The Comparative Pathology Workbench: Interactive Visual Analytics for Biomedical Data

Mike Wicks; Michael Glinka; Bill Hill; Derek Houghton; Mehran Sharghi; Ingrid Ferreira; David Adams; Shahida Din; Irene Papatheodorou; Kathryn  Kirkwood; Michael Cheeseman; Albert Burger; Richard Baldock; Mark J Arends

doi:10.1016/j.jpi.2023.100328

The Comparative Pathology Workbench: Interactive Visual Analytics for Biomedical Data

Mike Wicks, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Ingrid Ferreira, David Adams, Shahida Din, Irene Papatheodorou, Kathryn Kirkwood, Michael Cheeseman, Albert Burger, Richard Baldock, Mark J Arends

Research output: Contribution to journal › Article › peer-review

Abstract

Pathologists need to compare histopathological images of normal and diseased tissues between different samples, cases and species. We have designed an interactive system, termed Comparative Pathology Workbench (CPW), that allows direct and dynamic comparison of images at a variety of magnifications, selected regions of interest, as well as the results of image analysis or other data analyses such as scRNA-seq. This allows pathologists to indicate key diagnostic features, with a mechanism to allow discussion threads amongst expert groups of pathologists and other disciplines. The data and associated discussions can be accessed online from anywhere in the world. The Comparative Pathology Workbench (CPW) is a web-browser based visual analytics platform providing shared access to an interactive “spreadsheet” style presentation of image and associated analysis data. The CPW provides a grid layout of rows and columns so that images that correspond to matching data can be organised in the form of an image-enabled “spreadsheet”. An individual workbench can be shared with other users with read-only or full edit access as required. In addition, each workbench element or the whole bench itself has an associated discussion thread to allow collaborative analysis and consensual interpretation of the data.

The CPW is a Django-based web-application that hosts the workbench data, manages users and user-preferences. All image data are hosted by other resource applications such as OMERO or the Digital Slide Archive. Further resources can be added as required. The discussion threads are managed using WordPress and include additional graphical and image data. The CPW has been developed to allow integration of image analysis outputs from systems such as QuPath or ImageJ. All software is open-source and available from a GitHub repository

Original language	English
Journal	Journal of Pathology Informatics
Early online date	9 Aug 2023
DOIs	https://doi.org/10.1016/j.jpi.2023.100328
Publication status	E-pub ahead of print - 9 Aug 2023

Keywords / Materials (for Non-textual outputs)

Image visualisation
shared workspace
image spreadsheet
visual comparison
visual analytics
embedded discussion

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Wicks, M., Glinka, M., Hill, B., Houghton, D., Sharghi, M., Ferreira, I., Adams, D., Din, S., Papatheodorou, I., Kirkwood, K., Cheeseman, M., Burger, A., Baldock, R., & Arends, M. J. (2023). The Comparative Pathology Workbench: Interactive Visual Analytics for Biomedical Data. Journal of Pathology Informatics. Advance online publication. https://doi.org/10.1016/j.jpi.2023.100328

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title = "The Comparative Pathology Workbench: Interactive Visual Analytics for Biomedical Data",

abstract = "Pathologists need to compare histopathological images of normal and diseased tissues between different samples, cases and species. We have designed an interactive system, termed Comparative Pathology Workbench (CPW), that allows direct and dynamic comparison of images at a variety of magnifications, selected regions of interest, as well as the results of image analysis or other data analyses such as scRNA-seq. This allows pathologists to indicate key diagnostic features, with a mechanism to allow discussion threads amongst expert groups of pathologists and other disciplines. The data and associated discussions can be accessed online from anywhere in the world. The Comparative Pathology Workbench (CPW) is a web-browser based visual analytics platform providing shared access to an interactive “spreadsheet” style presentation of image and associated analysis data. The CPW provides a grid layout of rows and columns so that images that correspond to matching data can be organised in the form of an image-enabled “spreadsheet”. An individual workbench can be shared with other users with read-only or full edit access as required. In addition, each workbench element or the whole bench itself has an associated discussion thread to allow collaborative analysis and consensual interpretation of the data.The CPW is a Django-based web-application that hosts the workbench data, manages users and user-preferences. All image data are hosted by other resource applications such as OMERO or the Digital Slide Archive. Further resources can be added as required. The discussion threads are managed using WordPress and include additional graphical and image data. The CPW has been developed to allow integration of image analysis outputs from systems such as QuPath or ImageJ. All software is open-source and available from a GitHub repository",

