After years of hard work we're thrilled to announce our new Nature Methods paper: Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem. Another milestone for everyone working with Giotto! www.nature.com/articles/s41...

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. 🔗 www.biorxiv.org/content/10.1...

#EuroBioC2025 just started at @prbb.org in beautiful Barcelona. Looking forward to meeting friends and collaborators to discuss new generation of data structures and file formats for spatial/single-cell biology.

Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future. Thanks to my amazing team and collaborators—this is our award! 🙌 📽️ Keynote: Atlases, AI & virtual cells 📝 doi.org/10.1093/bioi...

🚀 Reminder: Bioconductor Developer Forum is this Monday! 🧵 Topic: R & Rust in Bioinformatics 🗓️ July 28 | 🕚 11am EDT / 5pm CEST 🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0... #Bioconductor #RStats #RustLang #OpenSource

We’re happy to share our new preprint form @N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat lab! 🎉 🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation. 🔗 biorxiv.org/content/10.1...

🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem! www.biorxiv.org/content/10.1...

🔬Hands-on workshops kick off the Berlin Summer Meeting 2025 #BSM2025! Attendees dove into real-time sequence search, nucleic acid analysis of environmental samples, spatial transcriptomics for infectious diseases, AI-assisted genomics, and a behind-the-scenes tour of single-cell omics 🧬🧑‍🔬 #mdcBerlin

I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm. What should one really care about? (1/5)

What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM: - OMERO-vitessce - IO-FAST initiative - @nfdi4bioimage.bsky.social Data Stewardship Talks, Workshops & Poster Session 2 up ahead today!🔬

As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...

Sums up a day in my life at the lab ...

Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants

The Innovations in Single Cell Omics conference in Berlin was amazing! Great talks and we even had a Night Science workshop! 🙏 @stefaniegrosswendt.bsky.social, Ashley Sanders, @simonhaas.bsky.social, @leifludwig.bsky.social, @elimereu.bsky.social, @larsplus.bsky.social & @alejofraticelli.bsky.social

📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20... Call for abstracts and registrations coming soon!

To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats Code along: www.youtube.com/watch?v=aaAN... #AcademicSky #codetutorials #Bioinformatics

Another semester done 🥳🥂 In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i... #AcademicSky

Time to join GESTALT – Global Alliance for Spatial Technologies – GESTALT – Global Alliance for Spatial Technologies Together we do more … www.nature.com/articles/s41... globalspatial.org

⏰ Final Reminder — EuroBioC2025 abstract submissions close today, 24 April! Don't miss the chance to share your work in Barcelona this September. Submit here: eurobioc2025.bioconductor.org/pages/submis...

⏳ Time’s running out! Submit your abstract for #EuroBioC2025 by 24 April. Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats. 👉 eurobioc2025.bioconductor.org/pages/submis...

Accurate cell segmentation remains a major issue for spatial transcriptomics. Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...

Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data www.huber.embl.de/group/posts/...

STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance www.biorxiv.org/content/10....

🧪 Finally!!! A single-cell atlas of the mouse seminal vesicle!!! (seriously though, it just might be the last major mammalian organ to undergo single cell sequencing). Check it out! pubmed.ncbi.nlm.nih.gov/40036847/#fu... @arturmansl.bsky.social @anashin.bsky.social @epididymosome.bsky.social

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment https://www.biorxiv.org/content/10.1101/2025.02.24.640007v1

We would like to thank Thore Buergel from Pheiron again for presenting at the Berlin Bioinformatics Social meeting. Check out Thore's work where they integrate massive biobank for inferring casual insight on targets! pheiron.com. @mdc-berlin.bsky.social @mdc-bimsb.bsky.social

With today’s and next releases (PyPI), we are gradually rolling out the new features developed during the hackathon. Find the full list of what we worked on in this pre-print: osf.io/preprints/bi... Thank you to all of the participants and to @cziscience.bsky.social for funding this wonderful event.

Quentin Blampey, Lotte Pollaris, @clarencemah.me Laurens Lehner @chiaraschiller.bsky.social @miguelib.bsky.social We worked on easing the learning curve of the SpatialData framework by improving the documentation and APIs. We prepared new beginner-friendly notebooks and introduced a new more...

... cross-language analysis pipelines possible based on the common SpatialData Zarr format. We are still early stage, but now you can start plotting SpatialData objects with ggplot, or use the spatialdata-io readers from R.

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!

@helucro.bsky.social @estellayixingdong.bsky.social @kevinyamauchi.bsky.social @arturmansl.bsky.social Dario Righelli, Louise Deconick, Vincent Carey Should you use R (Bioconductor) or Python (scverse) for spatial omics? Ideally, you won’t have to choose one. We are working toward making...

It’s been a real fun (& productive) event, as well as a great demo of how R/Bioc and Python/scverse communities can come together to pursuit mutually beneficial (vs. redundant/diverging) efforts. — Thanks @scverse.bsky.social & all of the SpatialData team for having us!

✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH Thanks @arturmansl.bsky.social‬ ! #Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats

Made a #short about my internal conflicts on academic publishing #AcademicSky #PhDlife "Stop asking me where I want to publish our paper. I don't care...I just want people to read it. And maybe learn from it. Even build on it. Ok?" Is this #hopecore or #hopelesscore youtube.com/shorts/GV7NJ...

What will you learn: - Post-processing of spatial omics data - Automated and manual image registration - Niche clustering - Multiple workflows for different spatial data types and data conversion module by @arturmansl.bsky.social

Learn how to analyze spatial omics data! Join our computational genomics course in 2025. Application deadline 30th January. compgen.mdc-berlin.de 🖥️ 🧬 🧪

Another paper that claims whose dataset are "publicly" available ... 😂

tidyplots is an R package to generate publication-ready plots for scientific papers tidyplots.org/ #rstats

I found this review quite informative: 1. Get rid of the skill set list, it doesn't say anything about you (exp: Python, R, bash etc.). 2. Be precise with your experience and summary and don't list your tasks. www.youtube.com/watch?v=qXPJ...

Join our upcoming workshop to learn more about our view on AI-assisted bioinformatics, multi-omics integration and spatial multi-omics. The course is for both R and Python users!!

I had amazing time at the European Society of Spatial Biology conference #ESSB meeting friends from @gestaltsp.bsky.social and from all over the world. I wanna congratulate Anja Hauser and @schapirolab.bsky.social for this glorious event. Below are a few take from last week:

Congrats to @coscialab.bsky.social & his colleagues! Their Deep Visual Proteomics pipeline is one of the highlighted @naturemethods.bsky.social's Spatial Proteomics approaches! He says "making DVP broadly accessible and advancing it to the multiomics space is a key mission" in his lab at #mdcBerlin.

The calm before the storm... #SpaceHack starts tomorrow! Looking forward to 3 intense days of addressing unsolved data analysis problems for #SpatialTranscriptomics. More here: spatialhackathon.github.io

Setting up Python, Julia, and R in Visual Studio Code (VSCode) on an M1 Mac towardsdatascience.com/setting-up-...

A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...

Check out our new tools for #SpatialTranscriptomics. It's called Sainsc: onlinelibrary.wiley.com/doi/10.1002/.... #Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...

New work reveals the impact of anxiety & depression on PhD students. "Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition." nature.com/articles/s41...

Thanks for sharing - PhD anxiety/depression is important to realize & address, and has been on the rise, more so after the pandemic. I think there are some take-aways here for us PIs, such as managing expectations and maybe talking about own anxieties too to remove potential taboo nature.

Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati... 13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...