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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
89 stars 30 forks source link

Rearrange tabs in napari #246

Closed lorenzocerrone closed 1 month ago

lorenzocerrone commented 1 month ago

Hey @qin-yu, I would like to propose the following changes.

qin-yu commented 1 month ago
  • merge the predictions and segmentation in a single Extra workflows (to save space for the upcoming training/dataset tab)
  • remove the watershed in segmentation and add back the functionalities in Main

These changes doesn't really affect me and might be new-user-friendly.

  • Always use the dropdown menu for Extra workflow (i.e., remove the TOO_MANY_WIDGES = False check). Having all the widgets open adds a lot of clutter to the UI.

I would like to have easier access to all widgets for more direct feedback ("on_change" events) during development, I propose to have an environment variable to allow this (that's why I did a TOO_MANY_WIDGES, but didn't have time to finish)

The workflow for me to segment or to show new users how to segment using PlantSeg is the following:

  1. (Add a model)
  2. Load an image
  3. (Gaussian blur)
  4. Run prediction
  5. Run watershed
  6. Run filter (the one I developed)
  7. Run GASP
  8. Run filter
  9. Export segmentation

So having "Data", "Main", and "Extra" doesn't add complexity for inference. I would say your proposal is nice overall.

qin-yu commented 1 month ago

Fixed by #249