That's exciting. From a hackathon in December 2023 (spatialhackathon.github.io/past.html) to a preprint in June 2025 (www.biorxiv.org/content/10.1...) to this publication out today (doi.org/10.1038/s415...).

This was a fun effort from our lab retreat (!) to recreate a "arms-length" benchmark (i.e., one that someone else created) using our Omnibenchmark framework. We all learned a lot in the process ..

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo ago

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation https://www.biorxiv.org/content/10.64898/2026.05.01.722166v1

We are excited to share our latest preprint on spatialFDA, a method for the statistical analysis of spatial omics data. bioconductor.org/packages/3.2...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 6mo ago

Differential co-localisation analysis of multi-sample and multi-condition experiments with spatialFDA https://www.biorxiv.org/content/10.64898/2026.04.13.718197v1

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 11mo ago

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

I'm very excited to share our latest preprint! We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells. We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1

🚀 Spatial Transcriptomics (Imaging) + Spatial-centric analyses by @helucro.bsky.social : the way to truly interrogate tissues!!! 📖 Read our pre-print on human tonsil architecture (full of tonsiLove ♥️) here: doi.org/10.1101/2025...

A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts

The tonsil is a highly compartmentalized organ in which different microanatomical structures orchestrate designated (immune) functions. We use this already well-studied tissue to survey spatial molecu...

doi.org

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data academic.oup.com/nar/article/...

Harnessing the potential of spatial statistics for spatial omics data with pasta

Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba

academic.oup.com

Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561

Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...

arxiv.org

Interested in spatial statistics for spatial omics data? Check out our new resource: pasta. We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome! arxiv.org/abs/2412.01561

pasta: Pattern Analysis for Spatial Omics Data

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...

arxiv.org