Omero (19)#
Browsing the Open Microscopy Image Data Resource with Python#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Omero, Python
Content type: Blog
https://biapol.github.io/blog/robert_haase/browsing_idr/readme.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
Content type: Workshop
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
Content type: Collection
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
Content type: Slide, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
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
Content type: Event, Publication, Documentation
OME Documentation#
Licensed CC-BY-4.0
Tags: Omero
Content type: Documentation
OME Event Database#
Tags: Omero, Research Data Management
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
Content type: Github Repository
OMERO Guide#
Licensed BSD-2-CLAUSE
Tags: Omero
Content type: Collection
OMERO documentation#
Licensed UNKNOWN
Tags: Omero
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
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000267/
OMERO walkthrough example#
Licensed BSD-2-CLAUSE
Tags: Omero
Content type: Document
OMERO walkthrough for facility managers#
Licensed BSD-2-CLAUSE
Tags: Omero
Content type: Document
https://omero-guides.readthedocs.io/en/latest/example_facility_manager.html
Omero Deployment examples#
Licensed BSD-2-CLAUSE
Tags: Omero
Content type: Collection
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
Content type: Collection, Video
RDM4mic#
Licensed UNKNOWN
Tags: Research Data Management, Omero
Content type: Collection, Video
User friendly Image metadata annotation tool/workflow for OMERO#
[‘Jens Wendt’]
Tags: Metadata, Workflow, Omero
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
Content type: Slides
[Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO#
[‘Vanessa Fuchs’, ‘Fiona Aphaia’, ‘Christian Schmidt’, ‘Tom Boissonnet’]
Licensed CC-BY-4.0
How to optimize microscopy data management using structured metadata annotations in OMERO, facilitating organization for processing, analysis, and eventual publication. The focus lies on enhancing data findability and usability through object-oriented organization, integrating OMERO with ImageJ/Fiji for image analysis, and implementing community-accepted metadata standards like REMBI to ensure data reproducibility and reusability.
Tags: Research Data Management, Bioimage Analysis, Omero
Content type: Slides
https://zenodo.org/doi/10.5281/zenodo.11109615