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    30 repositories

    • biomero-auto-container

      Public
      BIOMERO template container
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 6, 2026Nov 6, 2026

    • biomero-converter

      Public
      Convert db image format to Ome-Tiff and Ome-Zarr
      Python
      •
      Apache License 2.0
      •0•1•2•0•Updated Nov 6, 2026Nov 6, 2026

    • napari-meta-tiff

      Public
      napari tiff reader with extended metadata
      Python
      •
      MIT License
      •0•0•0•1•Updated Nov 6, 2026Nov 6, 2026

    • imaging-metadata-converter

      Public
      Convert acquisition metadata to custom model
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2026Nov 6, 2026

    • fair-segmentation

      Public
      FAIR organelle segmentation pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 6, 2026Nov 6, 2026

    • fair-metadata-integration

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2026Nov 6, 2026

    • NL-BIOMERO

      Public
      NL‑BIOMERO delivers a full containerized stack to run OMERO together with the BIOMERO 2.0 framework. It provides Docker/Podman configurations and Compose files …
      containersomerobiomero
      containersomerobiomero
      Python
      •
      Other
      •17•13•1•4•Updated Nov 5, 2026Nov 5, 2026

    • OMERO.biomero

      Public
      Plugin adding monitored, in-place uploads and workflows to OMERO Webclient
      webappomerobiomero
      webappomerobiomero
      JavaScript
      •
      GNU Affero General Public License v3.0
      •1•2•2•3•Updated Nov 5, 2026Nov 5, 2026

    • biomero-scripts

      Public
      Scripts for use with BIOMERO
      slurmhigh-performance-computingfair
      slurmhigh-performance-computingfairimage-analysisomerobioimaginghigh-throughput-screeninghigh-content-screeningcytominebiomero
      Python
      •
      GNU General Public License v2.0
      •2•5•3•2•Updated Nov 5, 2026Nov 5, 2026

    • biomero

      Public
      BIOMERO.analyzer - A python library for easy connecting between OMERO (jobs) and a Slurm cluster
      pythonslurmhigh-performance-computing
      pythonslurmhigh-performance-computingfairimage-analysisomerobioimaginghigh-throughput-screeninghigh-content-screeningcytomine
      Python
      •
      Apache License 2.0
      •6•29•5•2•Updated Nov 5, 2026Nov 5, 2026

    • BIOMERO.importer

      Public
      System that allows automatic importing of datasets via local network
      omerozarrngff
      omerozarrngffomero-importbiomerongff-zarr
      Python
      •
      GNU General Public License v2.0
      •0•3•2•0•Updated Nov 5, 2026Nov 5, 2026

    • BIOMERO.shallower

      Public
      Python library and CPU-only container for shallow OME-Zarr normalization in BIOMERO. Reuses verified canonical pixels while retaining new and changed image and …
      omeroiscccontent-identification
      omeroiscccontent-identificationbioimagingzarrngffngff-zarr
      Python
      •
      Apache License 2.0
      •0•1•1•0•Updated Nov 5, 2026Nov 5, 2026

    • biomero-schema

      Public
      A spec for BIOMERO workflows (internal)
      Python
      •
      Apache License 2.0
      •1•0•0•1•Updated Nov 5, 2026Nov 5, 2026

    • OMERO.forms

      Public
      Extension to OMERO.web to enhance metadata input and provide provenance
      webappomero
      webappomero
      Python
      •
      GNU Affero General Public License v3.0
      •8•9•0•1•Updated Nov 3, 2026Nov 3, 2026

    • BIOMERO.ZarrViewer

      Public
      BIOMERO OME-Zarr Viewer Extension
      JavaScript
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Nov 3, 2026Nov 3, 2026

    • ISA-REMBI-Metadata-Modules

      Public
      Repository to organize REMBI and ISA metadata modules
      2•2•2•2•Updated Oct 30, 2026Oct 30, 2026

    • vis-workflow

      Public
      Workflow visualiser
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2026Oct 27, 2026

    • OMERO.Analysis

      Public
      Analyse OMERO data
      JavaScript
      •
      Other
      •0•0•0•0•Updated Oct 27, 2026Oct 27, 2026

    • omero-web-zarr

      Public
      Implementation of OME-Zarr API with an omero-web app
      Python
      •
      GNU Affero General Public License v3.0
      •7•0•0•0•Updated Oct 21, 2026Oct 21, 2026

    • OMERO.DataQueryWorker

      Public
      Hardened bounded-query service for immutable DuckDB, SQLite, and CSV sources
      sqliteomerobioimaging
      sqliteomerobioimagingfastapiduckdb
      Python
      •
      Other
      •0•0•0•0•Updated Oct 15, 2026Oct 15, 2026

    • BIOMERO.WorkflowSkills

      Public
      Catalog for BIOMERO workflow skills
      Python
      •
      Other
      •0•0•0•0•Updated Oct 13, 2026Oct 13, 2026

    • imaging-metadata-consolidator

      Public archive
      Retired: see imaging-metadata-converter, which replaces it
      Python
      •0•0•0•0•Updated Sep 30, 2026Sep 30, 2026

    • NL-BioImageAnalysis-course2026

      Public
      Repository for the NL-BioImageAnalysis-course
      aideep-learningimage-processing
      aideep-learningimage-processingimage-analysisai-coding
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•2•1•0•Updated Sep 24, 2026Sep 24, 2026

    • omero-deployment-kit

      Public
      deployment solution for OMERO designed for research institutions that require production-ready OMERO server with minimal hassle
      Jinja
      •1•7•0•0•Updated Sep 10, 2026Sep 10, 2026

    • cowscript

      Public
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • omero-web

      Public
      Django-based OMERO.web client
      Python
      •41•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • ConvertLeica-Docker

      Public
      Python
      •
      Other
      •0•0•1•0•Updated Jul 23, 2026Jul 23, 2026

    • NL-BIOMERO-Local-Slurm

      Public
      A Slurm cluster using docker-compose
      hpccontainersslurm
      hpccontainersslurmbiomero
      Dockerfile
      •
      MIT License
      •276•6•1•0•Updated Apr 14, 2026Apr 14, 2026

    • biomero-workflows

      Public
      Gather workflows that can be used in BIOMERO
      Apache License 2.0
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • discussions

      Public
      0•0•0•0•Updated Feb 13, 2025Feb 13, 2025
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