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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 64 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 18

Repositories

Showing 10 of 98 repositories
  • 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 Nov 8, 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 Nov 8, 2024
  • qupath-extension-warpy Public

    ImgLib2 RealTransform brought to QuPath

    BIOP/qupath-extension-warpy’s past year of commit activity
    Java 20 Apache-2.0 5 8 0 Updated Nov 5, 2024
  • coLoc Public

    A Board Game to teach co-localization analysis

    BIOP/coLoc’s past year of commit activity
    12 CC0-1.0 0 3 0 Updated Nov 1, 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 Oct 31, 2024
  • BIOP/bigdataviewer-image-loaders’s past year of commit activity
    Java 5 GPL-3.0 0 4 0 Updated Oct 28, 2024
  • abba-documentation Public

    Documentation for ABBA - Aligning Big Brains & Atlases

    BIOP/abba-documentation’s past year of commit activity
    1 0 2 0 Updated Oct 23, 2024
  • BIOP/lightsheet-brain-workflows’s past year of commit activity
    Groovy 1 0 6 0 Updated Oct 21, 2024
  • 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 Oct 17, 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 Oct 15, 2024

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