search

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

Classic GUI is unavailable for PlantSeg 2.0. #350

Open athulrv opened 1 month ago

athulrv commented 1 month ago

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 commented 1 month ago

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 commented 4 weeks ago

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

AlexisMaizel commented 4 weeks ago

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 commented 4 weeks ago

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.