keywords = "Image visualisation, shared workspace, image spreadsheet, visual comparison, visual analytics, embedded discussion",

author = "Mike Wicks and Michael Glinka and Bill Hill and Derek Houghton and Mehran Sharghi and Ingrid Ferreira and David Adams and Shahida Din and Irene Papatheodorou and Kathryn Kirkwood and Michael Cheeseman and Albert Burger and Richard Baldock and Arends, {Mark J}",

note = "Funding Information: Chan-Zuckerberg Initiative Human Cell Atlas grant A-1708-02723, The Leona M. and Harry B. Helmsley Charitable Trust entitled “Human Gut Cell Atlas – Normal Intestine and Crohn's Disease”, grant reference number 1903-03783 and the Medical Research Council grant MR/V000292/1 entitled “The Genomic Atlas of Dermatological Tumours (DERMATLAS)”.We acknowledge the Chan-Zuckerberg Initiative (CZI) for initial funding and The Leona M. and Harry B. Helmsley Charitable Trust for continued funding that supported the project in which the Comparative Pathology Workbench was constructed, tested, and used. In addition, this publication is part of the Gut Cell Atlas Crohn's Disease Consortium funded by The Leona M. and Harry B. Helmsley Charitable Trust and is supported by a grant from The Helmsley Charitable Trust to The Universities of Edinburgh and Heriot-Watt, NHS Lothian and to the Wellcome Sanger Institute and the European Bioinformatics Institute. Please see www.helmsleytrust.org/gut-cell-atlas/. SD acknowledges the support of NHS Research Scotland via NHS Lothian. Funding Information: We acknowledge the Chan-Zuckerberg Initiative (CZI) for initial funding and The Leona M. and Harry B. Helmsley Charitable Trust for continued funding that supported the project in which the Comparative Pathology Workbench was constructed, tested, and used. In addition, this publication is part of the Gut Cell Atlas Crohn{\textquoteright}s Disease Consortium funded by The Leona M. and Harry B. Helmsley Charitable Trust and is supported by a grant from The Helmsley Charitable Trust to The Universities of Edinburgh and Heriot-Watt, NHS Lothian and to the Wellcome Sanger Institute and the European Bioinformatics Institute. Please see www.helmsleytrust.org/gut-cell-atlas/ . SD acknowledges the support of NHS Research Scotland via NHS Lothian. Funding Information: Chan-Zuckerberg Initiative Human Cell Atlas grant A-1708-02723 , The Leona M. and Harry B. Helmsley Charitable Trust entitled “Human Gut Cell Atlas – Normal Intestine and Crohn{\textquoteright}s Disease”, grant reference number 1903-03783 and the Medical Research Council grant MR/V000292/1 entitled “The Genomic Atlas of Dermatological Tumours (DERMATLAS)”. Publisher Copyright: {\textcopyright} 2023 The Authors",

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doi = "10.1016/j.jpi.2023.100328",

