Classic GUI is unavailable for PlantSeg 2.0.

[athulrv]

Its a pity that Classic PlantSeg GUI is not included in the 2.0 update. It has been very helpful in bulk image processing for biologists.

Is there any guideline how to install latest plantseg 1.x that includes Classic gui?

Best,
Athul

[qin-yu]

Bulk image processing in PlantSeg can be achieved with the new Headless Mode, which is not documented yet but an example config file is here: https://github.com/kreshuklab/plant-seg/blob/master/dag.yaml

[athulrv]

It would be great if a PlantSeg 1.8 version installation procedure is also available so people could still use the classic gui.

[AlexisMaizel]

I totally second @athulrv on this one. In the absence of documentation, it is important that we maintain existing workflows by having the possibility to (re-)install v1.8.x.

[lorenzocerrone]

Hi everyone,

I agree with the points raised. PlantSeg 1.8.x should continue to be documented, and we should provide minimal support to ensure it remains functional.

@athulrv, there seems to be a little misunderstanding. The classic PlantSeg GUI, as it was originally implemented, is not compatible with PlantSeg 2.

While it’s true that we don’t have a direct replacement, a new GUI version for batch processing is in development. This new interface will offer a user experience similar to the old GUI. In addition will also try to be able to accommodate more workflows like nuclei segmentation.

[athulrv]

Great if PlantSeg gui replacement can happen in 2.0. Any update on when it would be available? It would be great to have some documentation on how to install 1.8 version with classic gui.

[qin-yu]

Hey @athulrv and @AlexisMaizel, thank you for the advice. The installation guide for PlantSeg v1.8.1 can be found on the first page of the last chapter of the documentation: https://kreshuklab.github.io/plant-seg/chapters/plantseg_legacy/installation/. To make it more prominent, I have added the same link at both the beginning and the end of the installation tutorial page.

This issue should have been resolved by commit d031d78 by @lorenzocerrone. However, since he was preparing for I2K 2024 at the time of this commit, he might have forgotten to inform you.

@athulrv, if you have successfully installed v1.8.1 using the installation guide, feel free to close this issue. In the meantime, @AlexisMaizel has tried batch processing with PlantSeg v2, so PlantSeg v2 should be working now!

[athulrv]

@qin-yu thanks for the update and fix.

@AlexisMaizel, how did you perform batch processing with PlantSeg 2.0? using config file?

[qin-yu]

@athulrv yes you use a config file but a new one. Just open an image in PlantSeg Napari and perform what you want to automate, save that example output, and you can now export a workflow. This workflow file is what's used as the new config file.

We'll document it later.

[AlexisMaizel]

You basically only have to modify lines 28 and 29 of the YAML file to specify the paths to the Folder containing the input image and the path to the output folder.
I paste below the block of code to alter:

inputs:
- export_directory: /home/alexis/Desktop/Anamarija_data/Cells
  input_path: /home/alexis/Desktop/Anamarija_data/Cells/
  name_pattern: '{file_name}_export'

[qin-yu]

Related issue:

• Example config.yaml for current plant-seg version missing #340