ROI), and automated diagnosis classifications were performed too.Results: The experts’ diagnostic conformity was computed 4.2/5; i.e., at average 4.2 experts stated the same diagnosis of each case. The automated classification supported the summarized experts’ diagnoses in 38/47 cases. The experts interpreted the image quality diversely. Two of them evaluated with tendency of low, and two of them of high grades. The individual interactive image quality evaluations showed statistically significant relationship to the diagnostic accuracy (p<0.05). A helpful and correct automated ROI detection was stated in more than 95% of images.Conclusion: The study indicates that electronic transmission of acquired conventional cytology smears is a useful tool to get access to experts’ knowledge worldwide. The case related diagnostic agreement of experts can serve for gold standard of virtual cytology (for example conformity > 80%). Additional automated measurements might support the diagnosis. Implementation of virtual slide technology and automated ROI visualization are additional tools in order to support the diagnostic accuracy. Virtual international pathology institutions are able to successfully work together with or even replace conventional cytology laboratories.
DiagnomX GmbH
2017-12-28
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/253
10.17629/www.diagnosticpathology.eu-2017-3:253
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/253/552
Copyright (c) 2017 Gian Kayser, Stephan Borkenfeld, Essam Ayad, Armina Djenouni, Armaz Mariamidze, Armen Mkhitaryan, Klaus Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/129
2018-06-19T09:14:47Z
dpath:EP
The Use Of Smartphones As Adjuvant Tool In Cervical Cytologic Diagnosis
Ali, Leila
Moldovan, Valentin Tiberiu
Sajin, M.
Introduction/ BackgroundCervical cancer is still one of the world’s deadliest forms of cancer for women, and the Pap smear remains the main screening test for prevention and early detection. Pap test is convenient and inexpensive, but, as was reported, there are variation in the sensitivity and specificity. Current smartphones allow the acquiring and transmission of static digital images, representing a cost efficient form of telepathology. AimsWe report our experience in using smartphones and an instant messaging application to improve the cytologic diagnosis by teleconsultation. MethodsThe samples were conventional Pap smear and liquid base cytology slides. The images were taken by two of the authors, both junior pathologists, with the use of a Samsung Galaxy S3 Neo smartphone (8 MP, autofocus, Digital image stabilization) and a Zeiss PrimoStar micro- scope (415500-0057-000), 10x objective. We used the instant messaging application features to take the pic- tures and instantly send them to our fellow pathologist (if the images were resolution and focus suitable), then discuss the images in real time, using the chat optionsof the phone application. After reviewing the images together, and reaching to a conclusion, the images were submitted to an experienced pathologist in the same manner. They were reviewed a second time, and the results compared. ResultsThe most common diagnosis we discussed on was ASC-US (19 cases), followed by L-SIL (6 cases) and NILM (5 cases). After we analysed and compared the data, we found that the time frame for diagnosis has improved. For the cases with divergent opinion we asked a third opinion to a colleague for the difficult cases. Conse- quently a senior pathologist review the glass slides and we compared the results with the digital diagnosis. The camera resolution was not limitative in this case, the used field power being 10x, thus the resolution and de- tails were not impaired by the smartphone camera and instant messaging app limitations. Comparing our expe- rience with the interobserver agreement on ASCUS and LSIL categories on glass slides we consider ‘smartphone’ pathology a useful tool. The use of smartphones allows junior pathologists to transmit Pap test consultations to senior pathologists and to ask for second opinions among fellow colleagues, improving costly effective the diagnosis accuracy.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/129
10.17629/www.diagnosticpathology.eu-2016-8:129
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/129/267
Copyright (c) 2016 L. Ali, V. Moldovan, M. Sajin
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/275
2019-07-05T16:06:17Z
dpath:RES
Etiology and Pathogenesis of Sudden Cardiac Death
Guski, Hans
Kogan, Evgenya A.
Shvalev, Vadim N.
Background and definition: This article contributes to the current state of knowledge in etiology and pathogenesis of sudden cardiac death (SCD). SCD is a well - defined disease entity which recently approved international guidelines address (cardiac death within 1 hour). Etiology: The condition of coronary arteries contributes to common causes of SCD. Stenotic coronary artery sclerosis (80%) has been reported in most cases. In non-coronary causes (15%), cardiomyopathies (CMP) are frequently found, and alcoholic CMP dominates the CMP cohort. Genetically related causes are comparatively rare (5%). Pathogenesis: In pathogenesis, only the consecutives of coronary ischemia have been extensively studied, in contrast to non-coronary causes. Herein, only some (mostly infectious) forms of myocarditis have been investigated in detail. The pathogenesis of different causes of SCD is less well studied. These include pathologic changes of adrenergic and cholinergic heart nerves, of intra- and extra-cardiac ganglia and of the conduction system. Morphological changes that clearly explain SCD are still difficult to reproducibly detect in clinical-pathologic and forensic autopsy diagnosis because these lesions might morphologically at first manifest after 1 hour or even later. This statement holds particularly true for detecting early ischemic heart muscle cell deaths being the most common cause of SCD Conclusions: The reported methods and special staining have proven to be less suitable for routine diagnostics. Attempts are now undergoing to solve the problem by the use of specific antibodies. They provide evidence of immunoreactivity of ischemic damaged cardiomyocytes which can be detected even after prolonged postmortem lay times.
