output segmented result as Labels layer

[chili-chiu]

Requested feature

Describe the new feature you would like to see in the napari-segmenter plugin. Currently the segmentation outputs are saved as images with True/False values. The alternative is to save segmented result as labels layer, which assigns 0 as background and integers for objects. Saving as labels layer would allow direct property value extraction (for example using https://www.napari-hub.org/plugins/napari-skimage-regionprops).

Use case

What will this change enable you to do? To allow quantitative analysis of segmented result more directly. Also to enable possibly object segmentation not just semantic segmentation.

If this change is NOT made...

Check all that apply, by entering an x inside the brackets:

• [ ] I will not use the napari-segmenter plugin.
• [ ] I will be blocked from completing my current tasks.
• [x] I can accomplish what I need to accomplish, but it's tedious.
• [ ] Not a problem right this minute, but this is going to be a problem soon.
• [ ] Everything's fine! But it would be cool if this work happened at some point in the future.

Alternatives

Are there any other plugins or software that you would use in place of this feature? napari has Image Layer (right click) > Convert to Labels option to make the conversion, but could be tedious to do so if working with many images.

[schoinh]

Thanks for pointing this out! This is on our radar now.