Omero (42)

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Omero (42)#

Accessible Interactive Spatial-Omics Data Visualizations with Vitessce and OMERO#

Bortolomeazzi Michele

Published 2025-06-30

Licensed CC-BY-4.0

OMERO is the most used research data management system (RDM) in the bioimaging domain, and has been adopted as a centralized RDM solution by several academic and research institutions. A main reason for this is the ability to directly view and annotate images from a web-based interface. However, this feature of OMERO is currently underpowered for the visualization of very large or multimodal datasets. These datasets, are becoming a more and more common foundation for biological and biomedical studies, due to the recent developments in imaging, and sequencing technologies which enabled their application to spatial-omics. In order to begin to provide this multimodal-data capability to OMERO, we developed omero-vitessce (NFDI4BIOIMAGE/omero-vitessce), a new OMERO.web plugin for viewing data stored in OMERO with the Vitessce (http://vitessce.io/) multimodal data viewer. omero-vitessce can be installed as an OMERO.web plugin with PiPy (https://pypi.org/project/omero-vitessce/), and allows users to set up interactive visualizations of their images of cells and tissues through interactive plots which are directly linked to the image. This enables the visual exploration of bioimage-analysis results and of multimodal data such as those generated through spatial-omics experiments. The data visualization is highly customizable and can be configured not only through custom configuration files, but also with the graphical interface provided by the plugin, thus making omero-vitessce a highly user-friendly solution for multimodal data viewing. most biological datasets. We plan to extend the interoperability of omero-vitessce with the OME-NGFF and SpatialData file formats to leverage the efficiency of these cloud optimized formats.

Tags: Nfdi4Bioimage, OMERO, Include In Dalia

https://zenodo.org/records/15771899

https://doi.org/10.5281/zenodo.15771899


BHG2023-OMERO-ARC#

Andrea Schrader, Michele Bortolomeazzi, Niraj Kandpal, Torsten Stöter, Kevin Schneider, Peter Zentis, Josh Moore, Jeam-Marie Burel, Tom Boissonnet

Licensed CC-BY-4.0

Repository for documentation during the 2nd de.NBI BioHackathon Germany - 11.-15.12.2023 - OMERO-ARC project (in short: BHG2023-OMERO-ARC)

Tags: Nfdi4Bioimage, Bioinformatics, OMERO, Exclude From Dalia

Content type: Github Repository

NFDI4BIOIMAGE/BHG2023-OMERO-ARC


BIOMERO - A scalable and extensible image analysis framework#

Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A.J. Reits, Ron A. Hoebe, Przemek M. Krawczyk

Published None

Licensed CC-BY-4.0

The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments.

Tags: OMERO, Workflow, Bioimage Analysis, Exclude From Dalia

Content type: Publication

https://doi.org/10.1016/j.patter.2024.101024


Biomero#

Torec Luik, Johannes Soltwedel

Published 2024-07-24

Licensed APACHE-2.0

The BIOMERO framework, for BioImage analysis in OMERO, allows you to run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance compute (HPC) cluster, remotely through SSH.

Tags: OMERO, Github, Exclude From Dalia

Content type: Github Repository

NL-BioImaging/biomero


Browsing the Open Microscopy Image Data Resource with Python#

Robert Haase

Licensed CC-BY-4.0

Tags: OMERO, Python, Include In Dalia

Content type: Blog Post

https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html


Erick Martins Ratamero - Expanding the OME ecosystem for imaging data management | SciPy 2024#

SciPy, Erick Martins Ratamero

Published 2024-08-19

Licensed YOUTUBE STANDARD LICENSE

Tags: OMERO, Bioimage Analysis, Exclude From Dalia

Content type: Video, Presentation

https://www.youtube.com/watch?v=GmhyDNm1RsM


Fiji#

Licensed BSD-2-CLAUSE

Fiji is a popular free open-source image processing package based on ImageJ.

Tags: Imagej, OMERO, Exclude From Dalia

Content type: Online Tutorial

https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html


Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging#

Starts Oct 16, 2024, 9:00 AM, Ends Oct 17, 2024, 5:00 PM

Tags: Bioimage Analysis, OMERO, Research Data Management, Exclude From Dalia

Content type: Workshop

https://doi.org/10.5281/zenodo.14013025


Glencoe Software Webinars#

Chris Allan, Emil Rozbicki

Licensed UNKNOWN

Example Workflows / usage of the Glencoe Software.