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AU - Hill, Bill

AU - Houghton, Derek

AU - Sharghi, Mehran

AU - Ferreira, Ingrid

AU - Adams, David

AU - Din, Shahida

AU - Papatheodorou, Irene

AU - Kirkwood, Kathryn

AU - Cheeseman, Michael

AU - Burger, Albert

AU - Baldock, Richard

AU - Arends, Mark J

N1 - Funding Information: Chan-Zuckerberg Initiative Human Cell Atlas grant A-1708-02723, The Leona M. and Harry B. Helmsley Charitable Trust entitled “Human Gut Cell Atlas – Normal Intestine and Crohn's Disease”, grant reference number 1903-03783 and the Medical Research Council grant MR/V000292/1 entitled “The Genomic Atlas of Dermatological Tumours (DERMATLAS)”.We acknowledge the Chan-Zuckerberg Initiative (CZI) for initial funding and The Leona M. and Harry B. Helmsley Charitable Trust for continued funding that supported the project in which the Comparative Pathology Workbench was constructed, tested, and used. In addition, this publication is part of the Gut Cell Atlas Crohn's Disease Consortium funded by The Leona M. and Harry B. Helmsley Charitable Trust and is supported by a grant from The Helmsley Charitable Trust to The Universities of Edinburgh and Heriot-Watt, NHS Lothian and to the Wellcome Sanger Institute and the European Bioinformatics Institute. Please see www.helmsleytrust.org/gut-cell-atlas/. SD acknowledges the support of NHS Research Scotland via NHS Lothian. Funding Information: We acknowledge the Chan-Zuckerberg Initiative (CZI) for initial funding and The Leona M. and Harry B. Helmsley Charitable Trust for continued funding that supported the project in which the Comparative Pathology Workbench was constructed, tested, and used. In addition, this publication is part of the Gut Cell Atlas Crohn’s Disease Consortium funded by The Leona M. and Harry B. Helmsley Charitable Trust and is supported by a grant from The Helmsley Charitable Trust to The Universities of Edinburgh and Heriot-Watt, NHS Lothian and to the Wellcome Sanger Institute and the European Bioinformatics Institute. Please see www.helmsleytrust.org/gut-cell-atlas/ . SD acknowledges the support of NHS Research Scotland via NHS Lothian. Funding Information: Chan-Zuckerberg Initiative Human Cell Atlas grant A-1708-02723 , The Leona M. and Harry B. Helmsley Charitable Trust entitled “Human Gut Cell Atlas – Normal Intestine and Crohn’s Disease”, grant reference number 1903-03783 and the Medical Research Council grant MR/V000292/1 entitled “The Genomic Atlas of Dermatological Tumours (DERMATLAS)”. Publisher Copyright: © 2023 The Authors

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N2 - Pathologists need to compare histopathological images of normal and diseased tissues between different samples, cases and species. We have designed an interactive system, termed Comparative Pathology Workbench (CPW), that allows direct and dynamic comparison of images at a variety of magnifications, selected regions of interest, as well as the results of image analysis or other data analyses such as scRNA-seq. This allows pathologists to indicate key diagnostic features, with a mechanism to allow discussion threads amongst expert groups of pathologists and other disciplines. The data and associated discussions can be accessed online from anywhere in the world. The Comparative Pathology Workbench (CPW) is a web-browser based visual analytics platform providing shared access to an interactive “spreadsheet” style presentation of image and associated analysis data. The CPW provides a grid layout of rows and columns so that images that correspond to matching data can be organised in the form of an image-enabled “spreadsheet”. An individual workbench can be shared with other users with read-only or full edit access as required. In addition, each workbench element or the whole bench itself has an associated discussion thread to allow collaborative analysis and consensual interpretation of the data.The CPW is a Django-based web-application that hosts the workbench data, manages users and user-preferences. All image data are hosted by other resource applications such as OMERO or the Digital Slide Archive. Further resources can be added as required. The discussion threads are managed using WordPress and include additional graphical and image data. The CPW has been developed to allow integration of image analysis outputs from systems such as QuPath or ImageJ. All software is open-source and available from a GitHub repository

AB - Pathologists need to compare histopathological images of normal and diseased tissues between different samples, cases and species. We have designed an interactive system, termed Comparative Pathology Workbench (CPW), that allows direct and dynamic comparison of images at a variety of magnifications, selected regions of interest, as well as the results of image analysis or other data analyses such as scRNA-seq. This allows pathologists to indicate key diagnostic features, with a mechanism to allow discussion threads amongst expert groups of pathologists and other disciplines. The data and associated discussions can be accessed online from anywhere in the world. The Comparative Pathology Workbench (CPW) is a web-browser based visual analytics platform providing shared access to an interactive “spreadsheet” style presentation of image and associated analysis data. The CPW provides a grid layout of rows and columns so that images that correspond to matching data can be organised in the form of an image-enabled “spreadsheet”. An individual workbench can be shared with other users with read-only or full edit access as required. In addition, each workbench element or the whole bench itself has an associated discussion thread to allow collaborative analysis and consensual interpretation of the data.The CPW is a Django-based web-application that hosts the workbench data, manages users and user-preferences. All image data are hosted by other resource applications such as OMERO or the Digital Slide Archive. Further resources can be added as required. The discussion threads are managed using WordPress and include additional graphical and image data. The CPW has been developed to allow integration of image analysis outputs from systems such as QuPath or ImageJ. All software is open-source and available from a GitHub repository

KW - Image visualisation

KW - shared workspace

KW - image spreadsheet

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KW - visual analytics

KW - embedded discussion

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DO - 10.1016/j.jpi.2023.100328

M3 - Article

SN - 2153-3539

JO - Journal of Pathology Informatics

JF - Journal of Pathology Informatics

ER -

The Comparative Pathology Workbench: Interactive Visual Analytics for Biomedical Data

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

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Cite this