Areas of GUI improvement before v2.0.0-alpha - Githubissues

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

Areas of GUI improvement before v2.0.0-alpha #324

Open qin-yu opened 1 month ago

qin-yu commented 1 month ago

Here I summarise and expand discussions with @akreshuk and @lorenzocerrone.

In general, the user interface should have sequential layout and minimal options. Here are some details:

Logic Fix

[x] Hide watershed result once clustering result is added to the viewer
[x] Remove Scribble layers from proofreading init
[x] Update proofreading image selections

Formal Fix

[x] After prediction it should be proofreading (-> finetuning) -> extra
[x] Improve widget labels and make the case consistent
- [x] "Pick a file" in Data
- [x] "Run clustering" to "Run segmentation" in Main
- [x] "Pmap/Image" to "Boundary image" everywhere
- [x] "Save state" to "Save current proofreading snapshot"
- [x] "Stacked: 2D; 3D" to "Mode: 2D watershed; 3D watershed"
- [x] "Min-size"
- [x] "Extract correct labels" to "Freeze correct labels"
[x] change the name of the interface from "napari" to PlantSeg related
[x] fix "MutexWS" name/val correspondence
- 325

Missing widgets

[x] Add cropping widget
[x] Add label processing widgets

New Widgets

[x] create home/docs widget and fix warnings from Qt Main Window
- 329
[ ] have a one click solution for nuclei to avoid going back and forth

Widget Refactors

[ ] Show image dimension before letting users choose between, say, "ZYX" or "CZYX"
[x] Remove "Lifted Multicut" if we have nuclei-assisted fix or move to aggl. widget
[ ] Move "Add custom model" to prediction widget
~~Move tabs to top (not so Napary)~~

qin-yu commented 1 month ago

After discussion with @lorenzocerrone.

Don't forget to:

[x] Add cropping widget
[x] Add remove the biggest instance widget

Maybe we could:

[ ] have a one click solution for nuclei to avoid going back and forth

qin-yu commented 1 month ago

[x] Hide watershed result once clustering result is added to the viewer

qin-yu commented 1 month ago

[x] Remove Scribble layers from proofreading init

qin-yu commented 1 month ago

[x] change the name of the interface from "napari" to PlantSeg related
[x] create home/docs widget and fix warnings from Qt Main Window
- 329