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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 61 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

    25 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 18

Repositories

Showing 10 of 98 repositories
  • EasyXT-FIJI Public

    Commands and Classes for interfacing between Imaris and Fiji

    BIOP/EasyXT-FIJI’s past year of commit activity
    Java 12 2 22 0 Updated Sep 30, 2024
  • coLoc Public

    A Board Game to teach co-localization analysis

    BIOP/coLoc’s past year of commit activity
    12 CC0-1.0 0 1 0 Updated Sep 29, 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 Sep 26, 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 28 1 Updated Sep 23, 2024
  • abba_python Public

    ABBA, controlled from python

    BIOP/abba_python’s past year of commit activity
    Python 6 BSD-3-Clause 3 10 4 Updated Sep 23, 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 6 1 Updated Sep 18, 2024

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