Repositories list

• NucleusJ

  Public
  Java

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•11 pull request•Updated Apr 1, 2026Apr 1, 2026

• omeroXT

  Public
  An Imaris XTension to load images and ROIs from an OMERO server directly into Imaris.

  Java

  •

  GNU General Public License v2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2026Mar 10, 2026

• biom3d

  Public
  Easy Volumetric Segmentation with Deep Learning

  Python

  •

  GNU General Public License v3.0

  •77 forks•11 star•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• simple-omero-client

  Public
  Maven project to easily connect to OMERO.

  javamavenomero

  javamavenomero

  Java

  •

  GNU General Public License v2.0

  •88 forks•1111 stars•55 issues•00 pull requests•Updated Dec 10, 2025Dec 10, 2025

• omero_batch-plugin

  Public
  imagejomeroimagej-macros+ 1

  imagejomeroimagej-macrosimagej-plugin

  Java

  •

  GNU General Public License v2.0

  •44 forks•44 stars•88 issues•00 pull requests•Updated Nov 28, 2025Nov 28, 2025

• biom3d-mouse-embryo-training

  Public
  Scripts and macros used to train a Biom3D model for mouse embryos.

  ImageJ Macro

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 30, 2025Sep 30, 2025

• omero-hpc-script-biom3d

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 10, 2025Sep 10, 2025

• omero_macro-extensions

  Public
  imagejomeroimagej-macro

  imagejomeroimagej-macro

  Java

  •

  GNU General Public License v2.0

  •55 forks•66 stars•11 issue•00 pull requests•Updated Nov 19, 2024Nov 19, 2024

• sRNAPipe-cli

  Public
  CLI tool for bioinformatic in-depth exploration of small RNA-seq data

  rna-seqperltransposable-elements

  rna-seqperltransposable-elements

  Perl

  •

  Academic Free License v3.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• CLIFinder

  Public
  Perl

  •

  GNU General Public License v3.0

  •00 forks•33 stars•22 issues•00 pull requests•Updated Apr 10, 2024Apr 10, 2024

• sRNAPipe

  Public
  a GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data

  rna-seqgalaxytransposable-elements

  rna-seqgalaxytransposable-elements

  HTML

  •

  Academic Free License v3.0

  •33 forks•22 stars•11 issue•00 pull requests•Updated Apr 9, 2024Apr 9, 2024

• biosphere-biom3d

  Public
  Appliance Biosphere for biom3d

  Shell

  •

  GNU General Public License v2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 27, 2024Mar 27, 2024

• biosphere-omero-server

  Public
  Biosphere appliance for OMERO server.

  Shell

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 22, 2023Nov 22, 2023

• nj2_python

  Public
  NucleusJ 2.0 in Python

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 31, 2023Oct 31, 2023

• NucleusJ-tests-images

  Public
  Images for NucleusJ2 CI/CD tests

  11 fork•00 stars•00 issues•00 pull requests•Updated Aug 3, 2023Aug 3, 2023

• omero-plugins-workshop

  Public
  ImageJ Macro

  •

  BSD 2-Clause "Simplified" License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 7, 2023Mar 7, 2023

• update-site-activator

  Public
  Java

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 25, 2023Jan 25, 2023

• omero-toolbox-examples

  Public
  ImageJ Macro

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Sep 5, 2022Sep 5, 2022

• notebooks-team-probst-tatout

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 28, 2022Feb 28, 2022

• NucBase

  Public
  Small RNA aligner with graphical interface.

  C++

  •

  GNU Lesser General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2014Nov 12, 2014