Project Leads: This email address is being protected from spambots. You need JavaScript enabled to view it. , This email address is being protected from spambots. You need JavaScript enabled to view it.
Challenge Spatial omics technologies enable the mapping of DNA, RNA, proteins, lipids, and metabolites across tissue sections at cellular and subcellular resolution, generating datasets with exceptional potential for reuse across cancer research, neuroscience, developmental biology, infectious disease, and beyond.
However, despite their growing importance and parallels to next-generation sequencing in terms of reuse potential, spatial omics datasets remain fragmented, inconsistently annotated, and difficult to integrate. The absence of dedicated repositories, heterogeneous metadata practices, and limited adoption of existing standards such as REMBI and MIFA currently hinder FAIR data sharing and cross-study analysis.
Aim
To address these challenges, we will advance a unified, community-driven framework for spatial omics metadata and data packaging, building on the momentum of IO-FAST, prior BioHackathon efforts (4th BioHackathon Germany), and collaborations with the BioImage Archive as outlined in the following work packages.
WP1: Definition of a spatial-omics RO-Crate profile
We extend and refine the metadata model for SpatialData that we established in the last BioHackathon and formalize it into a new spatialomics RO-Crate profile, aligned with REMBI and MIFA guidelines and designed to support the full diversity of spatial omics technologies and workflows. We envision this part in a thinkathon style that will provide input for WP2. The framework will integrate with established resources including BioImage Archive, OMERO, SpatialData (scverse), and ArrayExpress, enabling interoperable, machine-readable data exchange across communities.
WP2: Generation of RO-Crates from real-world spatial multiomics data
We will translate the vision of WP1 into practical outputs through a datathon-style collaborative effort. Exemplary research data will be provided to the participants, e.g. from the BIA and not yet publicly available data, and we will work together to create structured RO-Crates using the profile produced in WP1 for these real-world spatial omics data.
WP3: Submission guidelines for RO-Crate submission to the BioImage Archive
In a nextstep we will generate guidelines to submit such RO-Crates to the BioImage Archive. Training material as well as instructions for submission will be prepared and tested.
WP4: Integration of the BioImage Archive submission workflow in Galaxy
The BIA submission guidelines for multimodal spatial omics data as RO-Crates will also be implemented as a prototype Galaxy workflow to integrate FAIR data processing with annotation and submission.
Alignment with the topics and activities of de.NBI (ELIXIR Germany)
This project will provide cutting-edge bioinformatics tools & services and strengthen ties between the German bioinformatics community, international bioinformatics networks, and industry partners. Moreover, the project aligns with multiple ambitions of the ELIXIR 2024-28 Scientific Programme, such as ambition 1.1 and ambition 2.1 (i) by connecting the BioImage Archive to the latest developments in spatial omics technologies through the development and expansion of workflows, metadata standards, tools, and training materials for the FAIR management of multimodal spatial omics data and (ii) by supporting the human and machine usability of multimodal data and metadata together with their deposition in a containerized standard format, respectively.