We celebrate the end of our three-day 🚀hackathon🚀 on spatial omics tools and methods in #Ghent #Belgium. A big thanks to all of the researchers across Europe. Check out our final slide deck and code! docs.google.com/presentation/d… github.com/saeyslab/VIB_H… #SpatialOmics24

🌟 Join me at #Scverse2024 for the "GPU-Accelerated Single-Cell Analysis with rapids-singlecell" workshop! 📍 Munich, Germany 🗓️ Sept 10-12 Don't miss out! Register now: [scverse.org/conference2024/] Explore the toolkit: [github.com/scverse/rapids…] scverse

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

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!

Which is more convenient: viewing the "Visium HD bins" as a collection of millions of vector geometries, or as a large multi-channel image given their grid arrangement? In the webinar, Quentin BLAMPEY, Wouter-Michiel Vierdag, and I will discuss code and use cases for both approaches.

Awesome week last week representing both napari and #SpatialData @scverse at @EuroSciPy2024. It was great to meet maintainers and contributors to the libraries we use. Also grateful for the opportunity to have a flashlight talk on #numpydantic and a little bit on #LinkML

First conference, first selfie with some of the incredible scverse core and volunteers! Feeling so grateful to be part of this amazing community pushing the boundaries of single cell analysis. 🖤🤍 #scverse2024

Happy to share Novae, our new foundation model for spatial transcriptomics data 💫 Load a pre-trained model and start using Novae in two lines of code! biorxiv.org/content/10.110… github.com/MICS-Lab/novae

scverse is at #SCG2024 Luca Marconato Danila Thanks to the organising committee. The first day was already EXCELLENT!

🧵 1/9 Delighted to announce that #DeepRVAT is out today in Nature Genetics! Here's a recap of our tweetorial from the preprint, with updates for some exciting new results. It's been a joy to work with Eva Holtkamp, as well as gagneurlab and Oliver Stegle.

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.

In September, I represented the SpatialData team at SCG 2024. I was honored to receive a best poster award; I want to thank my team (in particular Giovanni Palla, Tim, Wouter-Michiel Vierdag, Kevin Yamauchi, Sonja, ...) who made the project possible. In the pic, Danila and Mikaela Koutrouli from scverse.

I had the opportunity to present my work at BIOINFO 2024 in Gyeongju, Korea. It was great to meet previous colleagues from Heidelberg, Jeongbin Park and Hyobin Jeong, and be welcomed by such a vibrant research community!

Owkin and scverse are excited to announce their upcoming hackathon, focused on spatial omics data analysis. 📅 March 17-19, 2025 📍 Owkin office, Paris If you are a bioinformatician interested in spatial biology, this is your chance to make a contribution to open-source

The latest #scverse hackathon on spatial omics has really been a blast! A small example: Day 2 was planned from 8:30 am to 6:00 pm, yet we had people hacking until 9-10 pm! (pics 2-3). Looking forward to the new in-person event!

Join us in Paris at the Owkin headquarters to work together on spatial omics! #scverse

Join our next #ICGEBCapeTown International seminar by Luca Marconato from EMBL Oliver Stegle Lab 📅 25 February 2025 🕛 Noon - SAST 🇿🇦 🔗 email: [email protected] for link to register

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…

The Chan Zuckerberg Initiative Cell Science Meeting in Chicago just concluded. I had the opportunity to present the latest advancements in spatial omics within the #scverse ecosystem, highlighting our efforts to scale our infrastructure in preparation for the datasets of tomorrow.

💰 Travel Grants Available for scverse conference 2025! 💰 Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍 🧵 #scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant