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avweigel authored Mar 19, 2024
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Expand Up @@ -55,10 +55,14 @@ Tasks we support and approaches for those tasks:
- Chunked data, zarr, and n5
- OME-Zarr: a cloud-optimized bioimaging file format with international community support (doi: [10.1101/2023.02.17.528834](https://pubmed.ncbi.nlm.nih.gov/36865282/))
- Videos about N5 and Fiji can be found in [this playlist](https://www.youtube.com/playlist?list=PLmZHHIZ9Gz-IJA7HtW8quZcuLViz9Em6e). For other questions, join the discussion on the [Image.sc forum](https://forum.image.sc/tag/n5).
- [N5 plugins for Fiji](https://openorganelle.janelia.org/news/2023-02-06-n5-plugins-for-fiji)
- Script for converting [tif to zarr](https://github.com/yuriyzubov/tif-to-zarr)
- Read about chunked storage plugins in Fiji in this blog: [N5 plugins for Fiji](https://openorganelle.janelia.org/news/2023-02-06-n5-plugins-for-fiji)
- Script for converting tif to zarr can be found [here](https://github.com/yuriyzubov/tif-to-zarr)
- Segmentations
- A description of local shape descriptors used for affinities task. Read the blog [here](https://localshapedescriptors.github.io/). Example image from the blog showing the difference between segmentations:
- ![](https://localshapedescriptors.github.io/assets/img/detection_vs_segmentation_neurons.jpeg)
- CellMap Models
- [GitHub Repo](https://github.com/janelia-cellmap/cellmap-models) of published models
- For example, the COSEM trained pytorch networks are located [here](https://github.com/janelia-cellmap/cellmap-models/tree/main/src/cellmap_models/pytorch/cosem).
- [OpenOrganelle.org](https://openorganelle.janelia.org)
- ![](https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/mito_pred-seg.gif)
- Example of [unprocessed distance predictions](https://tinyurl.com/3kw2tuab)
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