Project-MONAI / Project-MONAI/MONAILabel
MONAI Label Pathology Tutorial (monailabel_HelloWorld_radiology_3dslicer)
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- Dominant language
- Python
- Stars
- 891
- Forks
- 269
- Avg merge
- 15h 41m
- Merged PRs (30d)
- 1
Description
Describe the bug
The pathology tutorial states that the MONAI Label extension works with versions of QuPath <=0.5.0, but I found it not working with version 0.5.0. I utilized version 0.4.3, and the extension was able to work with QuPath.
Server logs
If applicable attach 100+ lines of monailabel server logs which covers the error trace etc...
To Reproduce
Steps to reproduce the behavior:
- Go to tutorials/monailabel
/monailabel_pathology_nuclei_segmentation_QuPath.ipynb
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
Environment
Ensuring you use the relevant python executable, please paste the output of:
python -c 'import monai; monai.config.print_debug_info()'
Additional context
Add any other context about the problem here.
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 tutorials/monailabel/monailabel_pathology_nuclei_segmentation_QuPath.ipynb and compare its stated QuPath compatibility with the reported behavior in versions 0.5.0 and 0.4.3. Reproduce the extension failure with QuPath 0.5.0, then update the tutorial's compatibility guidance so it matches supported behavior and verify the tutorial with the supported version.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- documentation
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100