iiinova — where your digital self keeps evolving

Reposted by Artür Manukyan

BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 15/06/2026

"Bioconductor Spatial Data and Image Analysis Hackathon" doi.org/10.37044/osf.io/9ej32_v1 "We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and […] [Original post on fediscience.org]

One of the figures from the preprint. It shows a 2d image of tissue, colored with a red stain, showing the red and white image that we see. At the top there is the text "Overlay: Terra Image and Segmentation".

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Luke Zappia @lazappi.bsky.social · 10/06/2026

Excited that the {anndataR} 📦 publication is out academic.oup.com/bioinformati... 🎉! I hope this makes it easier to move single-cell data between R and Python and encourages people to take advantage of both languages. Check it out on @bioconductor.bsky.social bioconductor.org/packages/ann....

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Front Line Genomics @flgenomics.bsky.social · 01/05/2026

Ioannis Vlachos (Associate Professor of Pathology, Director of the Spatial Technologies Unit, Harvard Medical School) will be speaking at #FOGBoston! He’ll join a panel discussion on Spatial Technologies: What’s Real, What’s Hype, What’s Missing. More info: hubs.la/Q044gKQm0 @ioavlachos.bsky.social

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Wolfgang Huber @wkhuber.bsky.social · 28/05/2026

@helucro.bsky.social at CSAMA 2026 csama2026.bioconductor.eu

Helena L Crowell giving a lecture on spatial (transcript)omics in Brixen, South Tyrol on 2026-05-28.

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Wolfgang Huber @wkhuber.bsky.social · 29/05/2026

Thanks to input from @helucro.bsky.social, Daria Lazic, Hugo Gruson, Artür Manukyan and many others, there is now a whole new level of maturity and ease-of-use for spatial omics data, see helenalc.github.io/SpatialData....

helenalc.github.io

csama – SpatialData

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Bioconductor @bioconductor.bsky.social · 06/03/2026

📢 CSAMA 2026: Biological Data Science Summer School registrations are open for its 22nd edition, taking place in: 📍 Bressanone–Brixen, Italy 🗓 24–29 May 2026 🔗 Learn more and register: csama2026.bioconductor.eu #CSAMA2026 #Bioconductor

A scenic mountain landscape with steep rocky peaks and green forested slopes under a partly cloudy sky. Overlaid text reads: “CSAMA 2026 – Biological Data Science, 22nd Edition, Bressanone-Brixen, Italy, 24–29 May 2026.”

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Nikos Karaiskos @nukappa.bsky.social · 27/02/2026

🚀 We're looking for people to join Malva! 🧬 @danilexn.bsky.social Malva is the first search engine for single-cell genomics: we process massive amounts of sequencing data to enable ultrafast analysis of millions of cells. (1/4)

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Luca Marconato @lucamarconato.bsky.social · 02/02/2026

We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework. We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

embl.wd103.myworkdayjobs.com

Research Software Engineer - Spatial-omics

The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

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Helena Lucia Crowell @helucro.bsky.social · 02/02/2026

Registration now open for CSAMA! 📜 csama2026.bioconductor.eu Highly recommend for learning data science with a scenery, plus a fantastic crowd of students and faculty alike! 📸 from the traditional mid-week hike during last year’s edition.

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Wolfgang Huber @wkhuber.bsky.social · 15/01/2026

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps. ascona2026.sciencesconf.org

Poster session 2024, with Valentina Boeva, Constantin Ahlmann-Eltze and others

Wednesday afternoon hike incl. swim in the mountain river

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Dr. Jean Fan @jef.works · 15/01/2026

Thanks to the authors for sharing all components of this beautiful mouse embryo spatial transcriptomics data from cell gene counts to per-molecule coordinates: www.ahajournals.org/doi/full/10.... So I vibe coded an app to explore the 3D subcellular transcript organization: jef.works/CellCarto-Mo...

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Mine Doğucu @minedogucu.com · 14/01/2026

📖 Big news! We just released the first five chapters of our new book, Hello Data Science. It is a fully open-access resource written for beginners. Please help us spread the word! A few points about the book are below 👇 🔗 www.hellodata.science #rstats #datascience #tidyverse

A hex sticker with a text that reads Hello Data Science with green, yellow and pink scatterplot points in the background. There is a web address www.hellodata.science

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Boas Pucker @bpucker.bsky.social · 12/01/2026

“Analysis of Biological Data with Python” started today for biology bachelor students 🧬🐍 Want to learn Python for data analysis? Slides are freely available: github.com/bpucker/teac... #Python #DataAnalysis #Biology #OpenScience #BigData #Bioinformatics #DataScience @puckerlab.bsky.social

Figure illustrating some content of the Python course for biology students at UniBonn

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Wolfgang Huber @wkhuber.bsky.social · 17/12/2025

CSAMA 2026 - Biological Data Science Summer School Bressanone-Brixen, South Tyrol / Italy 24-29 May 2026 csama2026.bioconductor.eu Statistical & computational methods for single cell and spatial omics, with lectures and hands-on exercises in R/Bioconductor.

