plant-seg

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- [ ] version control #145

lorenzocerrone

wolny

export of models in BioImage Model Zoo format

1

Since plant-seg allows users to train models, it would be nice to write them out in [BioImage Model Zoo format](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md), or is this already possible?

k-dominik

Unnecessary check of preprocessing/prediction section configs when only using segmentation function

1

Now I try to run LMC but plantseg 1.6.0 checks my outdated cnn_pred part of config. Also, it reports error for model mismatch when I only want to use LMC.

qin-yu

Notify if a new plantseg release is out

3

It would be a nice feature to add a simple console notification that a new plantseg version has been released. Do you know if conda or git has a public...

lorenzocerrone

AssertionError: Sample size has to be bigger than the patch size

1

@wolny This error happens if the image is smaller that the patch size in any give dimension. I think this can be avoided by checking it in the `@widget_unet_predictions.model_name.changed.connect`. Do...

lorenzocerrone

support for passing dataset keys for Zarr files

1

Hi! I am wondering if it is possible to allow passing specific dataset keys for zarr files (changes anywhere load_stack/smart_load gets called). Right now, the data to be processed needs...

Mohinta2892

PyQT is not installed automatically, can't run napari interface

2

Hello, When I install plantseg with the command from documentation, it doesn't automatically install Napari's backend, adding `pyqt` explicitly helped: `mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge...

Buglakova

Error on the GASP segmentation using GUI: Need more labels than can be represented in the destination type

2


athulrv

- New structure for plantseg local files: before all plantseg user files were stored in `.plantseg_models`, and now: ``` .plantseg/ -------------/configs/ ------------/models/ -----------/user_dataset.yaml ``` - New module `dataset_tools` to handle...

lorenzocerrone