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
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
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
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
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
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
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
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
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
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
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
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
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 - 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
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
OME Documentation#
Licensed CC-BY-4.0
Tags: OMERO, Include In Dalia
Content type: Documentation
OME Event Database#
Tags: OMERO, Research Data Management, Exclude From Dalia
Content type: Collection, Event
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
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
OMERO Guide#
Licensed BSD-2-CLAUSE
Tags: OMERO, Include In Dalia
Content type: Collection
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
OMERO documentation#
Licensed UNKNOWN
Tags: OMERO, Include In Dalia
Content type: Documentation
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
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
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
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
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
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
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
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
RDM4mic#
Licensed UNKNOWN
Tags: Research Data Management, OMERO, Exclude From Dalia
Content type: Collection, Video
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
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
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
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
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
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