plant-seg
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kreshuklab
A tool for cell instance aware segmentation in densely packed 3D volumetric images
To transfer PlantSeg from [Heidelberg Collaboratory for Image Processing](https://github.com/hci-unihd) to [Kreshuk Lab](https://github.com/kreshuklab): - [ ] @lorenzocerrone may follow this guide to transfer: [Transferring a repository owned by your organization](https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#transferring-a-repository-owned-by-your-organization) -...
- by foreground filter #174 - by min_size - anything else?
Some of the networks we have in plantseg output foreground probability maps together with boundary predictions. This can be used in the segmentation post-processing step in order to filter background...
E.g. After GASP, the "Run Segmentation Fix from Nuclei" widget doesn't find the immediate GASP output in the drop down list. But if I GASP again, the previous renamed GASP...
E.g. 260 in Z shows 74. This image has x=y>1000 
Related posts: [Napari visualization in 3 planes](https://forum.image.sc/t/napari-visualization-in-3-planes/57768)
Add short videos with description for key functionalities: * proofreading (Lorenzo) * network prediction (Adrian) * segmentation (Adrian) * pre-/post-processing (Lorenzo)
To get the correct segmentation it's important that the objects on the new image are approximately the same size as in the training data. This doesn't necessarily mean that the...
F.Y.I. ```python !pip install -q condacolab import condacolab condacolab.install() ``` ```python !conda install -q -c conda-forge mamba # https://github.com/conda-incubator/condacolab/issues/60 with open('/usr/local/conda-meta/pinned', 'w') as f: f.write("python 3.10.*\npython_abi 3.10.* *cp310*\ncuda-toolkit 12.2.*") !mamba...
When I used the nuclear segmentation as seeds, there are errors from the lower-level libraries. Erosion of nuclei enables the algorithm to run. So maybe we should consider an erosion...
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A tool for cell instance aware segmentation in densely packed 3D volumetric images