plant-seg

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Heuristics for parameters: patch size, halo, and rescale factor

1

I'm planning the following enhancements to PlantSeg that could significantly improve its usability: - [x] #251 PlantSeg used a fixed halo that appeared optimal but was potentially influenced by a...

qin-yu

There has been a folder of tests, which inspired me to write tests for the model zoo module. Additionally, I observed some inconsistencies in the tests for the zarr module...

qin-yu

Cancel split/merge in proofreading

1

Hello, I would like to use the proofreading function and it looks like the split/merge would make it much faster, because it actually works in 3D. However, there's no way...

Buglakova

I've been analysing the differences from multiple models, maybe I should make it available in the GUI. - [ ] Proofreading assistant - [ ] Ensemble

qin-yu

## Re-train all PlantSeg models to eliminate hallucination during inference We have historically addressed the tiling artifact by using larger patch sizes. Recently, @Buglakova re-highlighted this issue in [Issue #190](https://github.com/hci-unihd/plant-seg/issues/190),...

qin-yu

PlantSeg pipelines do not reuse code

1

This adds to the complexity of code. e.g. - `UnetPredictions` class in `/g/kreshuk/yu/repositories/plant-seg-doc/plantseg/predictions/predict.py` and - `unet_predictions` function in `/g/kreshuk/yu/repositories/plant-seg-doc/plantseg/predictions/functional/predictions.py` need to be merged for easier maintenance.

qin-yu

Classic GUI is unavailable for PlantSeg 2.0.

4

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...

athulrv

Areas of GUI improvement before v2.0.0-alpha

4

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 -...

qin-yu

qin-yu

Possible issues in 1.8.1

1

Good afternoon, I am running the 1.8.1 version of plantseg on a linux Mint 22 machine. Everything works as intended but in some case I get the following error: ```...

PauCasanova