Helix/bwVisu/QuPath: Difference between revisions
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H Schumacher (talk | contribs) (Instructions for adding the Cellpose extension) |
H Schumacher (talk | contribs) m (Added troubleshooting section) |
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#* Go to Edit > Preferences > Cellpose/Omnipose |
#* Go to Edit > Preferences > Cellpose/Omnipose |
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#* Add the path to the Python executable: "/opt/cellpose/bin/python3.9" |
#* Add the path to the Python executable: "/opt/cellpose/bin/python3.9" |
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== Troubleshooting == |
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*'''Main window doesn't stay full size when other windows open''' |
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:-> Enlarge the main QuPath window with the mouse, instead of clicking on the "maximize" button. |
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Latest revision as of 16:44, 2 September 2025
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GPU support and CellPose are work in progress. |
QuPath offers a powerful set of tools for a wide range of image formats, including many whole slide formats.
Add Extensions
CellPose
The official installation and usage instructions for the extension can be found at https://github.com/BIOP/qupath-extension-cellpose.
To summarize:
- Install Cellpose
- Cellpose and the extra dependency scikit-image are already installed. This step can be skipped.
- Add the extension
- Install and setup the qupath-biop-catalog
- Add the Cellpose extension (Extensions -> Manage Extensions)
- Restart QuPath / the bwVisu Job
- First time setup
- Go to Edit > Preferences > Cellpose/Omnipose
- Add the path to the Python executable: "/opt/cellpose/bin/python3.9"
Troubleshooting
- Main window doesn't stay full size when other windows open
- -> Enlarge the main QuPath window with the mouse, instead of clicking on the "maximize" button.