cellpose-napari
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Best way to segment with multiple channels?
Quick question--I am trying to use cellpose-napari, but am working with irregular cell types where including a DNA stain as the nuclear channel for cellpose is essential to get proper segmentations. What is the best way to prepare images for this in Napari? Currently, I have tried two things:
Merge to stack
- Loading a multichannel image through drag and drop. This creates three different "layers" in Napari
- If we right click all the layers available (3) and "Merge to stack", this creates a "multi-channel" image (meaning that you appear to be able to scroll through the different channels) with an arbitrary color
- Cellpose segmentation, setting the correct channel as nuclear, and the correct channel as my cytoplasmic background, then fails:
15:58:29 : ERROR : MainThread : tuple index out of range
Merge to RGB
- Loading a multichannel image through drag and drop. This creates three different "layers" in Napari
- Setting the three channels to one of red, green, blue (through colormap)
- If we right click all the layers available (3) and "Merge to RGB", this creates an apparently "single-channel" image with three different colors (as previously specified, these are red, green and blue)
- Cellpose segmentation, setting the correct channel as nuclear, and the correct channel as my cytoplasmic background, then works
This suggests that segmenting a stacked image is not something that is possible in cellpose-napari. Is this accurate?