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 journalArticlepeer-review

Abstract / Description of output

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 languageEnglish
JournalJournal of Pathology Informatics
Early online date9 Aug 2023
DOIs
Publication statusE-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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