DiagnomX GmbH
2019-07-04
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/275
10.17629/www.diagnosticpathology.eu-2019-5:275
Diagnostic Pathology; Vol 5 No 1 (2019): Vol. 5 No. 1 2019
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/275/563
Copyright (c) 2019 Hans Guski, Evgenya A. Kogan, Vadim N. Shvalev
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/109
2019-08-22T16:01:36Z
dpath:RES
A sustainable visual representation of available histopathological digital knowledge for breast cancer grading
Traore, Lamine
Daniel, Christel
Jaulent, Marie-Christine
Schrader, Thomas
Racoceanu, Daniel
Kergosien, Yannick
Breast cancer grading, semantic annotation, knowledge formalization and modeling, standardization, computer aided diagnosis, high-content image exploration, digital pathology
Background: Recently, anatomic pathology (AP) has seen the introduction of several tools such as slide scanners and virtual slide technologies, creating the conditions for broader adoption of computer aided diagnosis based on whole slide images (WSI). This change brings up a number of new scientific challenges such as the sustainable management of the explicit and unambiguous semantics associated to the diagnostic interpretation of AP images by both humans (pathologists) and computers (image analysis algorithms) . In order to reduce inter-observer variability between AP reports of malignant tumors, the College of American Pathologists edited more than 60 organ-specific Cancer Checklists and associated Protocols (CAP-CC&P). Each checklist includes a set of AP observations that are expected to be reported by pathologists in organ-specific AP cancer reports. Our objective was to i) identify the available histopathological formalized knowledge from NCBO Bioportal and UMLS metathesaurus in the scope of the CAP CC&P for breast cancer grading and ii) to build a sustainable visual representation of this knowledge using UMLS semantic types.Methods: Our methodology was applied on the two breast cancer CAP-CC&Ps dedicated to invasive carcinoma (IC) and ductal carcinoma in situ (DCIS). We focused on a subset of quantifiable AP observations of the CAP-CCs - i.e. observable entities that could be computed by image analysis tools and on the corresponding notes in the protocols that unambiguously describe how pathologists should derive a high-level observation (e.g. Nottingham score) from low-level morphological characteristics observed in images (e.g. mitotic count or glandular/tubular differentiation).The notes were annotated manually by two AP experts (gold standard) and automatically by NCBO Annotator using the 508 ontologies available on the NCBO platform. A sub-set of reference ontologies was selected based on their capacities to automatically identify concepts in the notes and compared to the subset of ontologies selected based on their capacity to identify the concepts identified by experts (gold standard). Once automatically extracted from the notes, the concepts belonging to different ontologies, were integrated into a unique graph and organized according to UMLS semantic types.Results: The most relevant biomedical ontologies to be used for the annotation of the notes describing quantifiable observable entities of breast cancer CAP-CC&Ps are SNOMED-CT, LOINC, NCIT, NCI CaDSR Value Sets and PathLex. A visual representation integrating 25 concepts from the 5 different ontologies organized according to 11 UMLS semantic types was built to support AP experts for building a formal representation of the low-level quantifiable entities automatically extracted from the CAP-CC&Ps notes.Conclusion: The proposed approach and tools, based on the CAP-CC&Ps, aim at supporting AP experts in building a standard-based representation of low-level morphological abnormalities observed in cancer that can be quantified using image analysis tools. This effort is complementary to the Integrating the Healthcare Enterprise (IHE) initiative building a standard-based representation of high-level AP observations required in cancer AP reports. Additional efforts are needed to achieve a workable standard-based formal representation of histopathological knowledge integrating both observable entities reported by humans (pathologists) and quantifiable entities automatically computed by machines. Providing such unique formal representation paves the way for more efficient use of computer aided diagnosis in AP as well as for the development of new biomarkers based on automatic analysis of whole slide images (WSI).
DiagnomX GmbH
2016-06-28
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/109
10.17629/www.diagnosticpathology.eu-2016-2:109
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/109/228
Copyright (c) 2016 Lamine Traore, Christel Daniel, Marie-Christine Jaulent, Thomas Schrader, Daniel Racoceanu, Yannick Kergosien
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/157
2018-06-19T09:10:31Z
dpath:CAD
Computer-Assisted Inflammation Analysis Of Kidney-Graft Biopsy To Improve Risk Stratification In Allograft Rejection
Meas-Yedid, Vannary
Sicard, A.
Rabeyrin, M.
Koenigl, A.
Ducreux, S.
Dijoud, F.
Badet, L.
Morelon, E.
Olivo-Marin, J.-C.
Thaunat, O.
Introduction/ BackgroundKidney graft biopsy plays a key role in diagnosis of antibody-mediated rejection (AMR), the major cause of renal graft failure. The diagnosis of AMR requires the presence of i) donor specific antibodies (DSA), and ii) microvascular inflammatory lesions on kidney graft biopsy.AimsHistological assessment relies onBanffclassification [1] that has quantitative and qualitative limitations and faces in terms of diagnostic accuracy and risk prediction:1)  this grading is categorical with risks of threshold effect;2)     the nature of inflammatory cells is not considered. Hence we propose a new method of computerized image analysis in order to finely characterize the quality and intensity of graft inflammation.MethodsData57 kidney recipients fulfilled theBanffcriteria for AMR between 2004 and 2012 at the Lyon Hospitals. Double immunohistological stainings were performed with CD31 (capillaries) and respectively CD68 (macrophages), CD3 (T lymphocytes), CD66b (granulocytes), CD20 (B lymphocytes). 288 glass slides were scanned  (MiraxScan, 20x, NA=0.8).AlgorithmsThe goal is to quantify the number of immune cells in the different parts of the kidney cortex. Due to the biopsy preparation such as biopsy slicing and image quality staining many variations within the observed object could happen and result to incorrect image segmentation. Hence we combine color component images to extract Regions of Interest (ROI) based on the use of their contextual data information in order to correctly extract the capillaries and immune cells. The algorithms are implemented in the Icy software (http://icy.bioimageanalysis.org) [2]. In the workflow: 1) color deconvolution [3], 2) pre-processing step to segment the pixel staining, 3) extraction of stained objects by combined information. The color deconvolution separates the initial image into 3 component-staining images: blue component for nuclei, brown component for capillaries and the purple one for immune cells. These component images are first preprocessed, by gaussian filtering and then by the k-means classification to segment the images. We combine the segmented ROI and their spatial relation to extract the objects of interest.Results34 patients had C3d+ DSA and 23 had C3d- DSA. Al- though allograft survival was lower in the C3d+ group (p<0,001 by log-rank),Banffscores for AMR were similar in the 2 groups (3.4±1.1 vs 3.5±1.2, p=0.65). In contrast, our approach revealed notable differences in graft inflammation between the two groups. The number of CD68 cells in the capillaries and in the interstitium allows identifying patients with a risk of graft loss (HR=3.18, p<0.01 et HR=2.62, p=0.01 respectively). The combining C3d test and quantification of monocytes in interstitium allow clustering patients into 3 groups of renal prognosis: C3d-, C3d+/CD68 low and C3d+/CD68 high (p<0.0001 by log rank; C3d+/CD68 high vs C3d+/ CD68 low: HR=2.43, p=0.04; C3d+/CD68 low vs C3d-: HR=4.99, p=0.006).The isolated C3d test has an excellent value negative prediction (89,5% for the 1 year graft loss) but perfectible positive prediction (52,9%) [4] . The monocyte quantification allows to accurate the prognosis of patients in the C3d+ group. Using this novel reproducible approach for topological quantification of inflammation, we observed that histopathological features of complement-binding DSA are different from that of non-complement. The computer-assisted analysis of graft inflammation improves the risk stratification of graft loss.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/157
10.17629/www.diagnosticpathology.eu-2016-8:157
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/157/172
Copyright (c) 2016 V. Meas-Yedid, A. Sicard, M. Rabeyrin, A. Koenigl, S. Ducreux, F. Dijoud, L. Badet, E. Morelon, J.-C. Olivo-Marin, O. Thaunat
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/173
2018-06-19T09:09:06Z
dpath:STD
Anatomic Pathology Structured Report Under FHIR
Schrader, T.
