Support for GUI dataset/channel selection, follow #165

kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

https://kreshuklab.github.io/plant-seg/

MIT License

97 stars 31 forks source link

Support for GUI dataset/channel selection, follow #165 #173

Closed qin-yu closed 9 months ago

qin-yu commented 11 months ago

I plan to add these to GUI first then Napari. Do I need to watch out for something (cus I have limited experience with GUI)?

Use case: Alyona wanted to find out if PlantSeg can be used for her images
Her steps:
1. Install PlantSeg and run all models on the same images
2. Check which model give the best segmentation and probability map
3. She finds my generic plant nuclei model is the only capable model, to my surprise
4. But GUI can't give segmentation for some 2-channel network output

Maybe we should spend some time adding this to GUI.

wolny commented 11 months ago

hey @qin-yu, as disucssed with @lorenzocerrone let's implement it only for the multi-channel network output:

In legacy GUI, we should add the option you've added in config
In the napari GUI we should load the multi-channel output from the network in separate layers (one layer per channel) and the rest will work out of the box

qin-yu commented 9 months ago

I think I fixed this. Please check #184 @wolny @lorenzocerrone

lorenzocerrone commented 9 months ago

Yes we can close this

qin-yu commented 9 months ago

Wait a minute @lorenzocerrone It's not actually fixed until #184 is merged 🤣 I meant please review and see if it's fixed, though I thought it's fixed.

lorenzocerrone commented 9 months ago

Yeah sorry, I should have explained more :D

That part I have reviewed yesterday when we met and it was fine. But I will do the full PR review tomorrow :)