Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using StarDist
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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 file.

See Setup.

Version History

Version 1 (earliest) Created 1st Jun 2023 at 11:05 by Jean-Marie Burel

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Burel, J.-M., & Walczysko, P. (2023). Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using StarDist. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.493.1
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Created: 1st Jun 2023 at 11:05

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