Libramm, J.
Introduction/ BackgroundThe last version of profile for the structured report of IHE was created 2011(IHE). Many discussions took place to improve and adapt the model of described document models for clinical practice. The working group developed xxx templates to cover e.g. the main tumor locations and the requirements of various organizations about tumor documentation (e.g. CAP, national societies of pathology). The complexity of a Structured Report Document based on IHE and HL7 CDA structured increased. Up to now no German software vendor supports these templates directly. Another strategy was suggested by the German Working Group: the IHE should provide generic models usable for the other do- mains in pathology. But the general problem of missing implementation was not solved. The development of Fast Health Interoperability Resource (FHIR) began in 2012 and started a fascinating movement to prioritize the implementation over the theoretical correctness. The resources, documentation and examples are completely open and available under http://wiki.hl7. org/?title=FHIR .AimsIn a first approach we started to “translate†the structured pathology report based on the requirements of the technical framework. The aim was to analyze the usage of FHIR resources for the Anatomic Pathology Structured Report, simplify the document structure and increase the flexibility of document handling.MethodsAt first a complete report was created based on the CDA-XML-structure and model of the IHE Anatomic Pathology Working Group. The data based on a real, but anonymous case (many thanks to Prof. Haroske, Dresden, Germany). If possible each segment of CDA report was mapped to FHIR resources. The FHIR report consisting of different internal and external document fragments (resources) was evaluated by a public available FHIR communication server (http://spark.furore. com/fhir) to validate and verify this document.ResultsA first FHIR based structured report was created and validated against a public available FHIR server (http:// spark.furore.com/fhir). FHIR allows to create different document structures for any type of document: a document only with inside resources or a document with inside and outside (linked) resources. Our example consists of resources embedded in the main document file and linked resources. The FHIR document allows a great flexibility related to the document resources as well as data files. It is possible FHIR documents as XML, JSON (JavaScript Object Notation) or RDF (Resource Description Framework). Due to these various possibilities FHIR documents can be used in a web based application context easily.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/173
10.17629/www.diagnosticpathology.eu-2016-8:173
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/173/300
Copyright (c) 2016 T. Schrader, J. Libramm
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/189
2018-06-19T09:07:02Z
dpath:MIP
Diagnosis Of The Chronic Lymphocytic Leukemia (CLL) Using A Raman-Based Scanner Optimized For Blood Smear Analysis (M3s Project)
Fere, M.
Liu, L.H.
Gobinet, C.
Beljebbar, A.
Untereiner, V.
Angiboust, J.-F.
Manfait, M.
Gheldof, G.
Jacquemin, H.
Walbrecq, S.
Cornet, E.
Troussard, X.
Chatelain, B.
Angelo, J.
Chollat, M.
Klossa, J.
Piot, O.
Introduction/ BackgroundIn hematology, actual diagnosis of B chronic lymphocyte-leukemia (CLL) is based on the microscopic analysis of cell morphology from patient blood smear. However, new photonic technologies appear promising to facilitate and improve the early diagnosis, prognostic and monitoring of personalized therapy. The development of automated diagnostic approaches could assist clinicians in improving the efficiency and quality of health services, but also reduce medical costs.AimsThe M3S project aims at improving the diagnosis and prognosis of the CLL pathology by developing a multimodal microscopy platform, including Raman spectrometry, dedicated to the automatic analysis of lymphocytes.MethodsBlood smears were prepared on glass slides commonly used in pathology laboratories for microscopy. Two types of sample per patient were prepared: a conventional blood smear and a deposit of “pure†lymphocyte subtypes (i.e. normal B, CLL B, T and NK), sorted out in flow cytometry by using the negative double labeling technique. The second sample is used for the construction of a database of spectral markers specific of these different cell types. The preparations were analyzed with the multimodal machine which combines i) a Raman micro-spectrometer, equipped with a 532nm diode laser excitation source; ii) a microscope equipped with 40x and 150x lenses and a high precision xyz motorized stage for scanning the blood smear, and localizing x-y coordinates of representative series (~100 for each patient) of lymphocyte cells before registering three Raman spectra; these cells of interest being previously localized by an original method based on the morphology analysis. After the Raman acquisitions, the conventional blood smears were submitted to immunolabelling using specific antibodies. For the establishment of the Raman classifiers, this post-acquisition treatment was used as reference to distinguish the different lymphocyte sub-populations. Raman data were then analyzed using chemometric processing and supervised statistical classifiers in order to construct a spectral library of markers highly specific of the lymphocyte type and status (normal or pathological).ResultsCurrently, a total of 60 patients (CLL and healthy) were included in the study. Various classification methods such as LDA (Linear Discriminant Analysis), PLS-DA (Partial Least Square Discriminant Analysis), RF (Random Forest) and SVM (Support Vector Machine), were tested in the purpose to distinguish tumoral B lymphocytes from other cell types. These classification algorithms were combined with feature selection approaches. The best performances were around 70% of correct identification when a three-class model (B-CLL vs B-normal vs T and NK lymphocytes) was considered, and 80% in case of a two-class model (B-CLL vs B-normal lymphocytes). These encouraging results demonstrate the potential of Raman micro-spectroscopy coupled to supervised classification algorithms for leukemic cell classification. The approach can find interest more generally in the field of cyto-hematology. Further developments will concern the integration of additional modality such as Quantitative Phase Imaging on one hand to speed the exploration process of cells of interest to be probed, and on the other hand to extract additional characteristics likely to be informative for CLL diagnosis. In addition, the identification of prognostic markers will be investigated by confronting the photonic data to clinical patient information.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/189
