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

Early prediction of drug uptake by monitoring cell dynamics with deep learning, see our pre-publication at biorxiv.org/content/10.110…

Our #TissUUmaps applications note is out! and it's Open access! We thank OUP Bioinformatics 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

In situ sequencing visualized; don't miss out on Leslie's instructive and beautiful TissUUmaps videos: academic.oup.com/bioinformatics…

Zebrafish screening goes 3D; congratulations to Zhang & Allaou for cool open source HTS tools: osapublishing.org/boe/abstract.c…

Graph Neural Networks decipher in situ sequencing, read more at uu.se/en/news-media/… and febs.onlinelibrary.wiley.com/doi/10.1111/fe…

Unsupervised brain annotation - another nice use of in situ sequencing data, see rdcu.be/b8Kso

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…

Our new approach to decoding in situ sequencing data by deconvolution, ISTDECO, created together with Fred Hamprecht's lab, is now out on bioRxiv: biorxiv.org/content/10.110…. We hope it will come to use!

...and the first paper using spage2vec for finding cell niches in tissue: biorxiv.org/content/10.110…

We're looking for a new team member: join us in the Wählby lab/bio image informatics facility at Uppsala University/SciLifeLab Sweden, see scilifelab.se/career/bioinfo…

I haven't seen an official release so I'm sharing the news here about: github.com/wahlby-lab/Fla… A cool visualization tool for spatial transcriptomics. Easy to install and use. A big thanks to BIIF_Sweden Anna Klemm Carolina Wählby to make this tool available

The TissUUmaps gallery has a new project: The Human Developmental Lung Cell Atlas! 🫁 tissuumaps.github.io/gallery/ Go and take a look at the interactive visualization of the scRNA-Seq, spatial and interactome analyses accompanying the recent preprint: doi.org/10.1101/2022.0…

We (BIIF_Sweden) are hiring! #BioImageAnalysis position - permanent - in Uppsala, Sweden. Join us to work with researchers all over Sweden in their bioimage analysis projects. Closing date: October 21, 2022. forum.image.sc/t/bioinformati…

Deadline is approaching for our #BioImageAnalysis position, permanent, in Uppsala, Sweden. See details: forum.image.sc/t/bioinformati… P.S. this is how our social activities look like - mushroom picking and grilling in the woods around Uppsala. 🇸🇪🌲

Interested in learning how to analyze Spatial Omics Data? The course material from the NBIS Human Cell Atlas et al. course is now fully online. Schedule + Jupyter Notebooks + slides: uppsala.instructure.com/courses/58516/… Recordings: youtube.com/playlist?list=…

We're super proud to see the mapping of the human embryonic lung published in Nature Cell Biology (pubmed.ncbi.nlm.nih.gov/36646791/), with visualization powered by TissUUmaps (hdca-sweden.scilifelab.se/tissues-overvi…). Many thanks to the TM team!!!

Or read our preprint for more details: biorxiv.org/content/10.110…

Want to work at the intersection of morphometry and representation learning for bioimage analysis? We have TWO open postdoctoral positions! Each comes with its own challenging biological question, unique dataset, and exceptional team of collaborators! Details below👇

We are holding a #TissUUmaps webinar next Tuesday, 10:00 am CET. #TissUUmaps is a tool for GPU-accelerated interactive quality assessment and #visualization of large-scale #SpatialOmics and digital pathology data. Register here: scilifelab.se/event/tissuuma…