Looking back on the “BioImaging and the European Open Science Cloud” workshop

Looking back on the “BioImaging and the European Open Science Cloud” workshop

What a great opportunity to engage different stakeholders in a dialogue about Open Science, Open Data and the Sustainability of the EOSC!

Workshop crowd 2023

Scenes from the BioImaging and European Open Science Cloud workshop

The Euro-BioImaging Industry Board,  supported by the EOSC-Life project, organized this 1.5-day workshop with more than 85 participants online and on site in Heidelberg, Germany. We saw a great mix of attendees from our imaging facilities, companies in the imaging sector, EOSC-Life partners, policy and publishing.

The meeting kicked off with a first session on Image Data Analysis as a Service, in which several Euro-BioImaging Nodes shared insights into their capacities for offering these services to users and the workflows and pipelines they support.

Industry Board Coordinator Claudia Pfander and Industry Board Chair Herbert Schaden (ZEISS) officially opened the event, and Herbert  Schaden explained why keeping in control of the ever-increasing amount of imaging data is important for quality research and of high interest for industry. His talk was followed by presentations from different organizations supporting the road towards FAIRification, from the BioImage Archive to national initiatives such as I3D:bio. Speakers then joined the panel discussion on how to facilitate FAIR data generation.

After lunch and a tour of the Imaging Centre, speakers from the Euro-BioImaging Nodes and industry presented challenges & solutions for research data management at core facilities. Martin Tewinkel, EVIDENT Olympus & Industry Board Co-Chair, explored challenges from his perspective on (big) data management.

The next session was dedicated to the European Open Science Cloud, with talks from Ilaria Nardello of the EOSC Association, and presentations on specific Open Science developments that image analysts can use to make it easier to take their data & metadata to the cloud. These tools include the BAND virtual desktop, OME.Zarr and other next generation file formats (NGFF), as well Galaxy and other developments to link the user with different data (analysis) resources. Industry partners also shared some of their big data tools and developments. The day closed with a great panel discussion on how to bring image analysis tools into the cloud and connect to EOSC.

Day 2 opened with use cases from EOSC-Life, sharing results from different cloud-based solutions and tools developed with funding from the project, including success stories from EOSC-Life open calls. Presenters highlighted other EC projects in the wider EOSC landscape that will bring Open Imaging Data sets and tools such as machine learning and BioImage models to researchers.

The concluding panel discussion highlighted the efforts made on the level of the scientific community and policy makers to implement EOSC and explored how institutions, research infrastructures and journals could step up their game to support long-term sustainability.

We were lucky to see so many FAIR data and open science enthusiasts, witness the many fruitful discussion and explore future avenues for collaboration. We would like to thank all the speakers, chairs, participants and organizers for making this such a great event!

This meeting and EOSC-Life have received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087.

Online participation still possible: “BioImaging and the European Open Science Cloud”, 19-20 April 2023

Online participation still possible: “BioImaging and the European Open Science Cloud”, 19-20 April 2023

WS_Header_remote

This exciting 1.5-day workshop, organized by Euro-BioImaging and its Industry Board in collaboration with EOSC-Life, brings together the EOSC-Life community with imaging facilities and companies in the imaging field, to exchange on tools, workflows, data resources and data services with a specific focus on image data.

Topics will include:

  • Image Analysis as a service
  • Image Data Management for imaging facilities
  • FAIR image data and data services
  • Transitioning cloud-compatible tools and services to the EOSC
  • Imaging-related projects and initiative in the wider EOSC landscape

and discuss sustainability, funding models and opportunities for industry in our panel discussion. There will also be an opportunity to join some of the session remotely.

Download the full agenda.

You can now join this meeting remotely! 

09:00 – 10:30

Providing Image Data Analysis as a Service

User projects and access models for image analysis service provision

Coffee Break
11:00 – 11:15 Image data and why it matters to industry
11:15 – 12:30

FAIR data and image data services

Open Image Data repositories, Image Data Infrastructures and Services

Lunch Break
13:00 – 15:15

Image Data Management for facilities

Challenges and solutions for research data management at imaging facilities

Coffee Break
15:45 – 18:30 (incl. break)

Transitioning cloud-compatible tools and services to the EOSC

File formats, workflows, tools and commercial solutions in the cloud

Dinner

all times are CEST

09:00 – 10:15

Imaging in the EOSC landscape – projects and initiatives

EOSC-Life use cases, open call projects and image data projects in the wider EOSC landscape

Coffee Break and poster session
11:00 – 12:30

Panel discussion

Sustainability and long-term perspective for Imaging and EOSC

Lunch and departure

all times are CEST

EU flag
This meeting and EOSC-Life have received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087.
Workshop on “BioImaging and the European Open Science Cloud” 19-20 April 2023

Workshop on “BioImaging and the European Open Science Cloud” 19-20 April 2023

This exciting 1.5-day workshop, organized by Euro-BioImaging and its Industry Board in collaboration with EOSC-Life, brings together the EOSC-Life community with imaging facilities and companies in the imaging field, to exchange on tools, workflows, data resources and data services with a specific focus on image data.

The meeting will be organized as an in person event at Euro-BioImaging in Heidelberg, Germany.

We will hear about topics such as

  • Image Analysis as a service
  • Image Data Management for imaging facilities
  • FAIR image data and data services
  • Transitioning cloud-compatible tools and services to the EOSC
  • Imaging-related projects and initiative in the wider EOSC landscape

and discuss sustainability, funding models and opportunities for industry in our panel discussion. There will also be an opportunity to join some of the session remotely.

Download the draft agenda: Agenda_BioImaging_and_EOSC_v5

 

This meeting requires registration. Please sign up for the event here.

Deadline 1 March!

09:00 – 09:15 Welcome and opening
09:15 – 10:35 Providing Image Data Analysis as a Service

User projects and access models for image analysis service provision

Coffee Break
11:20 – 11:35 Image data and why it matters to industry
11:35 – 13:00 Image Data Management for facilities

Challenges and solutions for research data management at imaging facilities

Lunch Break
14:00 – 15:30 FAIR data and image data services

Open Image Data repositories, Image Data Infrastructures and Services

Coffee Break
16:00 – 18:30 (incl. break) Transitioning cloud-compatible tools and services to the EOSC

File formats, workflows, tools and commercial solutions in the cloud

Dinner

all times are CEST

09:00 – 10:15

Imaging in the EOSC landscape – projects and initiatives

EOSC-Life use cases, open call projects and image data projects in the wider EOSC landscape

Coffee Break and poster session
11:00 – 12:30

Panel discussion

Sustainability and long-term perspective for Imaging and EOSC

Lunch and departure

all times are CEST

EU flag
This meeting and EOSC-Life have received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087.
Virtual Pub Special “Data” Edition – September 9, 2022

Virtual Pub Special “Data” Edition – September 9, 2022

Data is THE hot topic in imaging these days. That’s why we’ve planned a two-part Special Edition of the Virtual Pub to cover the topic of “DATA” in Biological & Biomedical Imaging. These events will each be 2-hours long and will feature short presentations from academics and industry showcasing a range of image data management and analysis solutions for Biological & Biomedical imaging.

Part 1 on 9th July was a great success, and Frances Wong from University of Dundee won the prize for best presentation (as voted by the audience) for her talk “Making BioImage Data FAIR on a Global Scale: The Image Data Resource”. 

Part 2 of our Special Edition Virtual Pub Part 1 on the topic of “DATA in biological and biomedical imaging” will take place on Friday 9th September 2022.

From visualising 3D and 4D data to autonomous microscopy to deep learning – there is something for everyone, so don’t miss out!

With speakers from academia and industry and again a prize for the best short presentation voted for by our audience!

 

13:00-13:10 Welcome and Intro
13:10-13:25 Kinetically consistent data assimilation for plant PET sparse Time Activity Curve signals – Nicola D’Ascenzo, Instituto Neurologico Mediterraneo NEUROMED IRCCS
13:25-13:40 Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome – Yang Zhang, Carnegie Mellon University
13:40-13:55 Exploring high-content microscopic data  – Mike Woerdemann, Olympus Soft Imaging Solutions
13:55-14:10 Learning from users how to gain insights from microscopy images – a case study for applied AI towards autonomous image analysis – Luciano Lucas, Leica Microsystems
14:10-14:25 Spatial plot – new way to understand your microscopy data – Anna Paszulewicz, Imaris – Oxford Instruments
14:25-14:40 Piximi – a deep learning images to discovery tool – Beth Cimini, Broad Institute
14:40-14:45 Voting on the best presentation and Wrap-Up

all times are CEST

 

13:00-13:10

Welcome and Intro

13:10-13:25

Cloud-based interactive image data exploration with the Image Data Explorer – Jean-Karim Hériché, EMBL

13:25-13:40

Making BioImage Data FAIR on a Global Scale: The Image Data Resource – Frances Wong, University of Dundee

13:40-13:55

Multi-beam EM revolution – more data to insight Gerard Rauwerda, Technolution B.V.

