Repositories list

• biop-bash-scripts

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

  Shell

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

• bigdataviewer-image-loaders

  Public
  Java

  •

  GNU General Public License v3.0

  •0•5•4•0•Updated Oct 14, 2024Oct 14, 2024

• coLoc

  Public
  A Board Game to teach co-localization analysis

  Creative Commons Zero v1.0 Universal

  •0•12•1•0•Updated Oct 14, 2024Oct 14, 2024

• omero-hrm

  Public
  Python

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

• qupath-extension-abba

  Public
  QuPath extension for Aligning Big Brains and Atlases

  Java

  •

  Apache License 2.0

  •2•6•5•0•Updated Oct 13, 2024Oct 13, 2024

• ijl-utilities-wrappers

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

  Java

  •6•31•5•0•Updated Oct 13, 2024Oct 13, 2024

• bigdataviewer-biop-tools

  Public
  Another repo for bdv tools.

  Java

  •2•5•20•1•Updated Oct 10, 2024Oct 10, 2024

• BIOP-desktop

  Public
  JavaScript

  •0•9•7•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

• OMERO-scripts

  Public
  Series of script to make use of OMERO

  Groovy

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Sep 26, 2024Sep 26, 2024

• ijp-imagetoatlas

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

  Java

  •8•46•28•1•Updated Sep 23, 2024Sep 23, 2024

• abba_python

  Public
  ABBA, controlled from python

  Python

  •

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

  •3•6•9•4•Updated Sep 23, 2024Sep 23, 2024

• ijp-operetta-importer

  Public
  PerkinElmer Operetta Importer using BioFormats!

  HTML

  •

  GNU General Public License v3.0

  •3•9•5•0•Updated Sep 19, 2024Sep 19, 2024

• ijp-kheops

  Public
  Java

  •

  GNU General Public License v2.0

  •2•12•17•0•Updated Sep 18, 2024Sep 18, 2024

• lightsheet-brain-workflows

  Public
  Groovy

  •0•1•6•0•Updated Sep 18, 2024Sep 18, 2024

• abba-installer

  Public
  Repository backing the creation of standalone installers for ABBA

  Python

  •

  Other

  •0•1•14•0•Updated Sep 13, 2024Sep 13, 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•63•2•0•Updated Sep 12, 2024Sep 12, 2024

• abba-documentation

  Public
  Documentation for ABBA - Aligning Big Brains & Atlases

  0•1•2•0•Updated Aug 30, 2024Aug 30, 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

• bigdataviewer-playground-display

  Public
  Display additions for bigdataviewer using bigdataviewer-playground

  Java

  •0•2•0•0•Updated Jul 24, 2024Jul 24, 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

• 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 Jul 22, 2024Jul 22, 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•4•0•Updated Jul 17, 2024Jul 17, 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

  •388•0•0•0•Updated May 24, 2024May 24, 2024

• qupath-extension-biop-hrm

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 22, 2024May 22, 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 May 21, 2024May 21, 2024