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Image Data Services at Euro-BioImaging:

Community efforts towards FAIR Image Data and Analysis Services

Aastha Mathur, Euro-BioImaging ERIC

Defragmentation Training School – NEUBIAS Academy & EOSC-Life 2022

23rd of September, 2022

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ERIC MEMBERS

(16 COUNTRIES & EMBL)

NODES

FACILITIES

173

TECHNOLOGIES

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Euro-BioImaging Offers

Open access to biological and biomedical imaging technologies, with support from expert technical staff

Image data services for analysis, storage and sharing

Training opportunities for everyone

eurobioimaging.eu

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Euro-BioImaging Technologies

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Euro-BioImaging Technologies

Image Data Analysis as a service

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Understanding Image Data

Node: France BioImaging. doi: https://doi.org/10.1101/2021.05.28.446159

Size:

Single experiment -> Multiple Giga to Tera bytes
IDR contains 104 studies and makes up 307Tb

Format:

Diversity in instrumentation, proprietary file formats
For binary data and metadata

Complexity

Multimodal and correlative datasets

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Image data services @Nodes

Image Data Analysis as a Service

External users approach Nodes with their own data

Proof-of-Concept Study

at 10 Nodes

Adapted from: Herbert, S. et.al. BMC Biol 19, 136 (2021). https://doi.org/10.1186/s12915-021-01037-w. Euro-BioImaging Node: France BioImaging

Digital Imaging Multimodal Platform Neuromed

Swedish National Microscopy Infrastructure

Danish BioImaging

French BioImaging Node

Population Imaging Flagship Node Rotterdam

Advanced LM and Medical Imaging Node Brno

Finnish Advanced Light Microscopy

Advanced LM and EM Node Prague

Israel BioImaging

Austria BioImaging/CMI

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Image Data Services @Hub

Coordination with Community initiatives

QuarepLiMi

Global Bioimaging

Representation in European Landscape

European Open Science Cloud Association and Task Force

Projects like EOSC-Life, EOSC Future, BY-COVID, HealthyCloud

Supporting Open Image Data Repositories

BioImage Archive

Image Data Resource

Support Image Data Service provision

Expert Groups

Technical Support

EMPIAR

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Open Image data repositories

Bio-ImageArchive

at EMBL-EBI

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Open Image data repositories

Bio-ImageArchive

at EMBL-EBI

Swedlow, Jason R. et al. “A Global View of Standards for Open Image Data Formats and Repositories.” Nature Methods (December 2021 https://doi.org/10.1038/s41592-021-01113-7.

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Image Data Submission to Open Repositories

Open and FAIR Image data storage

Standardized file

and Metadata formats

Cloud compatible image analysis workflows

Large and information-rich image data

Bugra Özdemir �Image Data Specialist

Isabel Kemmer �FAIR Image Data Steward

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: AI services for Life Science Imaging

Service provision targeted to developers and users

Leveraging pre-existing projects and resources �BioImage Model Zoo

Address technical challenges in:

AI model storage, curation and usage
Easy access to cloud computing services
Annotated image data storage and access

Commitment to sustainable development and use of AI models for extended image data use and reuse

Project coordinated by Euro-BioImaging

Icons from bioimage.io

ai4life@eurobioimaging.eu

www.ai4life.eurobioimaging.eu

@AI4LifeTeam

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Empowering the imaging community with open

and FAIR image data & analysis services