Welcome to the BIOP GitHub organization! We are the BioImaging and Optics Platform, developing open-source tools and resources for biological image analysis and microscopy.
- Total Repositories: 83
- Primary Languages: Java, Python, Groovy, JavaScript, MATLAB
- Main Focus Areas: Image Analysis, Microscopy, Medical Imaging, Brain Mapping, Deep Learning Integration
- ijp-imagetoatlas ⭐ 56 - ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
- abba_python ⭐ 17 - ABBA controlled from Python
- abba-documentation - Documentation for ABBA
- abba-installer - Standalone installers for ABBA
- qupath-extension-cellpose ⭐ 84 - Cellpose/Omnipose integration for QuPath
- qupath-extension-warpy ⭐ 28 - ImgLib2 RealTransform for QuPath
- qupath-extension-abba ⭐ 7 - ABBA integration for QuPath
- qupath-extension-spotiflow ⭐ 4 - Spotiflow integration for QuPath
- qupath-biop-catalog ⭐ 5 - Catalog of QuPath extensions maintained by BIOP
- qupath-extension-biop - Collection of BIOP tools for QuPath
- qupath-scripts ⭐ 7 - Useful QuPath scripts (archived)
- ijl-utilities-wrappers ⭐ 40 - Wrappers for external software (Cellpose, Elastix, Ilastik)
- EasyXT-FIJI ⭐ 13 - Imaris-Fiji interface
- ijp-LaRoMe ⭐ 11 - Label to ROI conversion tools
- ijp-frc ⭐ 10 - Fourier Ring Correlation implementation
- ijp-operetta-importer ⭐ 10 - PerkinElmer Operetta Importer
- ijp-max-inscribed-circles ⭐ 8 - Fill masks with largest inscribed circles
- ijp-DEVILS ⭐ 5 - Display Enhancement for Visual Inspection in Large Stacks
- ijp-kheops ⭐ 20 - ImageJ plugin for KHEOPS
- bigdataviewer-image-loaders ⭐ 5 - Image loaders for BigDataViewer
- bigdataviewer-biop-tools ⭐ 5 - Collection of BigDataViewer tools
- quick-start-czi-reader ⭐ 4 - Fast-starting Bio-Formats CZI reader
- bigdataviewer-playground-display ⭐ 2 - Display additions for BigDataViewer
- bigdataviewer-selector - Source selection mode for BigDataViewer
- bigdataviewer-spimdata-extras - Extra settings for SpimData format
- BIOP-desktop ⭐ 14 - BIOP desktop application
- biop-desktop-doc - Documentation for BIOP-desktop
- napari-cotcotcot ⭐ 4 - CoTracker3 integration for Napari
- napari-figure ⭐ 4 - Figure creation tool for Napari
- ijp-imagetoatlas - ABBA: 2D section to 3D atlas registration
- abba_python - Python interface for ABBA
- abba-documentation - ABBA documentation
- abba-installer - Standalone ABBA installers
- ijp-atlas - Atlases and structures for ABBA
- lightsheet-brain-workflows - Lightsheet brain imaging workflows
- qupath-extension-cellpose - Cellpose/Omnipose for WSI analysis
- qupath-extension-warpy - Image transformations in QuPath
- qupath-extension-abba - ABBA integration
- qupath-extension-spotiflow - Spotiflow integration
- qupath-extension-biop - BIOP tools collection
- qupath-extension-biop-hrm - HRM integration
- qupath-biop-catalog - Extension catalog
- qupath-scripts - Useful scripts (archived)
- qupath-general-scripts - General scripts (archived)
- qupath-groovy-python-runner - Python integration proof of concept
- ijl-utilities-wrappers - External software wrappers
- ijp-LaRoMe - Label/ROI conversion utilities
- ijp-template-ij2 - ImageJ2 command template
- ijp-frc - Fourier Ring Correlation
- ijp-jacop-b - Colocalization analysis (JaCoP revamped)
- ijp-gabriel-graph - Gabriel graph analysis
- ijp-max-inscribed-circles - Inscribed circles
- ijp-quality-filter - ROI quality assessment
- ijp-operetta-importer - PerkinElmer Operetta importer
- ijp-kheops - KHEOPS integration
- ijp-DEVILS - Display enhancement for large stacks
- ijp-multi-stack-montage - Stack montage creation
- ijab-biop-channel-tools - Channel settings propagation
- ijp-siftalignmultichannel-ij2 - Multichannel SIFT alignment (archived)
- elastix_registration_server - Elastix server (archived)
- ijp-biop-run-macro - Macro runner with SciJava parameters
- ijm-bioplib - Common macro functions library
- ijp-localizej - Localization-based nanoscopy simulation
- EasyXT-FIJI - Imaris-Fiji interface
- pyimagej-scijava-command - PyImageJ notebooks
- bigdataviewer-image-loaders - Custom image loaders
- bigdataviewer-biop-tools - BIOP tools for BDV
