Jolene has done amazing work here. QUICHE is a dramatic improvement over cell neighborhood algos we've used in the past, gets immediately to a common question we ask often: how does spatial structure between two patient groups differ?

Stoked about our upcoming scverse and Owkin hackathon, focused on spatial omics data analysis. 📅 March 17-19, 2025 📍 Owkin office, Paris Apply now: lnkd.in/eWDD4uyc Details below.

Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!

Helena Lucia Crowell Estella Dong Kevin Yamauchi Artür Manukyan Dario Righelli Louise Deconinck Vincent Carey Should you use R (Bioconductor) or Python (scverse) for spatial omics? Ideally, you won’t have to choose one. We are working toward making cross-language analysis pipelines possible based on the...

... common SpatialData Zarr format. We are still early stage, but now you can start plotting SpatialData objects with ggplot, or use the spatialdata-io readers from R.

With today’s and next releases (PyPI), we are rolling out the new features developed during the hackathon. Find the full list of what we worked on in this pre-print: osf.io/preprints/bioh… Thank you to all of the participants and to CZI Science for funding this wonderful event.

The latest #scverse hackathon on spatial omics has really been a blast! A small example: Day 2 was planned from 8:30 am to 6:00 pm, yet we had people hacking until 9-10 pm! (pics 2-3). Looking forward to the new in-person event!

Join us in Paris at the Owkin headquarters to work together on spatial omics! #scverse

Our team SpaceAix won the Special Jury Award at the Paris Spatial+AI Hackathon for Glioblastoma. We made AI pipelines to integrate HE, single-cell, spatial, clinical data.Thanks Owkin Servier Thomas Clozel for being wonderful hosts, sharing data+resources to benefit patients!

We would like to thank Thore Buergel from Pheiron again for presenting at the Berlin Bioinformatics Social meeting CompBioBerlin. Check out Thore's work where they integrate massive biobank for inferring casual insight on targets! pheiron.com. MDC-BIMSB Max Delbrück Center

Interested in single cell genomics but need help getting started? Check out my lab's Single Cell Genomics Day on April 25. Talks will feature recent exciting computational and experimental advances and will be live-streamed at satijalab.org/scgd. Please RT/spread the word!

Interested in exploring Vevo Therapeutics’s massive Tahoe-100M single-cell perturbation dataset? #Scanpy now supports out-of-core analysis, powered by Dask—allowing you to seamlessly work with a single huge AnnData object without loading everything into memory. 🔗 theislab.github.io/vevo_Tahoe_100…

STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance biorxiv.org/content/10.110…

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows nature.com/articles/s4159… #spatialtranscriptome

ETH Zurich’s DeepSpot is a breakthrough in spatial transcriptomics. It predicts gene expression from routine H&E slides for scalable, cost-effective analysis. 👇

Happy to announce the first public release of rolv app. Rolv is your AI-powered research assistant for life sciences! It provides a new way to accelerate data analysis, literature reviews, and hypothesis generation. ✨ Core Features: AI-Assisted Data Analysis: Ask data analysis

⭐ Please consider joining our Single Cell Genomics group as Computational PhD Student! ♦️ We are hiring 2 Computational Biology PhD students to lead projects in immuno-oncology (IO) and immune-mediated inflammatory diseases (IMID), respectively. In #IO, we aim to delineate