13:55-14:10

HIVE- Efficient image data workflows – Peter Zehetmayer, ACQUIFER Imaging GmbH

14:10-14:25

Development and evaluation of an automatic approach for identification and assessment of Tumor-Infiltrating Lymphocytes in Breast Cancer – Valentina Brancato, IRCCS Synlab SDN

14:25-14:40

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers – Riccardo Gambino, Universita degli Studi di Torino

14:40-14:50

Voting for the best presenter & Wrap-up

all times are CEST

Recordings

Virtual Pub Special “Data” Edition – July 8, 2022

Virtual Pub Special “Data” Edition – July 8, 2022

Data is THE hot topic in imaging these days. That’s why we’ve planned a two-part Special Edition of the Virtual Pub to cover the topic of “DATA” in Biological & Biomedical Imaging. These events will each be 2-hours long and will feature short presentations from academics and industry showcasing a range of image data management and analysis solutions for Biological & Biomedical imaging.

From visualising large data sets, storing, managing, curating & sharing data and metadata – to image analysis tools and data repositories, there is something for everyone, so don’t miss out!

Join us this Friday 8th July 2022 for our Special Edition Virtual Pub Part 1 on the topic of “DATA in biological and biomedical imaging”.

With speakers from academia and industry and a prize for the best short presentation voted for by our audience!

Part 2 will take place on 9th September!

 

13:00-13:10

Welcome and Intro

13:10-13:25

Cloud-based interactive image data exploration with the Image Data Explorer – Jean-Karim Hériché, EMBL

13:25-13:40

Making BioImage Data FAIR on a Global Scale: The Image Data Resource – Frances Wong, University of Dundee

13:40-13:55

Multi-beam EM revolution – more data to insight Gerard Rauwerda, Technolution B.V.

13:55-14:10

HIVE- Efficient image data workflows – Peter Zehetmayer, ACQUIFER Imaging GmbH

14:10-14:25

Development and evaluation of an automatic approach for identification and assessment of Tumor-Infiltrating Lymphocytes in Breast Cancer – Valentina Brancato, IRCCS Synlab SDN

14:25-14:40

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers – Riccardo Gambino, Universita degli Studi di Torino

14:40-14:50

Voting for the best presenter & Wrap-up

all times are CEST

 

13:00-13:10

Welcome and Intro

13:10-13:25

Kinetically consistent data assimilation for plant PET sparse Time Activity Curve signals – Nicola D’Ascenzo, Instituto Neurologico Mediterraneo NEUROMED IRCCS

13:25-13:40

Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome – Yang Zhang, Carnegie Mellon University

13:40-13:55

Exploring high-content microscopic data  – Mike Woerdemann, Olympus Soft Imaging Solutions

13:55-14:10

Learning from users how to gain insights from microscopy images – a case study for applied AI towards autonomous image analysis – Luciano Lucas, Leica Microsystems

14:10-14:25

Spatial plot – new way to understand your microscopy data – Anna Paszulewicz, Imaris – Oxford Instruments

14:25-14:40

GliaMorph: A data analysis toolkit to quantify 3D glial cell morphology – Elisabeth Kugler, University College London

14:40-14:55

Piximi – a deep learning images to discovery tool – Beth Cimini, Broad Institute

14:55-15:00

Voting on the best presentation and Wrap-Up

all times are CEST

Virtual Pub Special “Data” Edition – July 8, 2022

Virtual Pub Special “Data” Edition – July 8, 2022

On 8th July 2022, Euro-BioImaging together with the Euro-BioImaging Industry Board will organize the next Special Edition of our Virtual Pub. 

Imaging Scientists and Image Data experts from academia and industry are invited to give a flash presentation on the topic of “DATA in imaging”.

Tell us about your work with image data analysis and image data management – whether it concerns an individual project, general data management strategies or any data or metadata related initiatives that you are involved in. We are looking forward to hearing about your image DATA solutions, which could address:

  • Analysing large data sets, whether it is your own acquired data or data from public repositories
  • Storing, managing, curating and sharing data – from Open data to proprietary or sensitive data
  • Developing image analysis tools for challenging data analysis problems
  • Visualizing and presenting complex data
  • Collecting and standardizing metadata

If you wish to present a 5 min flash presentation on this topic, please submit your abstract below.

Deadline 31 May 5:00 pm CEST.

There will be a prize for the best flash presentation selected by the audience!