iSCALE www.nature.com/articles/s41...

New online! Imaging-based multimodal profiling of single cells with STAMP

Very proud of these two! Anna Pascual Reguant | Kellie Wise A beautiful collaboration with Jasmine Plummer & Holger Heyn CNAG | St Jude Children’s Research Hospital #STAMP Imaging-based multimodal profiling of single cells with STAMP | Nature Reviews Genetics www.nature.com/articles/s41...

Congrats @hoheyn.bsky.social , @lgmartelotto.bsky.social and team!

Tracing colorectal malignancy transformation from cell to tissue scale www.biorxiv.org/content/10.1...

STAMP brings us non-destructive single-cell profiling without the sequencing www.omic.ly/stamp-brings...

Counting my lucky stars⭐️that not only do I get to work with these amazing scientists Jiwoon Park @christophermason.bsky.social but also give fun @cshlnews.bsky.social lectures together💪.Big thank you to @lgmartelotto.bsky.social Nicholas Navin Julea Vlassakis for uniting this #singlecell #dreamteam

Don’t forget to register to the seminar on June 27 and July 25: GESTALT - Seminar Series June 27 - 2025: Dr. Fei Chen July 25 - 2025: Dr. Hanchen Wang Please visit the Seminar Series Webpage for more information and registration: globalspatial.org/seminar-seri...

Awesome work by awesome people! Endless innovation by @lgmartelotto.bsky.social and team. Can’t wait to try it 💪

STAMP:Single cell Transcriptomics Analysis & Multimodal Profiling-cheap scprofiling-MILLIONS of cells, multimodal, pertubation expts & tissue atlas'ing at scale.Thx to brilliant colleagues @lgmartelotto.bsky.social Holger Heyn & our amazing teams. @cellpress.bsky.social www.cell.com/cell/abstrac...

“STAMP allows us to profile a million cells simultaneously, compared to tens of thousands typical of current methods, making it far more scalable,” said @jasmineplummer.bsky.social, PhD, St. Jude Center for Spatial Omics director.

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social www.cell.com/cell/fulltex...

👩‍🔬The lead authors of the study are Dr. @pascual-reguant.bsky.social & Emanuele Pitino (CNAG) with Felipe Segato Dezem (@stjuderesearch.bsky.social) Corresponding authors: Dr. @hoheyn.bsky.social (CNAG), Dr. @jasmineplummer.bsky.social (St. Jude) & Dr. @lgmartelotto.bsky.social (Univ. of Adelaide)

tidyplots is an R package to generate publication-ready plots for scientific papers tidyplots.org/ #rstats

Excited to share a new algorithm that we have been working on over the last year. 💡 idea is to extend mutual nearest neighbors for #spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄 Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪

It is so nice to spend quality time with your favorite people in the world before the end of the year! @jasmineplummer.bsky.social @alexswarbrick.bsky.social At Multi-Ome 2024 Btw: my best pic yet!

Happy to see our Damsel @bioconductor.bsky.social package published in Bioinformatics. Great work putting together this DamID sequencing and package from student Caitlin Page. Thanks to collaborators too @lonsbio.bsky.social academic.oup.com/bioinformati...

#singlecell to #spatial converts .. means a lot more python than r… great tool to help transition academic.oup.com/bioinformati...

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics #SingleCell 🧬🖥️ academic.oup.com/bib/article/...

Whole-brain spatial transcriptomics 🧪🤯 Congratulations to all the team @peruhlen.bsky.social

The Human Cell Atlas is yielding detailed maps of human tissues and systems throughout life, along with methods to handle single-cell data. Four scientists reflect in Nature on how the project is transforming our understanding of human biology. 🧪

Cool tool for segmentation free #spatial #transcriptomics onlinelibrary.wiley.com/doi/10.1002/...

The second preprint presents an experiment workflow and a broadly applicable computional framework to integrate sequencing-based and imaging-based spatial omics data for the SAME tissue slide to construct a single cell spatial omics atlas. www.biorxiv.org/content/10.1...

#LocationLocationLocation! Theis &co share @ Nature Methods @natureportfolio.bsky.social a probe set selection pipeline to identify cell types using spatial single cell omics! And it comes with its Python package (github.com/theislab/spa...) 😌💪 👉 doi.org/10.1038/s41592-024-02496-z

🚀 Ready to learn about Spatial Omics? Learn from @stemang.bsky.social & @lgmartelotto.bsky.social in this hands-on R/Bioconductor course! Master imaging vs. sequencing methods, experimental design & tidy data principles for cutting-edge spatial omics analysis www.physalia-courses.org/courses-work...

#Crispr and #spatial all in one … yes please… perturb-dbitseq. www.biorxiv.org/content/10.1...

This is why we are all in this field…to see, and one day to be able to produce work like this. Patho-DBiT-seq www.cell.com/cell/fulltex...

Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati... 13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...

Check out our new tools for #SpatialTranscriptomics. It's called Sainsc: onlinelibrary.wiley.com/doi/10.1002/.... #Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...