10.17629/www.diagnosticpathology.eu-2016-8:189
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/189/318
Copyright (c) 2016 M. Fere, L.H. Liu, C. Gobinet, A. Beljebbar, V. Untereiner, J.-F. Angiboust, M. Manfait, G. Gheldof, H. Jacquemin, S. Walbrecq, E. Cornet, X. Troussard, B. Chatelain, J. Angelo, M. Chollat, J. Klossa, O. Piot
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/115
2018-06-19T09:02:14Z
dpath:RES
Efficient pathology case distribution leveraging workflow and domain modeling, and flexible definition of policies
Bucur, Anca
van Leeuwen, Jasper
Vdovjak, Richard
Case distribution; digital pathology; workflow modeling and optimization; automatic dispatching; workflow engine; rules engine
BackgroundThe value of digital pathology and its potential to improve the current pathology practice are increasingly recognized, with a growing number of examples of successful implementation in a variety of use cases. While current widely-spread uses relate to research, consultation, second opinion and education, success stories are emerging demonstrating outcome and cost benefits of leveraging digital pathology for standard diagnosis as well. In all these cases optimization of pathology workflows, standardization and seamless integration in the environment are emphasized as prerequisites to reaching the desired improvements.AimsWe develop workflow-driven applications to enable clinical users to efficiently and effectively leverage deployed digital pathology solutions for faster diagnosis and better patient outcomes. The work addresses information integration requirements, and aims to identify and propose solutions for performance bottlenecks in existing processes. A process with potential for improvement is the case distribution to pathologists for diagnosis.Materials and MethodsWe propose an approach to workflow modeling and implementation that is open and flexible, and leverages existing standards (BPMN2.0) developed in the context of business process modeling and widely adopted in other domains. This enables efficient implementation and give us access to an existing platform (KIE) that delivers a workflow-engine (jBPM), a rule-engine (Drools), and a constraint satisfaction solver (OptaPlanner). By externalizing the definitions and implementations of tasks within the workflows, we build workflows that are adaptive to the environment and that can incorporate decision models and applications of the desired complexity. We selected case distribution for diagnosis as the first process to optimize and built an application that can be efficiently customized to the needs of each lab with respect to dispatching rules, operational domain model, optimization goals and visual elements.ResultsWe implemented a case distribution application that can be deployed within an integrated workflow implementation to optimize the distribution of cases to pathologists for diagnosis. To automatically assign cases to pathologists according to defined policies, the optimization component applies the defined policy model (scoring rules within the domain model). The schedules are generated according to the desired optimization goals, e.g. to improve throughput or turnaround. This application seamlessly connects with relevant systems in the environment, the LIMS and the IMS, in a loosely-coupled standard way through the integration engine to retrieve all needed data about the cases to be visualized and used in the dispatching decisions, and to provide the case assignation information to the IMS.ConclusionsThe optimization of the case distribution to pathologists for diagnosis has been identified in the literature as an important area when aiming at workflow improvements and automation of the processes in the pathology labs. A common theme emphasized by previous research identifying user needs and requirements for efficient digital pathology implementation is the use of standards to support adoption and the seamless integration with all relevant systems in the environment. Within a standards-based workflow-driven approach, we implement a case distribution application that optimizes the case assignation for diagnosis by modeling the local workflows and the requirements of each deployment site. The optimization component applies the local policy models (i.e. business rules, domain models with roles and characteristics, and optimization goals) to propose the most suitable solution for distributing the incoming case load among the available pathologists for diagnosis.
DiagnomX GmbH
2016-09-12
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/115
10.17629/www.diagnosticpathology.eu-2016-2:115
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/115/365
Copyright (c) 2016 Anca Bucur, Jasper van Leeuwen, Richard Vdovjak
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/65
2018-06-19T09:01:16Z
dpath:DIA
How do I diagnose metastatic giant cell tumor into lung
Kayser, Klaus
Borkenfeld, Stephan
Serguieva, Krasi
Kayser, Gian
Primary Osteosarcoma; Sarcoidosis; Tuberculosis; Interstitial pneumonitis and angiitis
This 26 years old male patient developed an osteoblastic tumor in the right os metatarsale I at the age of 21 years. The lesion was excised en bloc including the os cuneiforme and the m. extensor hallucis. After surgery a venal thrombosis occurred and was treated by thrombectomy and anti coagulation therapy. Five years later 9 intrapulmonary lesions were noted which were radiologically consistent with intra-pulmonary metastases. Two separate right and left lung surgeries were performed, and 17 active metastases of the left lung as well as 18 metastases of the right lung were excised. Post surgery course was inconspicuous. No cytostatic therapy was applied. The patient is still alive 13 years after surgery.Virtual Slides: www.diagnosticpathology.eu/vs/2015_1_65
DiagnomX GmbH
2015-08-15
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/65
10.17629/www.diagnosticpathology.eu-2015-1:65
Diagnostic Pathology; 2015
2364-4893
10.5072/www.diagnosticpathology.eu-2015-1
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/65/52
Copyright (c) 2015 Klaus Kayser, Stephan Borkenfeld, Krasi Serguieva, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/226
2018-06-19T08:58:25Z
dpath:QAM
Blur Quantification of Medical Images: Dicom Media, Whole Slide Images, Generic Images and Videos
Ameisen, D.
Auger-Kantor, J.
Ameisen, E.
Introduction/ Background
We have designed a quality assurance tool to quantify blur by quantifying the sharpness of custom-sized tiles composing an image, generating global results, detailed exchangeable logs and sharpness-maps regardless of their dimensions, quantity or acquisition rate [1]. We have now integrated the programming libraries and the standalone program we built to existing workflows and software, in order to improve quality assurance procedures.
Aims
When integrated in an acquisition workflow, the ability to map the quality of local areas inside an image allows to re-acquire parts of the image that were not scanned properly, or discard and re-acquire images when the global results fall under the thresholds set by the users. When integrated in an image analysis software, the regions of interest can be automatically chosen or suggested to the user according to the quality-map of the image to analyze, reducing the amount of incoherent analysis results. When integrated as a library in an image management platform, or as a standalone program in a storage server, a systematic quality check can detect de-calibration of the acquisition software, failed acquisitions that may be automatically deleted and users can be notified to re-acquire the images when below their quality-thresholds profiles. A quantified quality score can be inserted in each image’s metadata for traceability purposes. When integrated as a library in a local or remote image viewer, the best quality tiles can be sent first to the viewer, and magnification levels can be dynamically resampled for a better render.
Methods
One notable implementation, using our Java library, is inside the FlexMIm project [2], which includes 27 pathology laboratories in the Paris area (coordinated by APHP), research laboratories from University Paris 6 Paris 7, as well as 3 companies: TRIBVN, PERTIMM and Orange. All Whole Slide Images are systematically analyzed and mapped as they enter the platform. The focus map may be displayed on the web interface next to the thumbnail link to the WSI, or in the viewer as a semi-transparent layer over the WSI, or over the WSI map.
During the test phase and first integrations in laboratories and hospitals as well as in the FlexMIm project, more than 5000 whole slide images of multiple formats (Hamamatsu NDPI, Aperio SVS, Mirax MRXS, JPEG2000 …) as well as hundreds of thousands of images of various formats (DICOM, TIFF, PNG, JPEG ...) and videos (H264) have been analyzed using our standalone software or our C, C++, Java and Python libraries. Using default or customizable thresholds’ profiles, WSI are sorted as “acceptedâ€, “to reviewâ€, “to rescanâ€. In order to target the samples contained inside each WSI, special attention was paid to detecting blank tiles. Dynamic blank tile detection based on statistical analysis of each WSI was built and successfully validated for all our samples.
Results
More than 20 trillion pixels have been analyzed at a 3.5 billion pixels per quad-core processor per minute speed rate. Quantified results can be stored in JSON formatted logs or inside a MySQL or MongoDB database) or converted to any chosen data structure to be interoperable with existing software, each tile’s result being accessible in addition to the quality map and the global quality results. This solution is easily scalable as images can be stored at different locations, analysis can be distributed amongst local or remote servers, and quantified results can be stored in remote databases.
DiagnomX GmbH
2016-10-03
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/226
10.17629/www.diagnosticpathology.eu-2016-8:226
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/226/381
Copyright (c) 2016 D. Ameisen, J. Auger-Kantor, E. Ameisen
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/100
2018-06-19T09:04:46Z
dpath:CAS
Low Grade Well-circumscribed Well Differentiated Liposarcoma Developed in Fibroadenoma with Stromal adipose differentiation of the Breast; A Case Report
Ayad, Essam
Breast Fibroadenoma; Stromal Adipose differentiation; Well-differentiated liposarcoma.
Fibroadenomas are the most common breast tumor in adolescents and young women.They comprise  20% of benign breast masses and 12% of all breast masses in postmenopausal women. Smooth muscle metaplasia and adipose differentiation are uncommon forms of stromal differentiation encountered in a minority of fibroadenomas. Liposarcoma can arise from pre-existing benign lesions like phylloides tumour or from lipoid tissue in the breast. In this article we present a case of 38 year-old female who presented with a right breast mass which was clinically diagnosed as a case of fibroadenoma, but histologically showed a low grade well-circumscribed liposarcoma discovered in a pericanalicular type of fibroadenoma with stromal adipose differentiation. According to our knowledge, this the first case of a well-circumscribed liposarcoma arises in fibroadenoma of the breast. Virtual Slides: www.diagnosticpathology.eu/vs/2016_2_100/
DiagnomX GmbH
2016-02-04
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/100
10.17629/www.diagnosticpathology.eu-2016-2:100
Diagnostic Pathology; Vol 2 No 1 (2016): 2016
2364-4893
10.5072/www.diagnosticpathology.eu-2016-2
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/100/102
Copyright (c) 2016 Essam Ayad, MD
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/250
2018-11-26T16:07:14Z
dpath:REV
Epigenetics in lung cancer: What do DNA-methyltransferases do?
Fehrenbach, Uli
Kayser, MD, Gian
Despite recent advances in molecular characterization and targeted therapy approaches, lung cancer still remains the number one killer among malignant diseases worldwide. After understanding the impact of genetic mutations on malignant transformation, epigenetic changes have been focused on in recent times. Several studies could elucidate the potential of epigenetic alterations to not only increase invasiveness of cancer cells in cell culture and animal models but also to contribute to autonomous cellular growth and thus malignant transformation itself. Thus, epigenetic changes are nowadays acknowledged as a hallmark in cancer. Several enzymes are involved in the epigenetic equilibrium of DNA methylation and demethylation, one family being DNA methyl transferases (DNMT). Here, we give a review of the impact of DNMTs on the biology of lung cancer and additionally present some of our results within this context. Further, we are also giving a perspective on future treatment options arising from the current literature and our results.
DiagnomX GmbH
2017-08-11
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
application/xml
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/250
10.17629/www.diagnosticpathology.eu-2017-3:250
Diagnostic Pathology; Vol 3 No 1 (2017): 2017
2364-4893
10.5072/www.diagnosticpathology.eu-2017-3
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/250/543
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/250/544
Copyright (c) 2017 Uli Fehrenbach, Gian Kayser, MD
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/124
2018-06-19T09:14:11Z
dpath:DIM
Next Generation Biobanking - From Biorepository To Data Integration Center
Stephan, C.
Zünkeler, M.
Bieling, D.
Saeger, K.
Lohmann, S.
