#preprint alert 🚨 Can Large Language Models solve common #BioImageAnalysis coding tasks? And which #LLM performs best? 🙃🤓 Great collaboration with Christian Tischer, Jean-Karim Hériché, nico scherf and ... YOU? 🔬🖥️🅰️ℹ️🤝🚀 biorxiv.org/content/10.110…

I am excited to announce the new @MetaAI Segment Anything Model 2 (SAM) for videos as a napari🔬 plugin. Try it! github.com/JoOkuma/napari…

🚨𝐇𝐞 𝐋𝐚𝐛 job opportunity UC San Francisco 🚨: I'm hiring TWO postdocs - an experimentalist and a computational biologist. Join us to use cutting-edge single-cell and spatial technologies to unravel the mysteries of human tissues. opportunities.ucsf.edu/content/open-p…

Spatial data has its challenges to be visualized specifically together with single cell data, our neighbor labs Omer Ali Bayraktar Muzlifah Haniffa, and the team Tong LI 李彤 Dave Horsfall have cracked it with WebAtlas. nature.com/articles/s4159…

The NFDI4BIOIMAGE proposal is now on Zenodo! 🎉 With thanks to Christian Schmidt for herding the authorial cats and to said cool cats for making all of this happen. bit.ly/n4bi-proposal #bioimaging #rdm #FAIR #NFDI

WebAtlas for visualising single cell & spatial data online is out: rdcu.be/dRsKu With Muzlifah Haniffa Tong LI 李彤 Dave Horsfall+co, we aimed to open up sc/spatial data to biologists & clinicians without coding experience/infrastructure. Rambling🧵on why this matters

Out last week from the Bayrakter and Hannifa labs! WebAtlas offers user-friendly sharing and interactive navigation of integrated single-cell and spatial transcriptomic datasets. nature.com/articles/s4159…

It's great to be at #EMC2024 and learn more about all the different microscopy techniques. I will be presenting a poster on Fractal, our framework for scalable image analysis in OME-Zarrs on Wednesday afternoon (poster 58), feel free to stop by if you're there as well!

In case you missed this: we are hosting the #OME_NGFF_workflows_hackathon in November! Save the date and come have some bioimage analysis fun with us in Zürich!

Interactive analysis is considered one of the most challenging bioinformatics steps. 💡Seqera's #DataStudios makes this easier by bringing reproducible, containerized and interactive analytical notebook environments to your data in real-time. 👉Dive in: seqera.io/blog/data-stud…

Kota Miura is #ImagingTheFuture by working toward a more profound understanding of biology through increased access to bioimage analysis education

The recording for today's webinar will soon be available from EMBL-EBI Training. Meanwhile here are the notebooks 🤓 github.com/PMBio/spatiald… Thanks again for inviting me and Wouter-Michiel Vierdag, and thanks to the scverse for the collaborative effort in preparing the notebook.

Super stoked that Jordão Bragantini 's napari🔬 plugin for Meta's Segment Anything Model 2: napari-sam2, as well as our cell tracking software ultrack were showcased during Chris Cox's Keynote at Meta's Connect 2024. Jordao and I were in the audience; it was great fun!

Out today from the Gehlenborg lab! Vitessce is an interactive web-based visualization framework for exploration of multimodal and spatially resolved single-cell data. nature.com/articles/s4159…

Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.

Happy to share this summary of my recent work in the lab, piloting the use of PAXgene-fixed samples for 10x Xenium. Hoping to be able to make use of PFPE samples for cool genomics-transcriptomics

happy to see our cell2fate model out at Nature Methods. It is a completely new take on RNA velocity to disentangle complex cell trajectories from scRNA data & we have some very cool applications coming up! nature.com/articles/s4159…

Out today from the Singh and Way labs! Pycytominer is a user-friendly, open-source Python package that carries out key bioinformatics steps in image-based profiling. nature.com/articles/s4159…

The FIRST GloBIAS conference is happening in Kobe, Japan, and we launched the webpage and the registration form. Training school, Hackathon, Taggathon, and Symposium with talks, posters, open-source software lounge, call-4-help on stage! #BioimageAnalysis #GloBIAS

We have developed DELIVR, a user-friendly deep-learning pipeline for automatically detecting and analyzing cells from whole-brain images to map neuronal activity via cFOS. DELIVR uses virtual reality to substantially accelerate the generation of training data and is accessible to