Luca Marconato
@LucaMarconato2
Computational scientist at EMBL in the @OliverStegle lab. Deep learning methods and infrastructures for spatial multi-omics data.
The @ChanZuckerberg 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.
happy to see our cell2fate model out at @naturemethods. 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…
Join our next #ICGEBCapeTown International seminar by @LucaMarconato2 from @embl @OliverStegle Lab 📅 25 February 2025 🕛 Noon - SAST 🇿🇦 🔗 email: [email protected] for link to register
Join us in Paris at the @OwkinScience headquarters to work together on spatial omics! #scverse
Owkin and @scverse_team 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…
Owkin and @scverse_team 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!
Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!
I had the opportunity to present my work at BIOINFO 2024 in Gyeongju, Korea. It was great to meet previous colleagues from Heidelberg, @pjb7687 and @hyobin_jeong, and be welcomed by such a vibrant research community!
@LucaMarconato2 is giving a super nice tutorial on SpatialData @ BIOINFO2024, KSBi in Gyeongju, Korea.
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 @g_palla1, Tim, @WVierdag, @ky396, Sonja, ...) who made the project possible. In the pic, @gtcaa and @MKoutrouli from @scverse_team.
🧵 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 @Holtkamp_Eva, as well as @gagneurlab and @OliverStegle.
The recording for today's webinar will soon be available from @EBItraining. Meanwhile here are the notebooks 🤓 github.com/PMBio/spatiald… Thanks again for inviting me and @WVierdag, and thanks to the @scverse_team for the collaborative effort in preparing the notebook.
There’s still time to join tomorrow’s #webinar about SpatialData, an #OpenAccess data framework for spatial omics. Registration is free but essential: ebi.ac.uk/training/event… #bioinformatics #datascience #omics #multiomics #transcriptomics #singlecell #spatialomics
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_team is at #SCG2024 @LucaMarconato2 @gtcaa Thanks to the organising committee. The first day was already EXCELLENT!
First conference, first selfie with some of the incredible @scverse_team core and volunteers! Feeling so grateful to be part of this amazing community pushing the boundaries of single cell analysis. 🖤🤍 #scverse2024
Awesome week last week representing both @napari_imaging 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
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, @QuentinBlampey, @WVierdag, and I will discuss code and use cases for both approaches.
Your reaction to #VisiumHD data analysis may be somewhere between 🤓 and 😵. Wherever you land, join this webinar to see how intuitive and adaptable high-def #spatialtranscriptomics data exploration can be with tools like Bin2Cell & SpatialData. bit.ly/4dJoOpQ
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!
WebAtlas for visualising single cell & spatial data online is out: rdcu.be/dRsKu With @Muzz_Haniffa @BioinfoTongLI @Dave_Horsfall+co, we aimed to open up sc/spatial data to biologists & clinicians without coding experience/infrastructure. Rambling🧵on why this matters
🌟 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_team
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
📢 We're thrilled to announce that we are offering travel grants to cover registration fees and travel expenses for our #scverse2024 conference 🌏Researchers from low- and middle-income countries are especially encouraged to apply! 👉Apply now: scverse.org/conference2024…