Next iteration of in situ sequencing is now out as a preprint bioRxiv. We show improved robustness and flexibility of Hybridization-based in situ sequencing (HybISS) on human brain sections with goals towards a spatial human cell atlas.🧠🔬🧬 disq.us/t/3lupqeo

Two open positions (senior + postdoc) in digital image processing with life science applications in my lab at Uppsala University and SciLifeLab: uu.se/en/about-uu/jo… uu.se/en/about-uu/jo… #WahlbyLab #SciLifeLab

Dear friends, may I suggest you follow the one and only, Carolina Wählby . Joakim Lindblad Beth Cimini 🔬💻 📊 Ricardo Henriques Allen Goodman Anna Klemm MatsNilssonLab Markus M. Hilscher Philip J Harrison @GabrielePartel Pete Bankhead @npielawski SciLifeLab Emma Lundberg Rita Strack CellProfiler

L’unità e il lavoro di squadra sono da sempre i principi su cui si fonda la nostra Forza Armata e, in questo momento più che mai, sono fondamentali. Ed allora, come fanno da sempre le Frecce Tricolori ‘facciamo squadra’ 💪🏻, uniamo le forze 🏋🏻, insieme ce la faremo 🇮🇹!

Teaching online the next few weeks? Check out this Coding & Vision 101 Educational Lecture Series includes 12 videos produced by the Allen Institute for Brain Science to serve as an educational resource for the community. youtube.com/playlist?list=…

Phew, so much work! But finally submitted another paper. If you want to hear me embarrassing myself speaking english go to tissuumaps.research.it.uu.se/howto.html You can also visit if you are curious about our work! #TissUUmaps #geneExpression #spatialTranscriptomics

A scalable embedding algorithm that clusters scRNA-seq data by optimizing a clustering objective function and enables batch effects removal, from Mingyao Li Dept. of Biostatistics, Epidemiology & Informatics Katalin Susztak go.nature.com/35ZuhXt

Our #TissUUmaps applications note is out! and it's Open access! We thank @OUPBioinfo for a friendly process, the reviewers for their kind comments and constructive criticism, UppsalaUniLib for the OA agreements and European Research Council (ERC) for the funding. Carolina Wählby @GabrielePartel

🔬 Different microscopes output different image file formats making it challenging for scientists to compare. That's why we developed an #openscience software to help level the playfield. #microscopy alleninstitute.org/what-we-do/cel…

Hybridization-based in situ sequencing is now out on @NAR_Open! Fantastic work guys! @dgyllborg Xiaoyan Qian Markus M. Hilscher academic.oup.com/nar/advance-ar…

Great collaboration with Markus M. Hilscher and MatsNilssonLab! Take a look at the brain regions in our interactive viewer for spatial gene expression tissuumaps.research.it.uu.se/spatialcompart… Carolina Wählby Leslie S. Anna Klemm Giorgia Milli

#PhDdone ;)

I'm super proud to announce that our fantastic PhD students won the AI Sweden 'Adipocyte Cell Imaging Challenge': ai.se/en/news/ai-swe…

Come by my poster at #I2K2020 if you want to learn about how to visualize millions of in situ sequencing gene expression points and how you can use them to learn more about your cell types and spatial compartments! @Vi2UU Carolina Wählby Gabriele Partel

If you missed today's talk for in-situ RNA sequencing by MatsNilssonLab youtu.be/aQSSTr9E61M co-organized by Rong Fan

#CoMIR: Contrastive Multimodal Image Representation for Registration @ #NeurIPS2020 – solving your #multimodal #imageRegistration needs by first translating images to a shared virtual modality where the task is easier: github.com/MIDA-group/CoM… proceedings.neurips.cc/paper/2020/has… #MIDAgroup

Excited to share our data&model zoo sfaira: We provide 233 data sets, 55 organs, 3.1M annotated cells together with 8 pre-trained model classes, to replace manual workflows, facilitate method benchmarking & extension w private data. biorxiv.org/content/10.110… github.com/theislab/sfaira

The latest version of umap-learn is now out. Version 0.5 includes some major new features, including ParametricUMAP, DensMAP, AlignedUMAP, model composition, and model updating. Thank you to everyone who contributed! 1/14

Super-neat approach for fluorescence decoding of MERFISH, SeqFISH, ISS and any other image-based spatial transcriptomics technology!

So happy to see that spage2vec works so well to find cell niches from spatially multiplexed single cell data! Congrats Leslie S. (and all others) for this very interesting work!