Tags: OMERO, Exclude From Dalia

Content type: Video, Tutorial, Collection

https://www.glencoesoftware.com/media/webinars/


High throughput & automated data analysis and data management workflow with Cellprofiler and OMERO#

Sarah Weischer, Jens Wendt, Thomas Zobel

Licensed CC-BY-4.0

In this workshop a fully integrated data analysis solutions employing OMERO and commonly applied image analysis tools (e.g., CellProfiler, Fiji) using existing python interfaces (OMERO Python language bindings, ezOmero, Cellprofiler Python API) is presented.

Tags: OMERO, Data Analysis, Bioimage Analysis, Include In Dalia

Content type: Collection

https://zenodo.org/doi/10.5281/zenodo.8139353


High-content screening (HCS) workflows for FAIR image data management with OMERO#

Riccardo Massei, Wibke Busch, Beatriz Serrano-Solano, Matthias Bernt, Stefan Scholz, Elena K. Nicolay, Hannes Bohring, Jan Bumberger

Published 2025-05-09

Licensed CC-BY-4.0

This study demonstrates the use of Workflow Management Systems (WMS) and the OMERO platform to create reusable semi-automatic workflows for managing high-content screening (HCS) bioimaging data, improving data management efficiency, reducing errors, and providing a blueprint for future HCS data management systems.

Tags: Bioimage Analysis, OMERO, Include In Dalia

Content type: Publication

https://www.nature.com/articles/s41598-025-00720-0


I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#

Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Carsten Fortmann-Grote, Julia Dohle, Peter Zentis, Niraj Kandpal, Susanne Kunis, Thomas Zobel, Stefanie Weidtkamp-Peters, Elisa Ferrando-May

Published 2023-11-13

Licensed CC-BY-4.0

The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.

Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio, Include In Dalia

Content type: Slides, Video

https://zenodo.org/records/8323588

https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU

https://doi.org/10.5281/zenodo.8323588


KNIME Image Processing#

None

Licensed GPL-3.0

The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME.

Tags: Imagej, OMERO, Workflow, Exclude From Dalia

Content type: Tutorial, Online Tutorial, Documentation

https://www.knime.com/community/image-processing


Key-Value pairs scripts#

Licensed UNKNOWN

The key-value pairs are annotations in OMERO useful to describe thoroughly the data and can be added & edited via the OMERO.web interface.

Tags: OMERO, Exclude From Dalia

Content type: Documentation, Collection

https://guide-kvpairs-scripts.readthedocs.io/en/latest/


LEO#

Rodrigo Escobar Diaz Guerrero

Published 2025-01-08T10:20:30+00:00

Licensed MIT

Linking Electronic Lab Notebooks and other sources with OMERO objects

Tags: OMERO, Research Data Management, Electronic Lab Notebooks, Exclude From Dalia

Content type: Github Repository

NFDI4BIOIMAGE/LEO


NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#

Mohamed M. Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa A. F. Fuchs, Moritz Hoevels, Niraj Kandpal, Christoph Möhl, Joshua A. Moore, Astrid Schauss, Andrea Schrader, Torsten Stöter, Julia Thönnißen, Monica Valencia-S., H. Lukas Weil, Jens Wendt and Peter Zentis

Licensed CC-BY-4.0

Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, OMERO, Python, Research Data Management, Exclude From Dalia

Content type: Event, Publication, Documentation

NFDI4BIOIMAGE/Cologne-Hackathon-2023

https://doi.org/10.5281/zenodo.10609770


NFDITalk Cloud based image data science#

Josh Moore, Yi Sun

Published 2025-06-02

Licensed UNKNOWN

In this talk, we will be discussing OME-ZARR, a cloud-optimized format for scalable bioimage data management, and BARD, a cloud virtual desktop that provides a seamless way to run resource-intensive applications in the cloud, enabling users to access powerful computing environments from any device with a web browser.

