Tuesday 26 January 2027 | 09:00 – 18:30 

Sponsored by:

Bio-techne

A practical introduction to working with spatial omics data

Spatial omics data is large, multimodal and made up of numerous file formats, making it challenging to process, analyse and transfer for sharing using standard tools. 

This hands-on workshop will provide a practical introduction to working with spatial omics data - from metadata and pre-processing through to analysis and FAIR data management. The workshop will also explore the implications of making spatial omics datasets AI-ready. 

Using test datasets, live demonstrations and interactive sessions, participants will explore spatial omics data from sequencing-, image- and antibody-based technologies, including image overlay, segmentation, quantification and annotation.

Genome Dome Speaker

Workshop Leaders

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Speaker profile image for Teresa Zulueta-Coarasa

Teresa Zulueta-Coarasa

Technical Coordination Project Leader, EBI
Speaker profile image for Jan-Philipp Mallm

Jan-Philipp Mallm

Group Leader, Single Cell Open Lab, DKFZ German Cancer Research Center
Speaker profile image for Sam Jackson

Sam Jackson

Programme Manager for Human Genomics & Translational Data, Elixir Europe
Speaker profile image for Melina Velasquez

Melina Velasquez

Bioimaging Data Steward, EBI
Speaker profile image for Cindy Pamela Ulloa Guerrero

Cindy Pamela Ulloa Guerrero

Bioinformatician (Spatial Image Analysis), DKFZ
Speaker profile image for Amonida Zadissa

Amonida Zadissa

Associate Director of Informatics, UK Dementia Research Institute
Speaker profile image for Aybuke Kupcu Yoldas

Aybuke Kupcu Yoldas

BioImage Archive Data Project Leader, EBI
Speaker profile image for Nikolai Hecker

Nikolai Hecker

Senior Bioinformatician, UK Dementia Research Institute
Speaker profile image for Dan Marks

Dan Marks

Bioimaging Bioinformatician, EBI
Speaker profile image for Michele Bortolomeazzi

Michele Bortolomeazzi

Bioinformatician, DKFZ

    What to expect

    • Working with multimodal spatial data using the SpatialData framework 

    • Preprocessing spatial data, including cropping, segmentation and image registration 

    • Annotation and visualisation 

    • Metadata schemas, including JSON, JSON-LD and RO-Crate 

    • FAIR data management and data sharing 

    • Public data repositories and options for sharing spatial datasets 

    • AI-ready data and the implications for spatial omics.

    Who should attend

    The workshop is aimed at researchers working with spatial omics techniques and data formats, including postgraduate and PhD students, data stewards and postdocs. 

    It is suitable for beginners and intermediate users. Some knowledge of the command line is useful, while Python and R skills are helpful but not required. 

    Please note places are extremely limited.

    Your application is subject to approval and availability.

    What you will gain

    Participants will develop practical skills in: 

    • Loading, combining and processing spatial omics data 

    • Spatial data preprocessing and analysis 

    • Working with metadata schemas 

    • FAIR scientific practice 

    • Using curated test datasets 

    • Understanding data sharing options.

    What the conversation will focus on

    09:00 Introduction

    Introduction from IO-FAST, BioImage Archive and BioFAIR UK. 

    09:30 Metadata Structure & AI-ready Data

    Take part in the IO-FAST escape room and explore what it means for data to be AI-ready. 

    11:00 Networking Break

    11:20 DMP, RO-Crates & Metadata Containers

    A hands-on session exploring data management plans, RO-Crates and metadata containers. 

    12:30 Networking Lunch 

    13:30 SpatialData Framework

    Get hands-on with the SpatialData framework and explore how to load, combine and process spatial data. 

    14:30 Image Registration, Segmentation & Annotation

    Explore image registration, segmentation and annotation using Galaxy.

    15:50  BioFAIR UK Toolbox

    Explore tools and workflows from BioFAIR UK. 

    17:00 Submit data to the BioImage Archive

    A hands-on session focused on submitting spatial data to the BioImage Archive.

    18:10 Closing Remarks

    Wrap up discussion.

    18:30 Workshop Ends