Workshop (7)#
Bio-image Analysis ICOB 2023#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Kioto and Taipei 23/24#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Taipei#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bring your own data workshops#
Tags: Bioimage Analysis, Research Data Management
Content type: Workshop
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
Workshop-June2024-Madrid#
Licensed MIT
Tags: Bioimage Analysis
Content type: Workshop, Collection
[Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO#
[‘Vanessa Fuchs’, ‘Fiona Aphaia’, ‘Christian Schmidt’, ‘Tom Boissonnet’]
Published 2024-05-06
Licensed CC-BY-4.0
Description Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. Image processing and analysis is a standard procedure to retrieve quantitative information from biological imaging. Due to the complex nature of bioimaging files that often come in proprietary formats, it can be challenging to organize, structure, and annotate bioimaging data throughout a project. Data often needs to be moved between collaboration partners, transformed into open formats, processed with a variety of software tools, and exported to smaller-sized images for presentation. The path from image acquisition to final publication figures with quantitative results must be documented and reproducible. In this workshop, participants learn how to use structured metadata annotations in the image data management platform OMERO (OME Remote Objects) to optimize their data handling. This strategy helps both with organizing data for easier processing and analysis and for the preparation of data publication in journal manuscripts and in public repositories such as the BioImage Archive. Participants learn the principles of leveraging object-oriented data organization in OMERO to enhance findability and usability of their data, also in collaborative settings. The integration of OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. Moreover, users learn about community-accepted metadata checklists (REMBI) to enrich the value of their data toward reproducibility and reusability. In this workshop, we will provide hands-on training and recommendations on:
Structured metadata annotation features in OMERO and how to use them Types of metadata in bioimaging: Technical metadata, sample metadata, analysis metadata The use of ontologies and terminologies for metadata annotation REMBI, the recommended metadata for biological images Metadata-assisted image analysis streamlining Tools for metadata annotation in OMERO
The target group for this workshop This workshop is directed at researchers at all career levels who have started using OMERO for their microscopy research data management. We encourage the workshop participants to bring example data from their research to discuss suitable metadata annotation for their everyday practice. Who are the trainers (see trainer description below for more details)
Dr. Vanessa Fuchs (NFDI4BIOIMAGE Data Steward, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg)
Material Description Published here are the presentation slides that were used for input from the trainers during the different sessions of the programme. Additionally, a Fiji Macro is published that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, F100Research, https://doi.org/10.12688/f1000research.110385.2 Programme Overview Day 1 - April 29th, 2024 09.00 a.m. to 10.00 a.m.: Session 1 - Welcome and Introduction 10.00 a.m. to 10.30 a.m.: Session 2 - Introduction to the FAIR principles & data annotation 10:30 a.m. to 10:45 a.m.: Coffee break 10.45 a.m. to 12.00 a.m.: Session 3 - Data structure (datasets in OMERO) and organization with Tags 12.00 a.m. to 1.00 p.m.: Lunch Break 1.00 p.m. to 2.00 p.m.: Session 4 - REMBI, Key-Value pair annotations in bioimaging 2:00 p.m. to 2.30 p.m.: Session 5 - Ontologies for Key-Value Pairs in OMERO 2:30 p.m. to 2:45 p.m. Coffee break 2.45 p.m. to 3.45 p.m.: Wrap-up, discussion, outlook on day 2 Day 2 - April 30th, 2024 09.00 a.m. to 09.30 a.m.: Arrival and Start into day 2 09.30 a.m. to 11.30 a.m.: Session 6 - Hands-on : REMBI-based Key-Value Pair annotation in OMERO 11.30 a.m. to 12.30 a.m.: Lunch Break 12.30 a.m. to 1.15 p.m.: Session 7 - OMERO and OMERO.plugins 1.15 p.m. to 2.00 p.m.: Session 8 - Loading OMERO-hosted data into Fiji 2.00 p.m. to 2.15 p.m.: Coffee break 2.15 p.m. to 3.00 p.m.: Discussion, Outlook
Tags: Research Data Management, Omero
Content type: Workshop, Slides, Dataset
https://zenodo.org/records/11109616
https://doi.org/10.5281/zenodo.11109616