Training cellpose on brightfield images (R, G, and B channels)

[danidean]

Hi,
For training a cellpose model on brightfield images (Hematoxylin-DAB, H&E staining) based on Cellpose Training Template script what are modification required?

Thanks,

• Dean

[lacan]

Dear @danidean,
This will depend on what you want to do. If you want to do a training on the RGB image itself, you need to use the all_channels flag, but there is currently a bug with it on the cellpose side

[lacan]

Hi @danidean ,

Have you managed to train cellpose as you wanted? I can give you our current workaround, otherwise I will close this ticket as it is unrelated to the extension itself, but rather to cellpose proper.

[minhtran1309]

Hi, I also have the same issue and couldn't find a way to run CellPose in the Brighfield image. I always received an error message with the not found channel: ERROR: No channel found with name DAB.

I did the debug and confirmed that DAB is among the channels together with Hematoxylin, Optical density sum

[lacan]

If you do not set any channels in the builder, it will send the whole RGB image to cellpose