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# <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="28" align="center"> BIOMERO — BioImage Analysis in OMERO
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# <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="28" style="height:28px; width:auto; vertical-align:middle;"> BIOMERO — BioImage Analysis in OMERO
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[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![DOI](https://zenodo.org/badge/638954891.svg)](https://zenodo.org/badge/latestdoi/638954891) [![PyPI - Version](https://img.shields.io/pypi/v/biomero)](https://pypi.org/project/biomero/) [![PyPI - Python Versions](https://img.shields.io/pypi/pyversions/biomero)](https://pypi.org/project/biomero/) ![Slurm](https://img.shields.io/badge/Slurm-21.08.6-blue.svg) ![OMERO](https://img.shields.io/badge/OMERO-5.6.8-blue.svg) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/7530/badge)](https://bestpractices.coreinfrastructure.org/projects/7530) [![Sphinx build](https://github.com/NL-BioImaging/biomero/actions/workflows/sphinx.yml/badge.svg?branch=main)](https://github.com/NL-BioImaging/biomero/actions/workflows/sphinx.yml) [![pages-build-deployment](https://github.com/NL-BioImaging/biomero/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/NL-BioImaging/biomero/actions/workflows/pages/pages-build-deployment) [![python-package build](https://github.com/NL-BioImaging/biomero/actions/workflows/python-package.yml/badge.svg)](https://github.com/NL-BioImaging/biomero/actions/workflows/python-package.yml) [![python-publish build](https://github.com/NL-BioImaging/biomero/actions/workflows/python-publish.yml/badge.svg)](https://github.com/NL-BioImaging/biomero/actions/workflows/python-publish.yml) [![Coverage Status](https://coveralls.io/repos/github/NL-BioImaging/biomero/badge.svg?branch=main)](https://coveralls.io/github/NL-BioImaging/biomero?branch=main)
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> 🚀 **This package is part of <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" align="absmiddle"> BIOMERO 2.0** — For complete deployment and FAIR infrastructure setup, start with the [**NL-BIOMERO Documentation**](https://nl-bioimaging.github.io/NL-BIOMERO/) 📖
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> 🚀 **This package is part of <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" style="height:16px; width:auto; vertical-align:middle;"> BIOMERO 2.0** — For complete deployment and FAIR infrastructure setup, start with the [**NL-BIOMERO Documentation**](https://nl-bioimaging.github.io/NL-BIOMERO/) 📖
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The **BIOMERO** framework, for **B**io**I**mage analysis in **OMERO**, allows you to run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance compute (HPC) cluster, remotely through SSH.
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# <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="28" align="center"> BIOMERO 2.0
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# <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="28" style="height:28px; width:auto; vertical-align:middle;"> BIOMERO 2.0
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We have released an enhanced **BIOMERO** experience!
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<img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" align="absmiddle"> BIOMERO 2.0 is a complete ecosystem that includes:
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<img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" style="height:16px; width:auto; vertical-align:middle;"> BIOMERO 2.0 is a complete ecosystem that includes:
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- **BIOMERO.analyzer** (this Python library) - The core analysis engine
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- **BIOMERO.scripts** - OMERO scripts for HPC integration
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- **BIOMERO.importer** - Automated data import service
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![OMERO-Figure1_Overview_v5](https://github.com/NL-BioImaging/biomero/assets/68958516/ff437ed2-d4b7-48b4-a7e3-12f1dbf00981)
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For the <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" align="absmiddle"> BIOMERO 2.0 setup, see NL-BIOMERO for deployment; and for details on the design and FAIR features, see our latest preprint: [“BIOMERO 2.0: end-to-end FAIR infrastructure for bioimaging data import, analysis, and provenance”](https://arxiv.org/abs/2511.13611)
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For the <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" style="height:16px; width:auto; vertical-align:middle;"> BIOMERO 2.0 setup, see NL-BIOMERO for deployment; and for details on the design and FAIR features, see our latest preprint: [“BIOMERO 2.0: end-to-end FAIR infrastructure for bioimaging data import, analysis, and provenance”](https://arxiv.org/abs/2511.13611)
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## Deploy with NL-BIOMERO
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# BIOMERO Web Interface
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In addition to the BIOMERO.scripts, <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" align="absmiddle"> BIOMERO 2.0 introduces a modern web-based user interface through the [OMERO.biomero](https://github.com/NL-BioImaging/OMERO.biomero) web plugin. This plugin provides a more intuitive and user-friendly way to interact with BIOMERO workflows directly from the OMERO.web interface.
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In addition to the BIOMERO.scripts, <img src="https://raw.githubusercontent.com/NL-BioImaging/OMERO.biomero/refs/tags/v1.2.1/webapp/src/img/biomero-logo.svg" alt="BIOMERO" height="16" style="height:16px; width:auto; vertical-align:middle;"> BIOMERO 2.0 introduces a modern web-based user interface through the [OMERO.biomero](https://github.com/NL-BioImaging/OMERO.biomero) web plugin. This plugin provides a more intuitive and user-friendly way to interact with BIOMERO workflows directly from the OMERO.web interface.
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## Features
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