Zerbe, Norman
Hufnagl, Peter
Introduction/ BackgroundBiobanks and their operators are gaining popularity. However, they face a range of growing challenges. Many of these biobanks used to be smaller and midsized collections of data and samples, but are now being developed into centralized networks within clinics and consortia. These large biobanks require the integration of as many sources of information as possible, including imaging data in addition to any relevant structured data. This is especially the case in the field of virtual microscopy. Data collection is increasingly being orchestrated by workflow based systems and must eventually be incorporated entirely into rule based IT-processes.AimsIn order to achieve this goal, the Charité University Medicine Berlin, VMscope GmbH, and Kairos GmbH formed a consortium in the framework of the joint project, “Biobanking 3.0â€, which is funded by the German Federal Ministry for Education and Research (BMBF). Furthermore, after this successful project, a second KMU funded project called POST (Patient-centric Open Multi Center Study Tool) will begin in the autumn of 2015 to expand the data integration to pathology information systems in a standardized manner.MethodsOne of the project goals is to use an IT-platform with an integrated workflow-engine to orchestrate all necessary processes and document all findings. Defined SOPs during sample extraction and information acquisition can be executed, and all result data can be made available to local research groups as well as project partners.ResultsThus, the platform pursues the research approach of personalized medicine, which requires exact controlling of therapy cycles in a logical and chronological order.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/124
10.17629/www.diagnosticpathology.eu-2016-8:124
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/124/259
Copyright (c) 2016 C. Stephan, M. Zünkeler, K. Saeger, S. Lohmann, Norman Zerbe, Peter Hufnagl
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/265
2018-12-21T18:38:01Z
dpath:EDI
How to implement virtual microscopy in routine tissue – based diagnosis: Guidelines and Recommendations of the Federal Association of German Pathologists
Kayser, Klaus
Kayser, Gian
TMA non small cell lung cancer
Liver biopsy LALD (Lysosomal Acid Lipase Deficiency)
Dermtofibrosarcoma protuberans
Digital Pathology has jumped over the first barriers and enters the world of routine tissue – based diagnosis (surgical pathology) slowly and continuously. Several large pathology institutions use virtual slides (VS) for routine diagnosis, store the images in digital archives, and digitize their workflow according to the needs of laboratory (LIS) and hospital information system (HIS).Development and implementation of communication standards as well as adequate certification and quality control units are mandatory if an adequate and secure diagnosis and treatment of patients should be maintained or amended.The publication of the translated guidelines of the Federal Association of German Pathologists should give our readers the opportunity to read the well designed and substantial document in its original version. We include a few representative virtual slides in our editorial in order to demonstrate the actual performance of virtual microscopy.Thus, we offer our readers to comparing some issues of the virtual world with their own situation and to get informed about the essential procedures of accurate virtual microscopy implementation.
DiagnomX GmbH
2018-09-08
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/265
10.17629/www.diagnosticpathology.eu-2018-4:265
Diagnostic Pathology; Vol 4 No 1 (2018): 2018
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/265/558
Copyright (c) 2018 Klaus Kayser, Gian Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/135
2018-06-19T09:14:46Z
dpath:EP
Application Of Ki-67 Analysis In A Distributed Computing Infrastructure
Strutz, Marco
Lindequist, B.
Witt, M.
Heßling, H.
Hufnagl, P.
Krefting, D.
Introduction/ BackgroundOver the last few years, the protein Ki-67 [1] has been established as one of the most important biomarkers for cell proliferation in breast cancer. High Ki-67 values indicate high tumor growth and have direct impact on the patient’s treatment. Several automated image anal- ysis methods for identifying Ki-67-positive and negative tumor cells have been presented.AimsFor small regions of a virtual slide, the Ki-67 analysis can be realized within an acceptable period of time. However, to analyse an entire whole slide image (WSI [2])most of the current methods are not sufficient yet. On a typical office computer, the processing time of 3,752 tiles, which were extracted from a H–DAB stained WSI, exceeded 24 hours. Therefore, we propose an approach to significantly speed up the process of analysing entire WSIs by using a distributed computing infrastructure.MethodsTo evaluate the approach, an unmodified and validated [3] [4] analysis software for Ki-67 was deployed on a six node setup supporting two different software engines: Hadoop Streaming [5] and Apache Spark [6] . Both tools support the MapReduce methodology whereas Apache Spark offers alternative programing models. In addition, heat maps visualizing the Ki-67 scores for an entire slide were generated which can provide additional informa- tion for clinical research.ResultsFirst results on automated and reproducible tests have been produced. By processing 3,752 tiles the speedup turned out to increase linearly with the number of tiles. The overall processing time was improved by a factor of 10, more precisely from 28 hours on a typical office computer to three hours on a distributed environment. Further optimization strategies besides WSI partitioning will be considered. To achieve additional improvements in processing speed, the underlying algorithm of a Ki-67 analysis can be examined with focus on how to adapt it towards distributed processing workflows.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/135
10.17629/www.diagnosticpathology.eu-2016-8:135
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/135/273
Copyright (c) 2016 M. Strutz, B. Lindequist, M. Witt, H. Heßling, P. Hufnagl, D. Krefting
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/285
2022-04-08T14:54:52Z
dpath:CAS
Diffuse Lipomatosis of Thyroid Gland. Case Report and Review of Literature.
Xhemalaj, Daniela Flamur
Xhardo, Elona
Gradica, Fadil
Berdica, Leart
In normal thyroid glands, adipose tissue is distributed only under the capsule and along vessels.It is not usually present within the thyroid gland. Only a few adipose tissue -containing thyroid lesions have been reported to date.
Lipomatosis of thyroid gland is very rare condition,characterized by infiltration of adipose tissue in the thyroid gland.The pathophysiology of adipose tissue infiltration in the thyroid gland remains unclear.
We report a case of a 69-year-old female who presented in the Emergency Room of our hospital, complaining dysphaghia,dyspnea ,swelling of the neck and weight loss.
Her thyroid panel tests were in the range,ultrasound showed the typical appearance of multinodular goiter.A computed tomography revealed a rightward tracheal deviation and compression narrowing the tracheal lumen more than 50%.
