Abstract
Introduction There is a clinical need for Pathologists to compare histopathological images of normal and diseased tissues between different samples, cases, and species. Comparative pathology is limited by restricted availability of cross-species histopathological expertise. The Comparative Pathology Workbench (CPW) has been designed to allow direct and dynamic comparison of scanned whole slide images, or other clinical data such as radiological scans or research data such as spatial transcriptomics, or scRNA-seq in real time by pathologists and scientists anywhere across the world. This online tool allows pathologists to engage in meaningful expert discussion with other pathologists and other disciplines dynamically.
Methods The Comparative Pathology Workbench (CPW) is a free online web-browser based visual analytics platform and uses an interactive ‘spreadsheet’ style grid of presentation for both images and associated analysis data, to provide shared access to groups of users. Each ‘spreadsheet’ is called a Workbench or Bench, and this provides a grid of cells arranged in rows and columns, so that thumbnail images that correspond to matching data can be added to a cell and these cells can be organised in any way that the Bench creator sees fit.
No high-resolution image data is stored in the CPW system, instead, all such image data is hosted by other resource applications such as OMERO, with only references stored within the CPW. Low resolution data such as user generated charts and other images can be uploaded to the CPW directly as required. 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.
Results In figure 1, a Workbench hosted by the CPW, provides a visualisation of the differences in the morphology of a set of 30 terminal ileal fibrostenosing lesions, surgically resected from different Crohn’s disease patients, with a set of 30 normal terminal ileum controls.
These sections were collected in the context of the Human Gut Cell Atlas programme (https://www.ed.ac.uk/comparative-pathology/the-gut-cell-atlas-project).
A. A Bench displaying images of the histological sections.
Rows represent specific samples; columns represent specific stains and/or data related to these samples.
B. The Chain link icons represent links that were created between images, to notify the user that there is a relationship between such sections.
C. The Red–dashed box represents an accumulation of all data points quantified from annotations.
These represent the surface area of each region of the ileum wall, as well as the collagen area, stained by PSR & quantified using QuPath.
The summary data can be found in the last row as shown in ‘Data Summary’.
D. The CPW provides a ‘Bench Commentary’ facility for discussion about the Bench contents to further increase the interpretation & understanding of the histochemical analyses.
https://workbench-czi-cpw.mvm.ed.ac.uk/home/
Conclusions CPW has been successfully implemented in the DERMATLAS project of rare skin tumours from UK, Belgium, France, Canada, USA, and Mexico, and the Coeliac disease histopathology AI diagnosis project involving 17 UK pathologists. Future applications may include histopathological and endoscopic image analysis in clinical trials.
Methods The Comparative Pathology Workbench (CPW) is a free online web-browser based visual analytics platform and uses an interactive ‘spreadsheet’ style grid of presentation for both images and associated analysis data, to provide shared access to groups of users. Each ‘spreadsheet’ is called a Workbench or Bench, and this provides a grid of cells arranged in rows and columns, so that thumbnail images that correspond to matching data can be added to a cell and these cells can be organised in any way that the Bench creator sees fit.
No high-resolution image data is stored in the CPW system, instead, all such image data is hosted by other resource applications such as OMERO, with only references stored within the CPW. Low resolution data such as user generated charts and other images can be uploaded to the CPW directly as required. 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.
Results In figure 1, a Workbench hosted by the CPW, provides a visualisation of the differences in the morphology of a set of 30 terminal ileal fibrostenosing lesions, surgically resected from different Crohn’s disease patients, with a set of 30 normal terminal ileum controls.
These sections were collected in the context of the Human Gut Cell Atlas programme (https://www.ed.ac.uk/comparative-pathology/the-gut-cell-atlas-project).
A. A Bench displaying images of the histological sections.
Rows represent specific samples; columns represent specific stains and/or data related to these samples.
B. The Chain link icons represent links that were created between images, to notify the user that there is a relationship between such sections.
C. The Red–dashed box represents an accumulation of all data points quantified from annotations.
These represent the surface area of each region of the ileum wall, as well as the collagen area, stained by PSR & quantified using QuPath.
The summary data can be found in the last row as shown in ‘Data Summary’.
D. The CPW provides a ‘Bench Commentary’ facility for discussion about the Bench contents to further increase the interpretation & understanding of the histochemical analyses.
https://workbench-czi-cpw.mvm.ed.ac.uk/home/
Conclusions CPW has been successfully implemented in the DERMATLAS project of rare skin tumours from UK, Belgium, France, Canada, USA, and Mexico, and the Coeliac disease histopathology AI diagnosis project involving 17 UK pathologists. Future applications may include histopathological and endoscopic image analysis in clinical trials.
| Original language | English |
|---|---|
| Pages (from-to) | A286-A287 |
| Number of pages | 2 |
| Journal | Gut |
| Volume | 74 |
| Issue number | Suppl 1 |
| DOIs | |
| Publication status | Published - 23 Jun 2025 |
| Event | BSG Annual Meeting 2025 - Glasgow, United Kingdom Duration: 23 Jun 2025 → 26 Jun 2025 |
