plant-seg

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- [x] Unet predictions follow the AbstractStep like the rest of the pipeline - [x] New in-memory array loader and predictor - [x] Implement all steps as pure functions (preprocessing,...

lorenzocerrone

Found the code not working when I was doing LMC yesterday. `lifted_costs` is now created as a 1D `float64` array, `lifted_costs = np.zeros(len(lifted_labels), dtype="float64")`, in `elf`'s `lifted_problem_from_segmentation()`. Should fix #109...

qin-yu

2D segmentation of root meristem

1

Dear authors, I'm trying to run plant-seg on 2d confocal images of root meristems stained with FM4-64. I tried the confocal_2D_unet_bce_dice and the confocal_PNAS_2d model. Both models run smoothly after...

AlexStroh-git

using nuclear probabilities or segmentations from StarDist

9

Hi Thank you for making this software available. I would like to use nuclear prediction label map from StarDist for the Lifted MultiCut segmentation as part of the Plantseg workflow....

pr4deepr

Run plant-seg GUI and set either "Save Raw Data" on causes error

1

Default configs with patch 80x150x150 and 3D GASP Error ``` 2022-02-01 17:08:40,882 [ThreadPoolExecutor-0_0] INFO PlantSeg - Executing pipeline step: 'segmentation_postprocessing'. Parameters: '{'factor': [1.0, 1.0, 1.0], 'order': 0, 'save_raw': True, 'state':...

qin-yu

Currently while executing the PlantSeg pipeline it creates a directory structure which depends on whether some of the pipeline stages were enabled or not, and the directory names correspond to...

wolny

Execute multiple segmentation algorithms in a single PlantSeg run

1

It would convenient to execute multiple partitioning algorithms and save the results in a single h5 file, so that one can easily compare the results. We could make that option...

wolny

* Currently not functional - problem with running two servers? * Files mostly auto generated from npm, my code is in App.js * Working towards getting a list of tasks...

boykovdn

WIP

wolny

Problem running plant-seg on batch mode

2

Hello, When I try to run plant-seg on multiple images in a folder, after completing the predictions for the first image, I get the following message: [...] `File "h5py\_objects.pyx", line...

lcferme