Add option not to fill masks. Compression to TIFF files.

[hey2homie]

Often with the glial cells Cellpose fills in masks where the hole between processes is present. This affects the downstream morphological analysis and intensities computations. Added an option to disable this behaviour when calling eval.

Also, noticed that saved masks in .tif or .tiff format are quite large in size, so added compression which significantly reduced the size of the file.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 56.27%. Comparing base (cc4e62c) to head (0975ecf).
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@@            Coverage Diff             @@
##             main     #884      +/-   ##
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+ Coverage   56.26%   56.27%   +0.01%     
==========================================
  Files          16       16              
  Lines        3784     3785       +1     
==========================================
+ Hits         2129     2130       +1     
  Misses       1655     1655              

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[mrariden]

@hey2homie Can you post some example image/masks to demonstrate this issue?

[hey2homie]

Sure, this usually gets quite prominent with the ramified glia cells like on this two crops (left is grey-scale, right are masks with holes):

I've also added the possibility to filter out holes based on their area as single pixel holes are quite prominent. Need a bit more time to test though.

[hey2homie]

@mrariden, I've also added options to fill in holes that are less than certain threshold.

I've also added in the same PR option to save masks with/without holes in geojson format instead of using save_txt. This dramatically speeds up the exporting of the polygonal representation of the masks. Also allows to import segmentation results directly into QuPath without any extra hassle. Slightly modified part for saving outlines to account for possible holes in the masks.

I'll add tomorrow some tests and time measurements.

[hey2homie]

Here is example of plotted outlines:

Time it takes to save tiff, write coordinates and plot outlines for a single mask 512 by 512:

• Before

2024-03-21 17:17:04,229 [INFO] Started saving masks
2024-03-21 17:17:07,615 [INFO] Finished saving masks

2024-03-21 17:17:34,865 [INFO] Started saving masks
2024-03-21 17:17:38,305 [INFO] Finished saving masks

2024-03-21 17:17:41,645 [INFO] Started saving masks
2024-03-21 17:17:45,201 [INFO] Finished saving masks

• After

2024-03-21 16:08:24,113 [INFO] Started saving masks
2024-03-21 16:08:24,225 [INFO] Finished saving masks

2024-03-21 16:08:24,469 [INFO] Started saving masks
2024-03-21 16:08:24,495 [INFO] Finished saving masks

2024-03-21 16:08:24,526 [INFO] Started saving masks
2024-03-21 16:08:24,555 [INFO] Finished saving masks

Time it takes to save tiff, write coordinates and plot outlines for a single mask 26609 by 20824 with 28k objects:

• Before

2024-03-22 11:37:51,037 [INFO] Started saving masks
2024-03-22 12:25:36,460 [INFO] Finished saving masks

• After

2024-03-21 17:01:48,731 [INFO] Started saving masks
2024-03-21 17:02:43,550 [INFO] Finished saving masks

[lacan]

Is the fill_holes option also accessible from the CLI?

[carsen-stringer]

thanks @hey2homie ! these json masks, are they loadable in imageJ directly?

I think this is all great but I think I would make the polygon computation optional, only computed if the user requests to save to json (I can do that though)