[Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO
Creators: name: Fuchs, Vanessa Aphaia Fiona
name: Schmidt, Christian
name: Boissonnet, Tom
Publisher: name: Zenodo
Year: 2024
Subjects: FAIR
OMERO
Workshop
Open Educational Resources
Ontologies
REMBI
Metadata
Key-Value Pairs
Tags
Fiji
Bioimaging

description: 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
description: This work is funded the Deutsche Forschungsgemeinschaft (DFG, German  Research Foundation) - under the National Research Data Infrasstructure – NFDI 46/1 – 501864659- under the project I3D:bio, grant number 462231789