- bigdataviewer-playground-display - Display enhancements
- bigdataviewer-selector - Source selection mode
- bigdataviewer-spimdata-extras - SpimData extras
- bigdataviewer-uberdataset - Combined datasets
- bigdataviewer-omero - OMERO integration (archived)
- bigdataviewer-bioformats - Bio-Formats integration (archived)
- bigdataviewer_scijava - SciJava commands (archived)
- quick-start-czi-reader - Fast CZI reader
- BIOP-desktop - Main desktop application
- biop-desktop-doc - Desktop documentation
- abba_python - ABBA Python interface
- napari-cotcotcot - CoTracker3 plugin
- napari-figure - Figure creation plugin
- super-nice-pypi-package - PyPI package example
- OMERO-scripts ⭐ 3 - OMERO scripts collection
- omero-hrm - HRM integration for OMERO
- biop-bash-scripts ⭐ 11 - Bash utility scripts
- biop-operetta-tools - PerkinElmer Operetta tools
- biop-gitlab-admin - GitLab management tools
- gist-query ⭐ 3 - Query BIOP gists
- retire-update-site - Update site deprecation tool
- ArgoLight_analysis_tool ⭐ 2 - Microscope quality control
- nis-elements-macros - NIS Elements macros
- HuygensScripts - HuygensPro console scripts
- EasyXT ⭐ 3 - Imaris extension
- EasyXT-FIJI ⭐ 13 - Imaris-Fiji interface
- EasyXT-GUI - Imaris GUI
- XT-Views-Manager - Camera position management
- IPA4LSx ⭐ 26 - Image Processing & Analysis MOOC scripts
- IPA4LS - EPFL course materials
- pcb-02-fiji - Practical Course BIOP: Fiji
- coLoc ⭐ 13 - Colocalization board game
- BIOP-Educational-Figures - Educational figures
- renku-templates - RENKU templates
- renku-helpers - VNC preparation scripts
- tool-ibidi-slide-holder ⭐ 3 - 3D printed slide holder
- ijab-biop-channel-tools - Channel tools
- ijab-tracmit - Cell tracking on micropatterns
- ijab-biop-basics - Basic macro template
- ijab-biop-common-tools - Common tools & shortcuts
- ijab-mutli-manual-select - Manual selection tool
- ijab-sim-storm-tools - SIM-STORM tools
- ijab-ihc-ratio - IHC ratio analysis
- ijs-TrackMate - TrackMate Groovy scripts
- ijp-lima-biop - CellProfiler/FIJI bridge (archived)
- abba-documentation - ABBA documentation
- biop-desktop-doc - Desktop documentation
- qupath-biop-extensions-docs - QuPath extensions Javadoc
The following repositories are archived and no longer actively maintained:
- qupath-scripts - QuPath scripts
- qupath-general-scripts - General QuPath scripts
- qupath-biop-extensions - Legacy QuPath extensions
- elastix_registration_server - Elastix server
- ijp-siftalignmultichannel-ij2 - SIFT alignment
- bigdataviewer-omero - OMERO integration
- bigdataviewer-bioformats - Bio-Formats integration
- bigdataviewer_scijava - SciJava commands
- ijp-lima-biop - LIMA/CellProfiler bridge
- qupath-extension-cellpose - 84 ⭐
- ijp-imagetoatlas - 56 ⭐
- ijl-utilities-wrappers - 40 ⭐
- qupath-extension-warpy - 28 ⭐
- IPA4LSx - 26 ⭐
- ijp-kheops - 20 ⭐
- qupath-groovy-python-runner - 19 ⭐
- abba_python - 17 ⭐
- BIOP-desktop - 14 ⭐
- coLoc - 13 ⭐
Primary language for ImageJ/Fiji plugins, QuPath extensions, and BigDataViewer tools.
Used for Napari plugins, OMERO scripts, and analysis workflows.
Common for OMERO scripts, QuPath scripts, and utility tools.
Used for BIOP-desktop application.
Used for Imaris extensions (EasyXT).
Macro scripts for ImageJ/Fiji automation.
Bash scripts for system administration.
Interactive notebooks for analysis and documentation.
Our repositories cover various topics including:
- Image Analysis: QuPath, Fiji, ImageJ, Napari
- Brain Imaging: ABBA, atlas registration, lightsheet
- Deep Learning: Cellpose, Omnipose, Spotiflow, CoTracker
- Microscopy: OMERO, HRM, Operetta, ArgoLight
- File Formats: Bio-Formats, BigDataViewer, SpimData
- Collaboration: GitLab, Renku, C4Science
We welcome contributions and collaboration! Visit our repositories to:
- Report issues
- Submit pull requests
- Request features
- Ask questions
For more information about BIOP, visit our institutional page or reach out through our GitHub repositories.
Most repositories are open-source with various licenses. Please check individual repositories for specific license information.
Last updated: January 2026 Total repositories: 83