[GSoC2024]caMicroscope -finalReport-

GSoC2024_caMicroscope_finalReport.md

Google Summer of Code 2024

Contributor: Yuka Usui (@YukaUU)
Organization: caMicroscope
Project: Pathologist Annotation Behavior Report
Mentors: Ryan Birmingham

Overview

caMicroscope is a widely used open-source end-to-end platform for digital pathology. Many pathologists use caMicroscope to annotate WSI cases in their daily work.Annotating cancer cells requires specialized knowledge and experience. How pathologists annotate the slide and the different behaviors that different pathologist works on the same slide are very important. I collected, tracked, and visualized the annotation actions of every slide by graphing these data.

• caMicroscope - Pull Requests
  

Feel free to look into the PRs for clear description/details of individual features.

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The project consists of four parts:

1. Saving Marks include User's X, Y, Zoom, etc

The existing caMicroscope only tracked X, Y(image coordinate). I collected the position information and zoom level for each annotation and displayed them on the UI.

PR can be found here.

2. All annotations saved have (accurate image coordinate and zooming ) info saved

When annotating in multi-mode, the position information and zoom level are not saved correctly. I made adjustments to the database and the process of the data collecting to ensure the data are saved correctly.
PR can be found here.

3. Add Visualization Panel

In order to match the requirement of this project --- ""add web application (within caMicroscope) which is able to interpret and visualize user behavior data"", I created a panel that pathologists can visualize the annotation info while they are annotating the slide.

PR can be found here.

4. Add Visualization Dashboard

The purpose is same with #3. I created a dashboard page to show the annotation data which includes the number of the pathologists who annotated the same slide, the types of preset labels was used and several basic infomation.

PR can be found here.

Future Plans (To-do)

I would like to continue working on caMicroscope. What I can do is

1. Making visualization graphs more powerful by adding heatmap graphs of annotation etc.
2. Anything that can make this project better.

Acknowledgments

I am grateful to caMicroscope team and the organizer of Google Summer of Code for giving me this wonderful opportunity. I enjoyed the time spent working on this project and felt a great sense of accomplishment. Special thanks to Ryan Birmingham, my mentor for supporting me and giving me lots of advice throughout this project.

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Thank You :c)