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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 67 11

  2. ijp-imagetoatlas ijp-imagetoatlas Public

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

    Java 48 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 32 6

  4. IPA4LSx IPA4LSx Public

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

    25 16

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

    ImgLib2 RealTransform brought to QuPath

    Java 20 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 19

Repositories

Showing 10 of 98 repositories
  • OMERO-scripts Public

    Series of script to make use of OMERO

    BIOP/OMERO-scripts’s past year of commit activity
    Groovy 2 GPL-3.0 2 0 0 Updated Dec 20, 2024
  • 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 48 8 33 1 Updated Dec 20, 2024
  • ijp-atlas Public

    Repository containins Atlases and Atlas Structure for ABBA plugin

    BIOP/ijp-atlas’s past year of commit activity
    Java 0 GPL-3.0 0 3 0 Updated Dec 20, 2024
  • bigdataviewer-biop-tools Public

    Another repo for bdv tools.

    BIOP/bigdataviewer-biop-tools’s past year of commit activity
    Java 5 2 25 1 Updated Dec 20, 2024
  • ijp-kheops Public
    BIOP/ijp-kheops’s past year of commit activity
    Java 13 GPL-2.0 2 15 0 Updated Dec 20, 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 32 6 5 0 Updated Dec 20, 2024
  • bigdataviewer-playground-display Public

    Display additions for bigdataviewer using bigdataviewer-playground

    BIOP/bigdataviewer-playground-display’s past year of commit activity
    Java 2 0 0 0 Updated Dec 20, 2024
  • bigdataviewer-spimdata-extras Public

    Extra settings that can be stored in spimdata file format

    BIOP/bigdataviewer-spimdata-extras’s past year of commit activity
    Java 0 GPL-3.0 1 0 0 Updated Dec 20, 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 Dec 11, 2024
  • abba_python Public

    ABBA, controlled from python

    BIOP/abba_python’s past year of commit activity
    Python 7 BSD-3-Clause 3 9 0 Updated Dec 11, 2024

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