OMERO WORKSHOP Courses@CRG

The Open Microscopy Environment (OME) is an open-source software project that develops tools to enable access, analysis, visualization, sharing and publishing microscopy data. OMERO, a component of OME, is a client-server software, designed to efficiently manage, visualize and analyze microscopy images and associated metadata.

The workshop includes presentations from OME developers and experts in the field as well as open question sessions and multiple hands-on sessions. On Day 1, the OME Team will demonstrate how to manage, analyze and publish your data with OMERO. A hands-on practical experience using OMERO with datasets from a wide range of imaging modalities, including EM, time-lapse, confocal and super-resolution microscopy will be given. Day 2 will cover data analysis with OMERO using third party tools such as FIJI/ImageJ, CellProfiler and potentially napari and ilastik (hand-outs with workflows including Python and R usage with OMERO will be available).

Please note that the workshop is a hybrid event, allowing both on-site and online participation. On-site availability is limited to 18 places, while online participation is limited to 20 participants. Selections for participation will be based on the responses provided during registration. Successfully registered participants will receive additional course details during the first week of October. Any required workshop materials will be shared in advance.
If you would like to learn more about OME visit www.openmicroscopy.org for more info.

Main Goals

By the conclusion of this course, participants will have gained a comprehensive understanding of the following key topics:

FAIR data and ethics in bioimaging
Introduction to OMERO: core concepts, data management, metadata, search, Image Data Resource (IDR)
Working with metadata, File Annotations, Tagging, Key-Value pairs
OMERO.iviewer
Image analysis w/ OMERO: interfacing with Fiji/ImageJ
OMERO.parade
OMERO.figure
Advanced Image analysis w/ OMERO: interfacing with CellProfiler, napari, R, Python, and, possibly, ilastik.
Cloud-based image analysis with Next Generation File Formats (NGFF)

Organizers

Nadia Halidi, CRG
CRG Training

Speakers & Instructors

Jean-Marie Burel, University of Dundee
Petr Walczysko, University of Dundee
Emyr James, CRG
Nadia Halidi, CRG

Target audience and number of participants

The OMERO workshop will cover the use of OMERO and is targeted to experimental and imaging scientists and imaging core facility staff. Prior knowledge in microscopy, scripting and data analysis is not required.

Number of participants, dates and registration

Number of participants: 18 on-site + 20 online
Duration: 7th – 8th November 2023, from 9.00 am - 5.00 pm for both days.

Registration fee:

Presential participation: 250€+VAT
Online participation: 120€+VAT

Presential participation includes: didactic material and access to recordings, coffee breaks, lunches, networking event.
Online participation includes: didactic material and access to recordings.