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Stegle Lab @steglelab.bsky.social · 27/12/2025

We are looking for a Software Developer to work on R/Python interoperability for single-cell and spatial omics methods. 🔗 Apply here: jobs.dkfz.de/en/jobs/1683...

jobs.dkfz.de

Software Developer - Interoperability for Single-Cell and Spatial Omics Methods

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Dr. Jean Fan @jef.works · 05/01/2026

Every year, I give my lab (+myself) a "mini-sabbatical" to pursue independent learning. This year, I'm learning to use AI tools. So I made a short film to reflect on life/death + create art in an era where it can feel like AI has usurped the value of self-expression: youtu.be/YJjmKRlmI1Q

youtu.be

Come Take A Portrait With Me | a short film

YouTube video by Prof. Jean Fan

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Artür Manukyan @arturmansl.bsky.social · 27/12/2025

Amazing opportunity, we thank #Helmholtz ScienceServe Initiative for helping us recruit talented people to develop FAIR Software for spatial omics. You will also have the chance to join hackathons and workshop we organize with developers across @scverse.bsky.social and @bioconductor.bsky.social.

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Jasmine Plummer @jasmineplummer.bsky.social · 09/12/2025

Join us to the last #GESTALT seminar the year! Free for all GESTALT member. If you are interested in anything #spatialbiology come be part of our growing community GESTALT Seminar Series globalspatial.org/seminar-seri... December 19 10am EST @ioavlachos.bsky.social @lgmartelotto.bsky.social

globalspatial.org

Seminar Series – GESTALT – Global Alliance for Spatial Technologies

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Pau Badia i Mompel @paubadiam.bsky.social · 21/11/2025

scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄

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Lukas Weber @lmweber.bsky.social · 22/11/2025

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!

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Helena Lucia Crowell @helucro.bsky.social · 21/11/2025

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

bioconductor.org

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/11/2025

Orchestrating Spatial Transcriptomics Analysis with Bioconductor www.biorxiv.org/content/10.1101/202…

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Ursula von der Leyen @vonderleyen.ec.europa.eu · 10/11/2025

Switzerland is joining Horizon Europe! We are uniting two research powerhouses. For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more. Today is a good day for science, and for our EU-Switzerland partnership.

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GiottoSpatial @giottospatial.bsky.social · 02/10/2025

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...

nature.com

Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem - Nature Methods

Giotto Suite provides a comprehensive, flexible and scalable platform for technology-agnostic spatial omics analysis using R.

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Fabian Theis @fabiantheis.bsky.social · 28/09/2025

🚀 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...

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Artür Manukyan @arturmansl.bsky.social · 17/09/2025

#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.

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Fabian Theis @fabiantheis.bsky.social · 25/07/2025

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...

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Bioconductor @bioconductor.bsky.social · 25/07/2025

🚀 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

blog.bioconductor.org

Exploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025 – Bioconductor community blog

A blog for the Bioconductor community!

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Kamil Lisek @klisek.bsky.social · 22/07/2025

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...

biorxiv.org

Spatiotemporal dynamics of tumor microenvironment remodeling

During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...

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Reposted by Artür Manukyan

MDC-BIMSB @mdc-bimsb.bsky.social · 18/06/2025

🔬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

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Wolfgang Huber @wkhuber.bsky.social · 13/06/2025

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)

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Chris Schmidt @schmchris.bsky.social · 05/06/2025

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!🔬

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Artür Manukyan @arturmansl.bsky.social · 31/05/2025

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

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Stefanie Grosswendt @stefaniegrosswendt.bsky.social · 13/05/2025

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

(Some of the) speakers and co-organizers of the ISCO conference 2025

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Itai Yanai @itaiyanai.bsky.social · 13/05/2025

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

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scverse @scverse.bsky.social · 12/05/2025

📣 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!

scverse.org

scverse conference 2025

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Dr. Jean Fan @jef.works · 12/05/2025

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

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Dr. Jean Fan @jef.works · 05/05/2025

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

jean.fan

Jean Fan | Personal site

Personal website of Prof. Jean Fan

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Luciano Martelotto @lgmartelotto.bsky.social · 10/04/2025

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

globalspatial.org

GESTALT – Global Alliance for Spatial Technologies – GESTALT – Global Alliance for Spatial Technologies

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Bioconductor @bioconductor.bsky.social · 24/04/2025

⏰ 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...

eurobioc2025.bioconductor.org

submissions – European Bioconductor Conference 2025

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Bioconductor @bioconductor.bsky.social · 22/04/2025

⏳ 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...

Screenshot showing the EuroBioC2025 abstract submission deadline as April 24, 2025, and key conference dates for the Bioconductor community event in Barcelona, Spain.

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Nav @naveed-ishaque.bsky.social · 17/03/2025

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...

biorxiv.org

Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data

The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current c...

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Wolfgang Huber @wkhuber.bsky.social · 12/03/2025

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

huber.embl.de

Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data – Huber Group @ EMBL

Precision Oncology and Multiomics

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Ming Tommy Tang @tommytang.bsky.social · 12/03/2025

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

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umasschan-bmb.bsky.social @umasschan-bmb.bsky.social · 07/03/2025

🧪 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

a scatter plot showing the relationships between all the cells sequenced from the adult mouse seminal vesicle. major cell groupings include the secretory epithelium, basal cells, stroma, macrophages, and endothelial cells, among others.

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bioRxivpreprint @biorxivpreprint.bsky.social · 28/02/2025

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment www.biorxiv.org/content/10.1101/202…

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