error when plot.show_segmentation is called for 3D image

MouseLand / cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

https://www.cellpose.org/

BSD 3-Clause "New" or "Revised" License

1.27k stars 365 forks source link

error when plot.show_segmentation is called for 3D image #230

Closed sunyi000 closed 3 years ago

sunyi000 commented 3 years ago

Hi, the show_segmentaion for 3d image does not seem to work.. I have a 3D image in the correct shape requried by cellpose, if plot.show_segmentation is called, an error occurs from line 46 of the plot.py .. it seems that matplotlib requires an different shape. Thanks for any pointers and helps..

carsen-stringer commented 3 years ago

Unfortunately you cannot plot the 3D segmentation with that function. You could call it with slices of your masks and do a loop over the function if you want to visualize slices of the segmentation.

To do proper 3D mask visualization I've used ImageJ with labels saved as a tiff, there is probably a way to do this in napari as well