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1 | | -# <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 |
| 1 | +# <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 |
2 | 2 | [](https://opensource.org/licenses/Apache-2.0) [](https://zenodo.org/badge/latestdoi/638954891) [](https://pypi.org/project/biomero/) [](https://pypi.org/project/biomero/)   [](https://fair-software.eu) [](https://bestpractices.coreinfrastructure.org/projects/7530) [](https://github.com/NL-BioImaging/biomero/actions/workflows/sphinx.yml) [](https://github.com/NL-BioImaging/biomero/actions/workflows/pages/pages-build-deployment) [](https://github.com/NL-BioImaging/biomero/actions/workflows/python-package.yml) [](https://github.com/NL-BioImaging/biomero/actions/workflows/python-publish.yml) [](https://coveralls.io/github/NL-BioImaging/biomero?branch=main) |
3 | 3 |
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4 | | -> 🚀 **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/) 📖 |
| 4 | +> 🚀 **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/) 📖 |
5 | 5 |
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6 | 6 | 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. |
7 | 7 |
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8 | | -# <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 |
| 8 | +# <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 |
9 | 9 |
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10 | 10 | We have released an enhanced **BIOMERO** experience! |
11 | 11 |
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12 | | -<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: |
| 12 | +<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: |
13 | 13 | - **BIOMERO.analyzer** (this Python library) - The core analysis engine |
14 | 14 | - **BIOMERO.scripts** - OMERO scripts for HPC integration |
15 | 15 | - **BIOMERO.importer** - Automated data import service |
@@ -55,7 +55,7 @@ BIOMERO 1.0 consists of this Python library (`biomero`) and the integrations wit |
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56 | 56 |  |
57 | 57 |
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58 | | -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) |
| 58 | +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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60 | 60 |
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61 | 61 | ## Deploy with NL-BIOMERO |
@@ -228,7 +228,7 @@ You are encouraged to create your own custom scripts. Do note the copy-left lice |
228 | 228 |
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229 | 229 | # BIOMERO Web Interface |
230 | 230 |
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231 | | -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. |
| 231 | +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. |
232 | 232 |
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233 | 233 | ## Features |
234 | 234 |
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