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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 67 11

  2. ijp-imagetoatlas ijp-imagetoatlas Public

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

    Java 49 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 36 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 21 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
  • 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 49 8 37 0 Updated Feb 28, 2025
  • abba_python Public

    ABBA, controlled from python

    BIOP/abba_python’s past year of commit activity
    Python 10 BSD-3-Clause 4 10 0 Updated Feb 28, 2025
  • abba-installer Public

    Repository backing the creation of standalone installers for ABBA

    BIOP/abba-installer’s past year of commit activity
    Python 1 0 15 0 Updated Feb 28, 2025
  • bigdataviewer-biop-tools Public

    Another repo for bdv tools.

    BIOP/bigdataviewer-biop-tools’s past year of commit activity
    Java 5 2 26 1 Updated Feb 26, 2025
  • 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 36 MIT 6 3 0 Updated Feb 26, 2025
  • qupath-extension-biop-omero Public Forked from qupath/qupath-extension-omero-web

    QuPath extension to work with images through OMERO's Java API (raw)

    BIOP/qupath-extension-biop-omero’s past year of commit activity
    Java 5 GPL-3.0 11 6 0 Updated Feb 26, 2025
  • 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 Feb 25, 2025
  • BIOP/lightsheet-brain-workflows’s past year of commit activity
    Java 1 0 6 0 Updated Feb 24, 2025
  • qupath-extension-abba Public

    QuPath extension for Aligning Big Brains and Atlases

    BIOP/qupath-extension-abba’s past year of commit activity
    Java 6 MIT 2 5 0 Updated Feb 19, 2025
  • qupath-extension-biop Public

    An extension for QuPath with some tools made at the BIOP.

    BIOP/qupath-extension-biop’s past year of commit activity
    Java 1 Apache-2.0 3 1 0 Updated Feb 17, 2025

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