The patient underwent total thyroidectomy. The histopathological examination revealed that adipose tissue was diffusely distributed throughout the thyroid gland.There is no evidence of atypia or mitotic activity.
Capsular infiltration or amyloid deposition were not observed. Nuclear grooves or intranuclear cytoplasmic inclusions were not observed. Accordingly, diffuse lipomatosis of thyroid gland was diagnosed.
DiagnomX GmbH
2022-04-08
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/285
10.17629/www.diagnosticpathology.eu-2022-7:285
Diagnostic Pathology; Vol 7 No 1 (2022): Vol 7 No 1
2364-4893
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/285/576
Copyright (c) 2022 Daniela Flamur Xhemalaj, Elona Xhardo, Dr, Fadil Gradica, Prof.Asc, Leart Berdica, Dr
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/152
2018-06-19T09:28:24Z
dpath:VM
A Globally Optimum Parallelizable Whole Slide Image Registration Algorithm
Çapar, A.
Çöplü, T.
Türkmen, I.C.
Introduction/ BackgroundAdvancements in imaging, communication and computing technologies lead to commercially available digital slide scanners for pathology. These devices help to increase the quality of consultation, diagnosis, research, education and archiving processes as well as contribute to cancer research. At this point, high resolution imaging of the whole pathological specimen is one of the most important parts of the digitalization process. The imaged tiles must be perfectly combined to create the While Slide Image (WSI). In the literature, there are publicly available registration schemes to create the WSI [1] [2]. These methods mainly suffer from the high computational times and high computational resource usage (mainly RAM). To overcome these weaknesses, we have developed a novel, fast, globally optimum WSI registration algorithm.AimsIn this study, we plan to develop a new globally optimum WSI registration scheme for digital pathology. Time consumption, RAM usage, starting tile invariance and compliance to parallel processing are selected as the main design concerns of the registration algorithm.MethodsThe proposed registration scheme has 2 main steps: In the first step, Phase Correlation Method (PCM) given in [3] is utilized to compute the translational offsets between an image and its 4-neighbors. Since PCM requires computing Fourier and inverse Fourier transforms, only overlapping parts of neighbours plus an error region is used to reduce the amount of calculations. Then, all the translational offsets are stored in memory to be used in the global optimization step. In the second step iterations are run to globally optimize the registration according to the neighbouring tile relations. First, the priory knowledge from the motorized table is used to assign global coordinates to the tiles. Then, tiles best position is calculated by maximizing the translational offsets of the neighbors. Here, the tile coordinates are not updated, but the shift values both in X and Y coordinates are saved. After finishing the shift calculation process for all tiles, the shift map is updated, which concludes the first iteration. The iterations continue until zero shift is calculated for all images.ResultsThe performance of the proposed scheme is evaluated using 2 basic scenarios. In the first scenario, 40 different pathology slides are registered using the proposed scheme and then stitched using a bilinear blender. The resulting WSI’s are reviewed by 3 pathologists for stitching errors, and no faulty registration is recognized. In the second scenario, registration time and maximum RAM usage are employed to evaluate the performance of the proposed scheme under different number of tiles. In the evaluations the proposed scheme is compared with Grid Stitching algorithm [1] implemented in ImageJ using the same tile sets and the same PC. The results given in below table show that the proposed scheme has significant RAM and processing time advantages which are very important for real-world applications.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/152
10.17629/www.diagnosticpathology.eu-2016-8:152
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/152/314
Copyright (c) 2016 A. Capar, T. Cöplü, I.C. Türkmen
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/168
2018-06-19T09:08:24Z
dpath:QAM
Comparison Display Resolution On User Impact For Digital Pathology
Marchessoux, Cedric
Nave Dufour, A.
Espig, K.
Monaco, S.
Palekar, A.
Pantanowitz, L.
Introduction/ BackgroundDigital pathology images are very large, up to 100000x100000 pixels which are 30 to 50 times larger than a radiological image for which 12 Mega Pixels (MP) medical displays can be used. Higher resolution displays may have an important influence on digital pathology ergonomics. Three displays with varying resolutions were studied to determine their impact on user interaction.AimsOur hypothesis was that “with higher resolution displays, pathologists need less interaction such as panning and zooming actions and can focus more on image contentâ€. A psycho-physical study has been carried out for validating this hypothesis at the University of Pittsburgh Medical Center.MethodsThree experienced pathologists were selected. Seventy pathology including a wide variety of histological and cytological diagnoses were digitized (Aperio Scanscope XT scanner) and used in a previous study [Ava15]. Customized and optimized viewing software was used to display images and record pathologist’s interactions such mouse clicks, zooming and panning. Three medical displays with different different resolutions were used: 2MP (BARCO MDSC-2124), 4MP (BARCO MDPC-4130) and 12MP (BARCO MDCC-12133), all with the same maximum luminance. Scripts were used for statistical analyze and 1D, 2D, 3D plotting results. User interactions with each image were used to recreate videos documenting of their exact navigation with each digital slide.ResultsThe results of number of zooming and panning interactions are given in the Table 1, as well as averages. When display resolution was increased, the number of panning and zooming interactions significantly decreases for all three observers. For panning, there was on average 1172 panning actions for the 2MP and 951 actions for the 12MP display. For zooming actions, there was on average 12315 zoom actions for the 2MP and 2847 actions for the 12MP display. Between the 2MP and 12MP displays, the ratio of the number of zooms was 4:1 in favor of the 12MP monitor. On figure 1, the 3D plots of one case for the three monitors show the navigation through the slide and show lesser points for higher resolution display. With higher resolution the pathologist goes more directly to the Region Of Interest (ROI) for making the decision. Figure 2 shows more analysis of the zoom values across the cases for the three monitors. The pathologists have the tendency to remain close to a value of 1 with the 12 MP display where a value of 1 means that no zoom is applied. This is illustrated by the Figure 2 showing for observer 2 the boxplots of the zoom values for the three displays. It clearly shows that with higher resolution display the trend goes to get closer to one for the zoom value meaning no need to zoom in in the image. We used three different displays instead of one unique display with three different resolutions. Though using just one display would have reduced variability of differing LCD panels, pixel size and structure, it would not have been commercially or clinically realistic.Despite the limited number of pathologists, this study shows that display resolution used for digital pathology is important. Higher resolution monitors significantly help reducing the number of user interactions and thereby can minimize pathologist fatigue when reading digital slides.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/168
