Research Object Crate for Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using StarDist

The notebook shows how to load an IDR image with labels. The image is referenced in the paper "NesSys: a novel method for accurate nuclear segmentation in 3D" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the Image Data Resource. In this notebook, the image is loaded together with the labels and analyzed using StarDist. The StarDist analysis produces a segmentation, which is then viewed side-by-side with the original segmentations produced by the authors of the paper obtained via the loaded labels. ## Launch This notebook uses the [environment_stardist.yml](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/environment_stardist.yml) file. See [Setup](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/setup.md).

Author

Jean-Marie Burel

License

BSD-2-Clause

Contents