SpatiaLondon is built around four interconnected activities — from focused community discussions and hands-on training through to open standards and a flagship annual symposium. Click an activity to see its schedule.
Data Clubs
Focused, small-group discussions on the shared bottlenecks that slow spatial transcriptomics research. Each session is led by a network member and produces actionable notes feeding into our living, community-owned bottlenecks log. Sessions rotate across partner institutions in hybrid format.
Schedule — 6 sessions
Session 1 — High Dimensionality & Complex Data Structure
Lead: Gopal Krishna Ramadas Dhondalay (KCL)
- Curse of dimensionality and its impacts on clustering and neighbourhood graph construction
- Joint modelling of expression and spatial autocorrelation
- Trade-offs between PCA/UMAP and spatially aware methods such as graph-based smoothing
Session 2 — Batch Effects Across Slides, Platforms & Timepoints
Lead: Reuben Asher (UCL)
- Alignment of spatial datasets while preserving local spatial structure
- Overcorrection risk: removing real biological gradients
- Limitations of scRNA-seq integration methods when applied spatially
Session 3 — Resolution Limits & Segmentation Errors
Lead: Pietro Andrei (Francis Crick)
- Deconvolution algorithms for spot-based data
- Sensitivity of downstream DEGs to segmentation noise
- Boundary effects in dense tissues
Session 4 — Lack of Ground Truth for Benchmarking
- Reliance on simulated datasets vs real biological validation
- Metrics: ARI, NMI, and spatial coherence scores
- Difficulty benchmarking domain detection and cell–cell interaction inference
Session 5 — Multi-Modal Integration Challenges
Lead: Diana Perira (QMUL)
- Mapping dissociated single-cell data back to spatial coordinates
- Latent variable models vs anchor-based mapping
- Handling modality-specific noise and sparsity
Session 6 — Scalability & Computational Bottlenecks
Lead: Anthony Baptista (KCL)
- Sparse matrices, on-disk formats, and parallelisation
- GPU vs CPU trade-offs in image and transcript integration
- Algorithmic bottlenecks in neighbourhood graph construction
- Standardisation across platforms and reproducible benchmarks
Session 1 will be hosted at KCL. Venues and dates for remaining sessions will be confirmed and announced via the mailing list.
Training Workshops
Hands-on workshops teaching researchers and digital Research Technical Professionals how to work with spatial omics data in an interoperable, AI-ready, and FAIR-compliant way. Held monthly at HAB, Guy’s Campus, KCL. Places are limited — priority given to partner institution participants and early-career researchers.
Schedule — October 2026 to March 2027
Workshop 1 — Introduction to Coding for Spatial Biology Optional
- A gentle introduction to the programming tools used in spatial biology workflows. Recommended for those new to computational analysis.
Workshop 2 — Introduction to Spatial Biology: Data Acquisition & QC
- Overview of spatial transcriptomics platforms and technologies, from data acquisition through to quality control fundamentals.
Workshop 3 — Segmentation, QC, Batch Correction & ROIs
- Cell and tissue segmentation, quality control pipelines, batch correction strategies, and region-of-interest analysis.
Workshop 4 — From 3D to 2D: Cell Typing, Annotations & Neighbourhoods
- Cell type annotation workflows, moving between 3D tissue architecture and 2D representations, and neighbourhood analysis.
Workshop 5 — Downstream Analysis: Neighbourhoods & Networks
- Advanced downstream analysis including neighbourhood enrichment, cellular network inference, and spatially resolved interaction analysis.
Workshop 6 — AI Models & Spatial Biology
- Applications of machine learning and AI models in spatial biology — from foundation models to spatially aware deep learning approaches.
To register your interest email hab@kcl.ac.uk or subscribe to the mailing list for registration announcements.
Standards & Methods
Funded by the DisCouRSE+ programme, we are co-creating an open Spatial Methods Guide and a one-page Checklist that make best practice clear and usable across common platforms (Xenium, CosMx, Visium HD). All materials will be openly licensed (CC-BY/MIT) and published on GitHub with a DOI.
Spatial Methods Guide & Checklist — in development
The guide will cover minimal metadata and FAIR handover, quality control, reproducible pipelines, governance and sharing, and low-carbon compute.
Subscribe to be notified when v1.0 is published with DOI.
Subscribe to be notified when v1.0 is published with DOI.
Symposium
The SpatiaLondon Symposium brings the full London spatial biology community together for keynote talks, flash presentations, poster sessions, and networking — with dedicated space for early-career researchers and first-time presenters.
SpatiaLondon Symposium 2027
Registration and call for abstracts will be announced via the mailing list. Subscribe to be the first to know.
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