10.17629/www.diagnosticpathology.eu-2016-8:168
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/168/295
Copyright (c) 2016 C. Marchessoux, A. Nave Dufour, K. Espig, S. Monaco, A. Palekar, L. Pantanowitz
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/184
2018-06-19T09:09:45Z
dpath:EL
Open Access Publication In Pathology – Advantages, Constraints And New Tools
Carvalho, Rita
Borkenfeld, Stephan
Kayser, Klaus
Introduction/ BackgroundOpen access journals are financed by authors (i.e. re- search grants), rather than by readers or subscribers. This business model allows a world – wide uncontrolled distribution of medical information and scientific knowledge. The financial of shifting the finance and the opportunities for misuse raise significant concerns regarding non – scientific impact and article content integrity.AimsHerein we report and discuss ideas and experiences of open access publication focusing on diagnostic pathology.MethodsOur experiences are drawn from the open access online journal diagnosticpathology.eu. The journal offers the opportunity to publish case reports “beside the microscope†and to submit data for “interactive publicationâ€. Both tools are unique, and cannot be found elsewhere. For publication of suitable articles, we demand the submission of glass slides, which will become completely digitized (virtual slides, VS).ResultsThe journal is online since ten months, and the only completely independent open access journal in medicine. We have published several case reports under the headline “How do I diagnose…?†The presented form offers a guide through the article and permits a complete publication “besides the microscopeâ€, commonly in less than one hour. Automated links to reference search items are included as well as virtual slides. The strict publication format permits fast submission of unique or interesting cases, and, in addition, the implementation of the publication into a case – related open and flexible image date bank. ConclusionsThe mandatory inclusion of virtual slides is a unique quality control. The journal diagnosticpathology. eu is embedded in a cloud that will consist of an archive of published cases with virtual slides, an express review forum with a corresponding duty plan, an automated measurement system of histological slides, and open access atlases such as hazards of natural and artificial fibers (fine granulate) and a collection of all known pulmonary diseases.AcknowledgementThe financial support of the Verein zur Förderung des biologisch - technologischen Fortschritts in der Medizn e. V. is gratefully acknowledged.Â
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/184
10.17629/www.diagnosticpathology.eu-2016-8:184
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/184/326
Copyright (c) 2016 R. Carvalho, S. Borkenfeld, K. Kayser
http://creativecommons.org/licenses/by-sa/4.0
oai:ojs2.localhost:article/200
2018-06-19T09:07:53Z
dpath:TP
An Innovative Telepathology Solution For Developing Countries
Botteghi, M.
Masalu, N.
Stracca, V.
Amadori, D.
Introduction/ BackgroundThe increasing incidence of pathologies like tumors and infections is a significant public health burden in developing countries. The ability to provide early diagnosis, treatments, follow-up care has a strong impact on the survival. Telemedicine is of great utility in countries lacking appropriate healthcare facilities by allowing for the performance of good level healthcare practices. Sub-Saharan African Countries suffer a dramatic shortage of medical pathologists (in the range of 1 to 10 pathologists per 10 million people) and are also victims of digital divide. Vittorio Tison Association (Tison), IRST research cancer hospital and Patologi Oltre Frontiera NGO (APOF) cooperate in the sanitary mission founded in 1999 in Bugando Medical Centre (BMC), a hospital located in Mwanza, Tanzania. In that mission, during 2011 we started the development of our telemedicine project. The project utilizes a novel telematic platform oriented to several sanitary branches with a special focus in pathology and oncology. AimsThe main project goals are:to provide ICT and TLC services between healthcare facilities in developed and developing countries;to allow for simultaneous telepathology counselling sharing microscopy and radiology images, conference calling, remote diagnosis, double-blind evaluation, second opinion and the remote control of medical instrumentation;to perform e-learning and remote quality control;to carry out GCP clinical trials through data collection, monitoring and evaluation;to encourage and support scientific research;to reduce the knowledge gaps inherent to the digital divide. MethodsAPOF has been developing the BMC pathology lab from 2000 to 2008. In the meantime Tison took care of training in Oncology of local medical doctors, opened the BMC Oncology Department in 2010 and patronized the building of a new clinic dedicated to the Oncologic Institute. We started the development of the project in 2011 with a general assessment of the needs and lacks in local working procedures, related to the possible improvements in ICT. Our first step involved the Internet connections activation and the implementation of the project informatic core in the IT room of the BMC Oncologic Institute. The telematic link between IRST’s Italian site and BMC has been realized during the early pilot phase. We carried out several experimental sessions to investigate the compatibility of the main third-parts digital pathology products with our platform, choosing digital microscope Menarini D-SIGHT in association with D-SIGHT+ telepathology web-based application. Finally, on June 2015 we launched the BMC Telepathology Facility performing a complete demo of the system during the AORTIC East African Regional Meeting. ResultsWe validated the system in a wide range of conditions. Experimental data indicate an improvement of a factor up to 100 in the overall images transmission rate in comparison to the previous models. The pathology images remotely viewed are fully compliant with the diagnostic requirements in terms of definition and magnification. The platform is easy-to-use, all sanitary operators involved in the testing found it friendly and effective. The images browsing on the screen is very fast and precise, professional operators evaluated this solution equivalent to the use of the microscope. Our project is characterized by a high level of innovation which increases efficiency and efficacy of health practices and can boost the use of telepathology in developing countries.
DiagnomX GmbH
2016-06-16
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
application/pdf
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/200
10.17629/www.diagnosticpathology.eu-2016-8:200
Diagnostic Pathology; Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
2364-4893
10.5072/www.diagnosticpathology.eu-2016-8
eng
http://www.diagnosticpathology.eu/content/index.php/dpath/article/view/200/257
Copyright (c) 2016 M. Botteghi, N. Masalu, V. Stracca, D. Amadori
http://creativecommons.org/licenses/by-sa/4.0
22a6ae0a6dbaeecc076f106ecdfe168e