We're excited to release a #scanpy update for the analysis and visualization of #spatialTranscriptomics data, focussing on 10x Genomics Visium and MERFISH, thx Giovanni Palla. Tutorial at nbviewer.jupyter.org/github/theisla… Support for different data types and integration with #scRNAseq soon!

Our work on differential expression (DE) analysis downstream of trajectory inference (TI) is now published! A small thread on a few changes we have added since the preprint. nature.com/articles/s4146…

With widespread adoption of single-cell-omics technologies, developmental biologists are increasingly relying on the use of “gene expression trajectories” to study cell differentiation. What is the difference between a trajectory and a lineage? (1/4)

#Opensource software is essential to science. That’s why we’re awarding 23 grants to support open source tools that accelerate biomedical research and serve the larger scientific community. chanzuckerberg.com/newsroom/award…

Happy to be part of this project. Congratulations to @rcannood and Wouter Saelens

Generalizing RNA velocity to transient cell states through dynamical modeling go.nature.com/30m2ak0

The Nature Immunology perspective Martin Guilliams and I wrote is out. We ask does tissue imprinting restrict macrophage plasticity? Using the lung as a case study we propose a revised model of macrophage plasticity. nature.com/articles/s4159…