Image Data: data management, standard image file format for sharing big image data in the cloud, and image data repositories

Online course

Image Data: data management, standard image file format for sharing big image data in the cloud, and image data repositories

This online course will focus on several key areas including data management of image data using OMERO open source data management solution, cloud-based sharing of image data using next-generation image file format, and image data repositories including Image Data Resource (IDR) and EMPIAR (Electron Microscopy Public Image Archive) as well as new developments within BioImage Archive.

This course was made possible with the funding from Chan Zuckerberg Initiative and the European Union’s Horizon 2020 research and innovation programme under grant agreement No.824087.

Date & Time: 27-29 January, 12:00 - 14:30 CET (11:00 - 13:30 GMT; 16:30 - 19:00 IST; 19:00 - 21:30 SGT; 20:00 - 22:30 JST)

Target audience: This course is open to staff of imaging infrastructures and imaging core facilities (light microscopy, electron microscopy, & biomedical imaging) and image analysts from all over the world.

Number of participants: this course is limited to 50 participants

Apply here:

https://www.surveymonkey.com/r/imagedatacourse

Application deadline:

11 January 2021, 17:00 CET/Applications are now closed

Contents of the course

This 3-day online course (2.5 hours per day including a short break) will include OMERO workshop during day 1, workshop on image file format for sharing big image data in the cloud during day 2, and workshops & lectures on image data repositories, IDR and EMPIAR during day 3.

Workshop: OMERO

OMERO, developed by OME, is an open source, enterprise software platform for image data management and analysis. We will demonstrate data import, organisation, viewing, searching, annotation and publishing. After we cover the basics of OMERO, we will demonstrate manual data processing and automated processing workflows using a range of open source applications running alongside OMERO. We will demonstrate how to integrate OMERO with a variety of processing tools such as ImageJ/Fiji, ilastik, CellProfiler, and how to store analytical results alongside the image data for further analysis or publication.

OMERO workshop will be delivered by members of OME team, Petr Walczysko and Jean-Marie Burel.

https://www.openmicroscopy.org/omero/

Workshop: Towards a community standard image file format for sharing big image data in the cloud

Differences in nomenclature and data formats in BioImaging data inhibit sharing. For users, translating between data formats is imperfect, time-consuming and must be performed repeatedly. Combined with the growing number of formats and advancements in both data volume and complexity, translation is increasingly a bottleneck. We will present recent work on a next-generation format that aims to enable a one-time conversion of datasets to a common format as well as the ability to store them on highly-parallel object storage. We propose that such a next-generation format can revolutionize the sharing of bioimaging data by expediting access and driving discovery. We imagine the same strategy is amenable to image repositories like the BioImage Archive or Image Data Resource, but also a large number of lab and institutional tools.

This workshop will be delivered by Christian Tischer, EMBL Heidelberg and Josh Moore from OME team.

Workshop: Image Data Resource (IDR)

This workshop will provide a complete overview of Image Data Resource (IDR). We will show how to browse and search the data in IDR and briefly explain the submission process. We will then demonstrate how to integrate a variety of image processing tools such as ImageJ/Fiji, ilastik, and CellProfiler in a Jupyter notebook environment and use these for analysis of the images and metadata stored in IDR.

IDR workshop will be delivered by Petr Walczysko and Jean-Marie Burel from OME team.

https://idr.openmicroscopy.org/about/

Lecture: Electron Microscopy Public Image Archive (EMPIAR) & BioImage Archive

The Electron Microscopy Public Image Archive (EMPIAR), a public resource for raw, 2D electron microscopy images will be demonstrated long with the updates within BIoImage Archive that stores and distributes biological images that are useful to life-science researchers.

This lecture will be given by Gerard Kleywegt and Ardan Patwardhan from EMBL-EBI.

https://www.ebi.ac.uk/bioimage-archive/about-us/

https://www.ebi.ac.uk/pdbe/emdb/empiar/

Apply here:

https://www.surveymonkey.com/r/imagedatacourse

Application deadline:

11 January 2021, 17:00 CET

Eligibility criteria:

This course is open to staff of imaging infrastructures and imaging core facilities (light microscopy, electron microscopy, & biomedical imaging) from all over the world