Project-MONAI / Project-MONAI/MONAI
Generalized Stain Normalization
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- Dominant language
- Python
- Stars
- 8.7k
- Forks
- 1.6k
- Avg merge
- 5d 1h
- Merged PRs (30d)
- 20
Description
Stain normalization in MONAI consists of two components stain extraction and stain normalization. Right now, they are specific to Hematoxylin and Eosin stains but both of these components can be generalized to supports any or at least many stains.
#3505 generalized normalization part to be independent of the stain matrix but the stain extraction needs further investigation to see whether it can be generalized to common stains in histopathology. Also it would be great to know if we can use our stain normalization with arbitrary predefined stain matrices.
Moreover, changes are needed to be fit into the overall structure of MONAI Pathology #4005.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Review the current stain extraction and normalization components, then read issue #3505 for the existing normalization generalization and issue #4005 for the MONAI Pathology structure. Investigate support for common stains and arbitrary predefined stain matrices; done means the components fit the planned pathology structure and work beyond only Hematoxylin and Eosin.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- computer-vision
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100