Repositories list

• OMERO-scripts

  Public
  Series of script to make use of OMERO

  Groovy

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Dec 20, 2024Dec 20, 2024

• ijp-imagetoatlas

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

  Java

  •8•48•33•1•Updated Dec 20, 2024Dec 20, 2024

• ijp-atlas

  Public
  Repository containins Atlases and Atlas Structure for ABBA plugin

  Java

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Dec 20, 2024Dec 20, 2024

• bigdataviewer-biop-tools

  Public
  Another repo for bdv tools.

  Java

  •2•5•25•1•Updated Dec 20, 2024Dec 20, 2024

• ijp-kheops

  Public
  Java

  •

  GNU General Public License v2.0

  •2•13•15•0•Updated Dec 20, 2024Dec 20, 2024

• ijl-utilities-wrappers

  Public
  Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)

  Java

  •6•32•5•0•Updated Dec 20, 2024Dec 20, 2024

• bigdataviewer-playground-display

  Public
  Display additions for bigdataviewer using bigdataviewer-playground

  Java

  •0•2•0•0•Updated Dec 20, 2024Dec 20, 2024

• bigdataviewer-spimdata-extras

  Public
  Extra settings that can be stored in spimdata file format

  Java

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• abba-installer

  Public
  Repository backing the creation of standalone installers for ABBA

  Python

  •

  Other

  •0•1•14•0•Updated Dec 11, 2024Dec 11, 2024

• abba_python

  Public
  ABBA, controlled from python

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•7•9•0•Updated Dec 11, 2024Dec 11, 2024

• bigdataviewer-image-loaders

  Public
  Java

  •

  GNU General Public License v3.0

  •0•5•4•0•Updated Dec 10, 2024Dec 10, 2024

• qupath-extension-abba

  Public
  QuPath extension for Aligning Big Brains and Atlases

  Java

  •

  MIT License

  •2•6•5•2•Updated Dec 9, 2024Dec 9, 2024

• ijp-operetta-importer

  Public
  PerkinElmer Operetta Importer using BioFormats!

  HTML

  •

  GNU General Public License v3.0

  •3•9•8•0•Updated Nov 25, 2024Nov 25, 2024

• ArgoLight_analysis_tool

  Public
  Code to control the quality of images taken with our microscopes

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•1•0•Updated Nov 13, 2024Nov 13, 2024

• lightsheet-brain-workflows

  Public
  Groovy

  •0•1•6•0•Updated Nov 12, 2024Nov 12, 2024

• qupath-extension-warpy

  Public
  ImgLib2 RealTransform brought to QuPath

  Java

  •

  Apache License 2.0

  •5•20•8•0•Updated Nov 5, 2024Nov 5, 2024

• coLoc

  Public
  A Board Game to teach co-localization analysis

  Creative Commons Zero v1.0 Universal

  •0•12•3•0•Updated Nov 1, 2024Nov 1, 2024

• abba-documentation

  Public
  Documentation for ABBA - Aligning Big Brains & Atlases

  1•1•2•2•Updated Oct 23, 2024Oct 23, 2024

• biop-bash-scripts

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

  Shell

  •8•10•9•0•Updated Oct 15, 2024Oct 15, 2024

• omero-hrm

  Public
  Python

  •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

• BIOP-desktop

  Public
  JavaScript

  •0•9•8•0•Updated Oct 8, 2024Oct 8, 2024

• EasyXT-FIJI

  Public
  Commands and Classes for interfacing between Imaris and Fiji

  Java

  •

  Other

  •2•12•22•0•Updated Sep 30, 2024Sep 30, 2024

• qupath-extension-cellpose

  Public
  an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

  Jupyter Notebook

  •

  Apache License 2.0

  •11•67•3•0•Updated Sep 12, 2024Sep 12, 2024

• qupath-extension-biop-omero

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

  Java

  •

  GNU General Public License v3.0

  •12•4•6•0•Updated Aug 23, 2024Aug 23, 2024

• ij2-LocalizeJ

  Public
  HTML

  •1•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• quick-start-czi-reader

  Public
  A bio-formats image reader for CZI that starts faster

  Java

  •0•4•6•0•Updated Jul 24, 2024Jul 24, 2024

• bigdataviewer-selector

  Public
  Source Selection mode for BigDataViewer

  Java

  •0•1•2•0•Updated Jul 22, 2024Jul 22, 2024

• biop-desktop-doc

  Public
  The documentation of the BIOP-desktop

  0•1•2•0•Updated Jun 27, 2024Jun 27, 2024

• super-nice-pypi-package

  Public
  blabla

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•3•Updated Jun 20, 2024Jun 20, 2024

• cellpose

  Public
  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •411•0•0•0•Updated May 24, 2024May 24, 2024