Tags: Bioimage Analysis, OMERO, Exclude From Dalia

Content type: Video

https://www.youtube.com/watch?v=bzfmE29S270


OME Documentation#

Licensed CC-BY-4.0

Tags: OMERO, Include In Dalia

Content type: Documentation

https://www.openmicroscopy.org/docs/


OME Event Database#

Tags: OMERO, Research Data Management, Exclude From Dalia

Content type: Collection, Event

https://www.openmicroscopy.org/events/


OMERO - HCS analysis pipeline using Jupyter Notebooks#

Riccardo Massei

Licensed MIT

Material and solutions for the course ‘Bioimage data management and analysis with OMERO’ held in Heidelberg (13th May 2024) - Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks. Main goal of the workflow is to show the potential of JN to perform reproducible image analysis in connection with an OMERO instance. In this specific example, we are performing a simple nuclei segmentation from raw images uploaded in OMERO.

Tags: Teaching, Bioimage Analysis, Notebooks, Python, OMERO, Include In Dalia

Content type: Github Repository

rmassei/2024-jn-omero-pipeline


OMERO - QuPath#

Rémy Jean Daniel Dornier

Licensed CC-BY-NC-SA-4.0

OMERO-RAW extension for QuPath allows to directly access to the raw pixels of images. All types of images (RGB, fluorescence, …) are supported with this extension.

Tags: Bioimage Analysis, OMERO, Exclude From Dalia

Content type: Online Tutorial

https://wiki-biop.epfl.ch/en/data-management/omero/qupath


OMERO Guide#

Licensed BSD-2-CLAUSE

Tags: OMERO, Include In Dalia

Content type: Collection

https://omero-guides.readthedocs.io/en/latest/


OMERO and ARC Workflow#

Niraj Kandpal, Peter Zentis, Monica Valencia-Schneider, Astrid Schauss

Published 2025-04-15

Licensed CC-BY-4.0

A tutorial for OMERO and ARC Interoprability and (meta)data exchange. This describes the relevant metadata to transfer from OMERO to ARC and the other way round.

Tags: Bioimage Analysis, OMERO, Include In Dalia

Content type: Slides

https://zenodo.org/records/15225616


OMERO documentation#

Licensed UNKNOWN

Tags: OMERO, Include In Dalia

Content type: Documentation

https://omero.readthedocs.io/en/stable/


OMERO for microscopy research data management#

Thomas Zobel, Sarah Weischner, Jens Wendt

Licensed ALL RIGHTS RESERVED

A use case example from the Münster Imaging Network

Tags: Nfdi4Bioimage, OMERO, Research Data Management, Exclude From Dalia

Content type: Publication

https://analyticalscience.wiley.com/do/10.1002/was.0004000267/


OMERO walkthrough example#

Licensed BSD-2-CLAUSE

Tags: OMERO, Include In Dalia

Content type: Document

https://omero-guides.readthedocs.io/en/latest/example.html


OMERO walkthrough for facility managers#

Licensed BSD-2-CLAUSE

Tags: OMERO, Include In Dalia

Content type: Document

https://omero-guides.readthedocs.io/en/latest/example_facility_manager.html


Omero Deployment examples#

Licensed BSD-2-CLAUSE

Tags: OMERO, Include In Dalia

Content type: Collection

ome/omero-deployment-examples


Omero-tools#

Johannes Soltwedel

Licensed CC-BY-4.0

This repository contains a collection of tools for working with OMERO. Such tools can be working with the OMERO command line interface to transfer datasets between repositories, etc.

Tags: OMERO, Bioimage Analysis, Exclude From Dalia

Content type: Github Repository

https://biapol.github.io/omero-tools/


Open Microscopy Environment YouTube channel#

YouTube channel collecting videos and webinar recordings about the Open Microscopy Environment (OME), the Next Generation File Format OME-NGFF, the Image Data Resource (IDR), the Omero platform and Omero plugins.

Tags: OMERO, Exclude From Dalia

Content type: Collection, Video

https://www.youtube.com/OpenMicroscopyEnvironment


Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy#

Riccardo Massei, Björn Grüning

Published 2024-12-02

Licensed CC-BY-4.0

Tags: OMERO, Galaxy, Metadata, Nfdi4Bioimage, Include In Dalia

Content type: Tutorial, Framework, Workflow

https://training.galaxyproject.org/training-material/topics/imaging/tutorials/omero-suite/tutorial.html


Plugin “omero-batch-plugin”#

Licensed GPL-2.0

An ImageJ plugin to run a script or macro on a batch of images from/to OMERO.

