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      SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images

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          Abstract

          The demand for accurate and reproducible phenotyping of a disease trait increases with the rising number of biobanks and genome wide association studies. Detailed analysis of histology is a powerful way of phenotyping human tissues. Nonetheless, purely visual assessment of histological slides is time-consuming and liable to sampling variation and optical illusions and thereby observer variation, and external validation may be cumbersome. Therefore, within our own biobank, computerized quantification of digitized histological slides is often preferred as a more precise and reproducible, and sometimes more sensitive approach. Relatively few free toolkits are, however, available for fully digitized microscopic slides, usually known as whole slides images. In order to comply with this need, we developed the slideToolkit as a fast method to handle large quantities of low contrast whole slides images using advanced cell detecting algorithms. The slideToolkit has been developed for modern personal computers and high-performance clusters (HPCs) and is available as an open-source project on github.com. We here illustrate the power of slideToolkit by a repeated measurement of 303 digital slides containing CD3 stained (DAB) abdominal aortic aneurysm tissue from a tissue biobank. Our workflow consists of four consecutive steps. In the first step (acquisition), whole slide images are collected and converted to TIFF files. In the second step (preparation), files are organized. The third step (tiles), creates multiple manageable tiles to count. In the fourth step (analysis), tissue is analyzed and results are stored in a data set. Using this method, two consecutive measurements of 303 slides showed an intraclass correlation of 0.99. In conclusion, slideToolkit provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic data sets.

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          Statistical methods for assessing agreement between two methods of clinical measurement.

          In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old. Such investigations are often analysed inappropriately, notably by using correlation coefficients. The use of correlation is misleading. An alternative approach, based on graphical techniques and simple calculations, is described, together with the relation between this analysis and the assessment of repeatability.
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            Management of abdominal aortic aneurysms clinical practice guidelines of the European society for vascular surgery.

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              When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry--the red, brown, and blue technique.

              Once focused mainly on the characterization of neoplasms, immunohistochemistry (IHC) today is used in the investigation of a broad range of disease processes with applications in diagnosis, prognostication, therapeutic decisions to tailor treatment to an individual patient, and investigations into the pathogenesis of disease. This review addresses the technical aspects of immunohistochemistry (and, to a lesser extent, immunocytochemistry) with attention to the antigen-antibody reaction, optimal fixation techniques, tissue processing considerations, antigen retrieval methods, detection systems, selection and use of an autostainer, standardization and validation of IHC tests, preparation of proper tissue and reagent controls, tissue microarrays and other high-throughput systems, quality assurance/quality control measures, interpretation of the IHC reaction, and reporting of results. It is now more important than ever, with these sophisticated applications, to standardize the entire IHC process from tissue collection through interpretation and reporting to minimize variability among laboratories and to facilitate quantification and interlaboratory comparison of IHC results.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                5 November 2014
                : 9
                : 11
                : e110289
                Affiliations
                [1 ]Department of Vascular Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
                [2 ]Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
                [3 ]Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
                University of Torino, Italy
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: BN JvH FM PvD GP. Performed the experiments: BN. Analyzed the data: BN. Contributed reagents/materials/analysis tools: BN JvH FM PvD GP. Wrote the paper: BN JvH FM PvD GP.

                Article
                PONE-D-14-29166
                10.1371/journal.pone.0110289
                4220929
                25372389
                72ed6d1d-de73-4d57-b86d-d1d5ddf8e054
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 10 July 2014
                : 11 September 2014
                Page count
                Pages: 10
                Funding
                The authors have no support or funding to report.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Histology
                Histological Examination
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Computer and Information Sciences
                Computer Applications
                Computer Architecture
                Pipelines (Computing)
                Computer Software
                Open Source Software
                Computing Methods
                Programming Languages
                High Level Languages
                Engineering and Technology
                Signal Processing
                Image Processing
                Medicine and Health Sciences
                Research and Analysis Methods
                Computational Techniques
                Database and Informatics Methods
                Bioinformatics
                Imaging Techniques
                Image Analysis
                Specimen Preparation and Treatment
                Custom metadata
                The authors confirm that, for approved reasons, some access restrictions apply to the data underlying the findings. The slideToolkit is hosted on github.com. Raw image data are available upon request due to ethical restrictions. Summarized data is available in the manuscript and in the supplemental files. Readers may contact Gerard Pasterkamp ( g.pasterkamp@ 123456umcutrecht.nl ) to request the raw, anonymized image data.

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