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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 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 32 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
  • BIOP/lightsheet-brain-workflows’s past year of commit activity
    Groovy 1 0 10 0 Updated Sep 12, 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 3 0 Updated Sep 12, 2024
  • BIOP/BIOP-desktop’s past year of commit activity
    JavaScript 9 0 7 0 Updated Sep 12, 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 10 2 Updated Sep 10, 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 45 8 27 1 Updated Sep 9, 2024
  • abba_python Public

    ABBA, controlled from python

    BIOP/abba_python’s past year of commit activity
    Python 6 BSD-3-Clause 3 9 4 Updated Sep 6, 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 13 0 Updated Sep 5, 2024
  • BIOP/ijp-kheops’s past year of commit activity
    Java 12 GPL-2.0 2 16 0 Updated Sep 5, 2024
  • biop-bash-scripts Public

    Bash scripts to simplify your life (let's hope so!)

    BIOP/biop-bash-scripts’s past year of commit activity
    Shell 9 8 9 0 Updated Sep 5, 2024
  • BIOP/bigdataviewer-image-loaders’s past year of commit activity
    Java 5 GPL-3.0 0 4 0 Updated Sep 4, 2024

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