Tags: OMERO, Imagej, Imagej Macro, Github, Exclude From Dalia

Content type: Github Repository

GReD-Clermont/omero_batch-plugin


Plugin “omero-cli-transfer”#

Erick Martins Ratamero, jean-marie burel, Will Moore, Guillaume Gay, Christoph Moehl, et al.

Published 2024-09-14

Licensed GPL-2.0

An OMERO CLI plugin for creating and using transfer packets between OMERO servers.

Tags: OMERO, Exclude From Dalia

Content type: Github Repository

ome/omero-cli-transfer


Plugin “simple-omero-client”#

Pierre Pouchin, Rdornier, kekunn, jean-marie burel

Licensed GPL-2.0

A wrapper library which can be called from scripts in Fiji, but can mostly be used in Maven projects to wrap calls to the underlying OMERO Java Gateway.

Tags: OMERO, Github, Fiji, Exclude From Dalia

Content type: Github Repository

GReD-Clermont/simple-omero-client


RDM4mic#

Licensed UNKNOWN

Tags: Research Data Management, OMERO, Exclude From Dalia

Content type: Collection, Video

https://www.youtube.com/@RDM4mic


Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users#

Anett Jannasch, Silke Tulok, Chukwuebuka William Okafornta, Thomas Kugel, Michele Bortolomeazzi, Tom Boissonnet, Christian Schmidt, Andy Vogelsang

Published 2024-09-14

Licensed CC-BY-4.0

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis.

Tags: Nfdi4Bioimage, OMERO, Bioimage Analysis, Exclude From Dalia

Content type: Publication

https://onlinelibrary.wiley.com/doi/10.1111/jmi.13360


User friendly Image metadata annotation tool/workflow for OMERO#

Jens Wendt

Tags: Metadata, Workflow, OMERO, Include In Dalia

Content type: Forum Post

https://forum.image.sc/t/user-friendly-image-metadata-annotation-tool-workflow-for-omero/87925/1


Welcome to BioImage Town#

Josh Moore

Licensed CC-BY-4.0

Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023

Tags: OMERO, Bioimage Analysis, Nfdi4Bioimage, Exclude From Dalia

Content type: Slides

https://zenodo.org/doi/10.5281/zenodo.10008464


omero-arc#

Christoph Moehl, Peter Zentis, Niraj Kandpal

Published 2023-12-18T16:11:04+00:00

Licensed GNU GENERAL PUBLIC LICENSE V3.0

Library to export OMERO projects to ARC repositories

Tags: OMERO, Research Data Management, Exclude From Dalia

Content type: Github Repository, Software

cmohl2013/omero-arc


omero-ontop-mappings#

Carsten Fortmann-Grote, andrawaag, Jerven Bolleman

Published 2024-09-13T08:01:09+00:00

ONTOP module for querying OMERO with SPARQL

Tags: OMERO, Exclude From Dalia

Content type: Github Repository

German-BioImaging/omero-ontop-mappings


omero-quay#

Alexis Lebon, Anatole Chessel, Raphael Braud-Mussi, Marine Breuilly, Denis Ressnikoff, Dorian Kauffmann, Elvire Guiot, Emmanuel Faure, Perrine Gilloteaux, Guillaume Gay, Guillaume Jean-François, Jerome Mutterer, Paulette Lieby, Julio Mateos-Langerak, Guillaume Maucort, Marc Mongy, Mylene Pezet, Sotirios Papadiamantis, Théo Barnouin, Mathieu Vigneau

Published 2023-06-16

Licensed MPL-2.0

omero-quay is a microscopy data transport layer between data management tools. Currently, it supports the iRODS — OMERO architecture built at France BioImaging fbi-omero.

Tags: Data Management, OMERO, Exclude From Dalia

Content type: Gitlab Repository

https://gitlab.in2p3.fr/fbi-data/omero-quay


omero-vitessce#

Michele Bortolomeazzi

Published 2024-11-25T10:51:01+00:00

Licensed AGPL-3.0

OMERO.web plugin for the Vitessce multimodal data viewer.

Tags: OMERO, Exclude From Dalia

Content type: Github Repository

NFDI4BIOIMAGE/omero-vitessce