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Delete multiple ROIs in GUI #718
Delete multiple ROIs in GUI #718
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Codecov Report
@@ Coverage Diff @@
## main #718 +/- ##
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Coverage 63.39% 63.39%
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Files 14 14
Lines 2964 2964
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Hits 1879 1879
Misses 1085 1085 |
All test look good, just need final testing on Mac & Windows. |
# Conflicts: # cellpose/gui/gui.py # cellpose/gui/guiparts.py
@carsen-stringer resolved conflicts, integrated |
Hi Michael, I am quite new with cellpose, I downloaded it recently (last month) and I am now starting to use it for my analysis. The segmentation works for most cells that I want to select, however I have many masks over debris that I need to correct. I started deleting ROIs one by one, but it takes very long time (over an hour) since the masks automatically save each time in the seg.npy file. I saw this https://github.com/MouseLand/cellpose/issues/501 post where you linked this post to delete multiple ROIs in GUI. Thank you very much for your time. Kind regards, Leire Iglesias |
@LeireIglesiasC This feature is not currently merged into the main branch of cellpose, and that's why you don't see it. For the moment you can speed up deleting cells by disabling autosaving the _seg.npy file (File drop down -> Disable autosave checkbox). You will need to update your cellpose version since this feature was only added last week. You can do that with:
Or you can install this version of cellpose (the delete multiple feature) with these commands:
If you do the latter please let us know your experience using the delete multiple feature! |
Hi @mrariden , Thank you very much for your fast response. I tried both options you gave, the first one works perfectly! I updated the cellpose version and without the automatic saving the whole process is much faster. Leire |
Ah this merge broke the disable autosave feature by replacing the |
Add functionality to GUI to allow 'batch' deletion of masks:
Current implementation is a button that starts batch deletion mode and masks can be selected/deselected until pressing the 'done' button. Once the 'done' button is pressed, the masks are removed from the relevant state variables and the mask is saved once.
Task list:
Write tests?manual
tags are properly updatedAddresses: