Export ROIs directly to ImageJ

[mrariden]

Allows exporting outlines to .zip archive of .roi files using roifile ImageJ as mention in #581. This introduces a new dependency, roifile.

• Left the "Save Outlines" functionality as it was both in the GUI and in the command line args
• Added --save_rois command line flag
• Added GUI button similar to existing "save outlines" functionality

Did not update docs (how/should I do this?)

[carsen-stringer]

Thanks you so much, this looks great and super useful! I just need to test it, will get to it soon. The documentation can be added here: https://github.com/MouseLand/cellpose/blob/main/docs/outputs.rst

[mrariden]

Cellpose segmentation:

Save the ROIs:
Going into CP GUI -> save outlines as .zip

Use the ROIs in FIJI/ImageJ:

1. Open image
2. Import ROIs using File -> open. Recent versions will autodetect that the file is an roi archive
3. Click 'show all' to display the rois on the image.
   

Note that the roifile library appends rois to existing archives. So, if the user removes rois after saving the removed rois will still be there when the user saves again. I circumvented this by deleting the file before writing, but this may not be ideal for images with many ROIs.

I added ctrl+R shortcut for the function in the GUI, and updated relevant docs.

[codecov-commenter]

Codecov Report

Merging #643 (c8fdf9a) into main (b709064) will decrease coverage by 0.09%.
The diff coverage is 25.00%.

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@@            Coverage Diff             @@
##             main     #643      +/-   ##
==========================================
- Coverage   37.40%   37.31%   -0.09%     
==========================================
  Files          20       20              
  Lines        5355     5378      +23     
==========================================
+ Hits         2003     2007       +4     
- Misses       3352     3371      +19     

Impacted Files	Coverage Δ
cellpose/gui/gui.py	7.53% <0.00%> (-0.01%)	⬇️
cellpose/gui/guiparts.py	12.69% <ø> (ø)
cellpose/gui/menus.py	7.96% <0.00%> (-0.37%)	⬇️
cellpose/io.py	62.43% <25.00%> (-0.85%)	⬇️
cellpose/gui/io.py	8.46% <28.57%> (+0.12%)	⬆️
cellpose/__main__.py	64.47% <50.00%> (-0.20%)	⬇️
cellpose/cli.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

[mrariden]

@carsen-stringer Can you review and potential merge?

[carsen-stringer]

thanks this looks great!