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: WS_draft_program_v1

More information and registration here in January 2023!

 

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 – 10:30 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
11:00 – 12:30 Panel discussion

Sustainability and long-term perspective

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!

Special “Cold” Edition of the Virtual Pub!

Special “Cold” Edition of the Virtual Pub!

On 10th December 2021, Euro-BioImaging together with the Euro-BioImaging Industry Board will organize another special edition of the Virtual Pub. This time, owed to the season of the year, we will focus on the theme of “COLD” and evoke a little celebratory spirit with exciting talks from our community.

 

Please join us on Friday, December 10th at 13:00 CET!

Join via internet:

https://us02web.zoom.us/j/760003029  

 

AGENDA

TimeTitlePresenter
13:00 - 13:05Welcome
13:05 - 13:20Cryopreserved cells regeneration monitored by atomic force microscopy and correlated with state of cytoskeleton and nuclear membraneJan Přibyl,
CEITEC,
Masaryk University
13:20 - 13:35Potential interplay between cold receptor (TRPM8) and the hemodynamic function during anesthesia and hypothermiaMathilde Boisseau,
INSERM
13:35 - 13:50Cool Images with or without Cooling of the Image Sensor?Gerhard Holst,
Excelitas PCO GmbH
13:50 - 14:05Cold exposure affects the quantification of brown adipose tissue volume and activity by 18F-FDG-PET-CTFrancisco M. Acosta,
University of Turku
14:05 - 14:20Cryogenic super-resolution fluorescence imaging in vitrified specimensRainer Kaufmann,
University of Hamburg
14:20 - 14:30Wrap-up & Conclusion

“Living Collaborations” – webinar on 28 Oct 2021 10am CEST

“Living Collaborations” – webinar on 28 Oct 2021 10am CEST

collaborations_hands

Knowledge exchange, training, co-development and open innovation are often cited as key objectives of academia-industry collaboration, but making the relevant contacts and implementing joint projects requires a good network and defined areas of collaboration. 

We would like to invite you to a webinar sharing examples form our Euro-BioImaging network on different areas for collaboration, and discuss with a panel of facility and company representatives how to make these collaboration come alive.

Find out more and register for the event.