🚀 Our paper on spatialproteomics is now out in @natmethods.nature.com Spatialproteomics is a Python package for analyzing highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem. www.nature.com/articles/s41...

How do >1600 transcription factors (TFs) bind across hundreds of cell types? Experimentally profiling every combination isn't practically doable. But relying on DNA motifs isn't a great alternative -- they lack both sensitivity and specificity. #Genomics #GeneRegulation 👇

Cell segmentation for spatial transcriptomics isn’t so easy, right? We thought so too. A wonderful group lead by @garybader.bsky.social and @rgottardo.bsky.social put together a perspectives piece on where things stand, the challenges, and what’s next. Check it out: arxiv.org/pdf/2606.09675

Just analysed 48 single nuclei samples with scprocess and went from fastq files to cell-type annotation in a couple of weeks!! Really recommend this pipeline developed by @willmacnair.bsky.social and team, thank you for making it public!! github.com/marusakod/sc...

GitHub - marusakod/scprocess: Snakemake pipeline for processing single cell data

Snakemake pipeline for processing single cell data - marusakod/scprocess

github.com

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 · 3mo 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 · 4mo 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

Join us next week for the second free webinar in our spatial transcriptomics series: www.ebi.ac.uk/training/eve... Daria Lazic (EMBL Heidelberg) presents 'Imaging-based spatial transcriptomics: methods, preprocessing, and quality control' on 25 February | 14:30 UK time.

Omnibenchmark (omnibenchmark.org): transparent, reproducible, extensible and standardized orchestration of solo and collaborative benchmarks arxiv.org/abs/2409.17038 🧬💻🧪

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 · 10mo ago

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

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