Bioimage data management and analysis with OMERO
Location
DKFZ main building (INF 280)
room: D137e (seminar room of the DKFZ library)
Date
May 13th, 9 am to 6 pm.
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.
Since 2023, the DKFZ offers the image data management platform OMERO for all DKFZ researchers.
In this workshop, participants learn how to use OMERO to organize their data and enrich the bioimage data with structured metadata annotations.
We also focus on image analysis workflows in combination with OMERO based on the Fiji/ImageJ software and using Jupyter Notebooks. In the last part, we explore how OMERO can be used to create publication figures and prepare bioimage data for publication in a suitable repository such as the Bioimage Archive.
This workshop consists of four modules. Participants can book individual modules or the whole day (May 13th).
Module 1 (9 am - 10.15 am):
Basics of OMERO, data structuring and annotation
Module 2 (10.45 am - 12.45 pm):
OMERO and Fiji
Module 3 (1.45 pm - 3.45 pm):
OMERO and Jupyter Notebooks
Module 4 (4.15 pm - 6. pm):
Publication-ready figures and data with OMERO
The target group for this workshop
This workshop is directed at researchers at all career levels who plan to or have started to use 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.
Eligibility:
This workshop is directed at researchers from DKFZ and University of Heidelberg
Prerequisites:
Users should bring their laptops and have access to the internet through one of the following options:
- eduroam
- DKFZ Dienst
- VPN connection to their institutional networks to access OMERO
Who are the trainers?
Dr. Riccardo Massei (Helmholtz-Center for Environmental Research, UFZ, Leipzig) - Data Steward for Bioimaging Data in NFDI4BIOIMAGE
Dr. Michele Bortolomeazzi (DKFZ, Single cell Open Lab, bioimage data specialist, bioinformatician, staff scientist in the NFDI4BIOIMAGE project)
Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)
Costs
The workshop is free of charge for both members of Heidelberg University and DKFZ members. Places are limited to 20 participants.
Preparation, prior experience/skills
You should have worked with microscopy data in your research before. A basic knowledge of OMERO is an asset. You could watch the I3D:bio's OMERO training material videos to acquire the basic knowledge (~45 min in total).
Module 2: Basic knowledge of Fiji/ImageJ is an asset. Module 3: Basic knowledge of Python/Jupyter Notebooks is an asset.
Program and more information
Find the preliminary program here: https://indico.dkfz.de/event/973/timetable/#20240513
! Registration ist closed since the maximum number of participants is reached !
Registration is limited to 20 participants per module.
Registration is open until May 3rd, or until the maximum number of participants is reached.
Organizer:
in the course of the NFDI4BIOIMAGE consortium project, and in collaboration with the I3D:bio project.
Hosts:
Dr. Michele Bortolomeazzi (DKFZ Heidelberg)
Dr. Riccardo Massei (UFZ Leipzig)
Dr. Christian Schmidt (DKFZ Heidelberg)
