Interested in Smart Microscopy? Join the discussion!

Interested in Smart Microscopy? Join the discussion!

Towards community standards in Adaptive Feedback Microscopy

Adaptive Feedback or ‘Smart’ Microscopy is an emerging field that is gaining importance e.g. in the context of large image data acquisitions and investigation of rare events by creating a feedback between the 4-dimensional detection of specific features to be imaged and tailored acquisition workflows. While there are several software solutions for microscopy control that can be used to implement smart-microscopy workflows, there is no reference specification on what functionalities are needed, or how these workflows could be implemented.

After the successful 2022 Euro-BioImaging/ Industry Board workshop, we set up a working group with participants from academia and industry to establish such a standard specification and to put forth desired workflows, then in dialog we find functionality requirements, reach common terminologies, and share these with the community for feedback and improvement. Ultimately, we want to help facilitate the development of smart-microscopy applications, and enable their execution across imaging-systems with similar modalities.

The group was first presented at ELMI 2023. More information can be found on Zenodo. In the second half of 2023, we aim to develop several use cases and collect feedback from the community (via GitHub).

Are you interested to learn more or join the discussion? Please sign up here.

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.