Add Cellpose v3.0.1 #1390
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Add Cellpose v3.0.1 #1390
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pavanvidem
commented
Feb 28, 2024
pavanvidem
commented
- Currently uses container as a requirement
- Added 6 more tests
- The output tiffs are completely black. No idea if that's normal. It is not a Galaxy issue. Standalone also generates black images.
bgruening
reviewed
Feb 28, 2024
tools/cellpose/cellpose.xml
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| help="Interpolated flows at the true image size. This option will create smoother ROIs when the cells are large but will be slower in case"/> | ||
| <param argument="flow_threshold" type="float" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/> | ||
| <param argument="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/> | ||
| <param argument="niter" type="integer" value="0" label="Number of iterations" |
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add min/max ? also to other params?
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It is hard to find min/max for all the params. Tried to add as much as I could.
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