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      QuPath: Open source software for digital pathology image analysis

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          Abstract

          QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

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          NIH Image to ImageJ: 25 years of image analysis.

          Lynda C. Schneider, Wayne S Rasband (2013)
          For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
          Article 0 comments Cited 4147 times – based on 0 reviews     Review now
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            Metadata matters: access to image data in the real world

            Melissa Linkert, Curtis Rueden, Chris Allan … (2010)
            Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.
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              Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): Explanation and Elaboration

              Douglas G. Altman, Lisa McShane, Willi Sauerbrei … (2012)
              The REMARK “elaboration and explanation” guideline, by Doug Altman and colleagues, provides a detailed reference for authors on important issues to consider when designing, conducting, and analyzing tumor marker prognostic studies.
              Article 0 comments Cited 313 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Manuel Salto-Tellez: m.salto-tellez@qub.ac.uk
                Peter W. Hamilton: p.hamilton@qub.ac.uk
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 4 December 2017
                Publication date PMC-release: 4 December 2017
                Publication date Collection: 2017
                Volume: 7
                Electronic Location Identifier: 16878
                Affiliations
                [1 ]ISNI 0000 0004 0374 7521, GRID grid.4777.3, Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, ; Belfast, Northern Ireland UK
                [2 ]ISNI 0000 0000 9565 2378, GRID grid.412915.a, Tissue Pathology, Belfast Health and Social Care Trust, Belfast, ; Northern Ireland, Northern Ireland UK
                [3 ]ISNI 0000 0004 0374 7521, GRID grid.4777.3, Centre for Experimental Medicine, Queen’s University Belfast, ; Belfast, Northern Ireland UK
                [4 ]ISNI 0000 0004 0374 7521, GRID grid.4777.3, Cancer Epidemiology and Health Services Research Group, Centre for Public Health, Queen’s University Belfast, ; Belfast, Northern Ireland UK
                Author information
                http://orcid.org/0000-0001-9160-283X
                Article
                Publisher ID: 17204
                DOI: 10.1038/s41598-017-17204-5
                PMC ID: 5715110
                PubMed ID: 29203879
                SO-VID: 6fe84731-6303-4a2a-a0f5-abc5ca445479
                Copyright © © The Author(s) 2017
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 20 July 2017
                Date accepted : 21 November 2017
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Uncategorized
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