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@BIOP

BioImaging And Optics Platform (BIOP)

All the code that is publicly available/published by the BioImaging And Optics Platform (BIOP)

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  1. qupath-extension-cellpose qupath-extension-cellpose Public

    an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

    Jupyter Notebook 60 11

  2. ijp-imagetoatlas ijp-imagetoatlas Public

    ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)

    Java 45 8

  3. ijl-utilities-wrappers ijl-utilities-wrappers Public

    Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

    Java 31 6

  4. IPA4LSx IPA4LSx Public

    ImageJ Macro Scripts showcased during Image Processing and Analysis for Life Scientists MOOC on EdX

    24 16

  5. qupath-extension-warpy qupath-extension-warpy Public

    ImgLib2 RealTransform brought to QuPath

    Java 19 5

  6. qupath-groovy-python-runner qupath-groovy-python-runner Public

    A proof of concept to run python segmentations and recovering the results within QuPath

    Groovy 17

Repositories

Showing 10 of 98 repositories
  • ijp-imagetoatlas Public

    ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)

    BIOP/ijp-imagetoatlas’s past year of commit activity
    Java 45 8 29 1 Updated Sep 19, 2024
  • bigdataviewer-biop-tools Public

    Another repo for bdv tools.

    BIOP/bigdataviewer-biop-tools’s past year of commit activity
    Java 5 2 14 1 Updated Sep 19, 2024
  • BIOP/bigdataviewer-image-loaders’s past year of commit activity
    Java 5 GPL-3.0 0 3 0 Updated Sep 19, 2024
  • ijp-operetta-importer Public

    PerkinElmer Operetta Importer using BioFormats!

    BIOP/ijp-operetta-importer’s past year of commit activity
    HTML 8 GPL-3.0 3 5 0 Updated Sep 19, 2024
  • BIOP/ijp-kheops’s past year of commit activity
    Java 12 GPL-2.0 2 16 0 Updated Sep 18, 2024
  • ijl-utilities-wrappers Public

    Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

    BIOP/ijl-utilities-wrappers’s past year of commit activity
    Java 31 6 5 1 Updated Sep 18, 2024
  • BIOP/lightsheet-brain-workflows’s past year of commit activity
    Groovy 1 0 6 0 Updated Sep 18, 2024
  • abba-installer Public

    Repository backing the creation of standalone installers for ABBA

    BIOP/abba-installer’s past year of commit activity
    Python 1 0 14 0 Updated Sep 13, 2024
  • qupath-extension-cellpose Public

    an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

    BIOP/qupath-extension-cellpose’s past year of commit activity
    Jupyter Notebook 60 Apache-2.0 11 2 0 Updated Sep 12, 2024
  • BIOP/BIOP-desktop’s past year of commit activity
    JavaScript 9 0 7 0 Updated Sep 12, 2024

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