Project-MONAI / Project-MONAI/MONAI
An optimized solution to run HoverNet on patholgy WSI
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- Dominant language
- Python
- Stars
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- 5d 1h
- Merged PRs (30d)
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Description
Is your feature request related to a problem? Please describe.
I am trying to use a trained model in HoverNet to infer many SVS whole slide images. I followed every thing in tutorial, except changing PILReader to WSIReader: like
https://github.com/Project-MONAI/tutorials/blob/6be932f821c9ce4e795748dde7574beea8f8ea2c/pathology/hovernet/inference.py#L69
LoadImaged(keys="image", reader=WSIReader, backend="cucim", level=0)
I have tried the backend as either cucim or tifffile. But both cannot do the job quickly. It is more than 4 hours (not finished yet) in a single WSI. This will make the tool unfeasible for use. Also cucim gives "cuda out of memory" on multi-gpu.
Describe the solution you'd like
I think the limiting step here has something to do with post-processing after inference. There must be a way multi-thread that using something like dask.
CC: @KumoLiu might help triage the problem?!
Update:
All the runs with either cucim or tifffile stopped after about 5 hours with "cuda out of memory" error
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
Start with pathology/hovernet/inference.py and the linked tutorial, comparing the PILReader example with the WSIReader configuration using cucim or tifffile. Profile inference and post-processing on a representative SVS whole-slide image; done means processing is substantially faster and avoids the reported CUDA out-of-memory failures.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, pytorch
- Domain
- machine-learning, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100