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SlicerScope extension

Key Investigators

• Yi Gao (Shenzhen University)
• Steve Pieper (Isomics)
• Andras Lasso (Queen’s University)

Project Description

SlicerScope is a microscopy tool for operating on slides like histopathology (H&E) images.

Objective

1. Objective A. Add the SlicerScope, an open platform for whole slide histopathology image as a Slicer extension.
2. Objective B. Add the nucleus segmentation module into the extension.

20220701 What’s been done in the week

1. With the help from Steve and Andras, the extension has been submitted to the extension manager. We will keep watching it’s bugs and make improvements.
2. The extension has been renamed to “BigImage” to better reflect its nature.

Approach and Plan

1. It’s currently already on github. The extension s4ext file has been updated and the pull-request has been created. We will review the extension with the benevolent dictators.
2. Add the nucleus segmentation (non-deep learning version) to a module under this extension.

Progress and Next Steps

1. The extension and the module has already been pushed to github

Illustrations

Background and References

See this webpage for more details.

Xiaxia Yu, Bingshuai Zhao, Haofan Huang, Mu Tian, Sai Zhang, Hongping Song, Zengshan Li, Kun Huang, Yi Gao, “An Open Source Platform for Computational Histopathology,” in IEEE Access, vol. 9, pp. 73651-73661, 2021, doi: 10.1109/ACCESS.2021.3080429.