iiinova — where your digital self keeps evolving

Reposted by Helena Lucia Crowell

Joel Lüthi @joelluethi.bsky.social · 21/09/2026

I'm happy to announce the fall 2026 Open Bioimaging Practices Meetup schedule. We'll have 3 exciting meetings about developments in the OME-Zarr space: - OME-Zarr viewers - Multiplexed Image analysis in OME-Zarr - Spatial OMICs in OME-Zarr See www.biovisioncenter.uzh.ch/en/events/Op... (🧵 1/10)

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetups

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Wolfgang Huber @wkhuber.bsky.social · 16/09/2026

A commentary on "Training as infrastructure for biological data science in wartime Ukraine" doi.org/10.1038/s415... (Nat. Genet.)

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Wolfgang Huber @wkhuber.bsky.social · 24/08/2026

I wrote up a short blog post about this year's Ukrainian Biological Data Science Summer School, which took place over two weeks in July: www.huber.embl.de/group/posts/... @mikelove.bsky.social @helucro.bsky.social @ladaisa.bsky.social

huber.embl.de

Ukrainian Biological Data Science Summer School 2026 – Huber Group @ EMBL

Uzhhorod, 11 - 25 July 2026: the fourth edition

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Stevie Ped @smped.bsky.social · 19/08/2026

Reminder for all members of the Bioconductor community. Nominations close at the end of the month. If you're unsure, please reach out on the Bioc chat or through your networks

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Bioconductor @bioconductor.bsky.social · 10/07/2026

🌟 Bioconductor 2026 CAB & TAB nominations are open! Join our advisory boards to support community growth or guide technical strategy. 📅 Apply by Aug 31 CAB: forms.gle/qXwPqEzPET45... TAB: forms.gle/MLYBYDgdbU1C... #Bioconductor #RStats

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

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Helena Lucia Crowell @helucro.bsky.social · 17/06/2026

Little blog post, preprint included, re: spatial/image Bioc hackathon on a little Venetian island — Thank you @wkhuber.bsky.social and especially @davi1893.bsky.social (and Elena!) for organizing and securing this 🤩 location 🤩 — Let’s do it again!

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Helena Lucia Crowell @helucro.bsky.social · 15/06/2026

Fantastic effort by Lori et al. 👏 Win-win for reviewers & contributors alike!

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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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Reposted by Helena Lucia Crowell

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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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 07/06/2026

"2nd SpatialData Hackathon: Frameworks, Formats and Interoperability" doi.org/10.37044/osf.io/s6bph_v1 "The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of […] [Original post on fediscience.org]

Figure 1: Comparison of Zarr, bioimaging and single-cell/spatial omics packages across scverse and Bioconductor ecosystems that interface with SpatialData objects on disk (“Database-icon” by Zahra Ibrahem is licensed under CC BY-SA 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-sa/4.0/?ref=openverse.)

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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 · 07/05/2026

📢 We’re excited to launch the BiocAsia Seminar Series, bringing together the Asia-Pacific Bioconductor community through shared learning and connection. The series will begin with two speakers: Prof Matt Ritchie & Dr Helena Crowell 📅 12 May ⏰ 4:00-5:00 pm AEST 🔗 Register to attend: bit.ly/42gczgl

adelaide.zoom.us

Welcome! You are invited to join a webinar: BiocAsia Seminar Series. After registering, you will receive a confirmation email about joining the webinar.

Please join us for the first in the BiocAsia Seminar Series. This session will feature two talks from some fantastic Bioconductor contributors. Prof Matt Ritchie (WEHI, Melbourne, Australia) "Developing...

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Reposted by Helena Lucia Crowell

Mark Robinson @markrobinsonca.bsky.social · 06/05/2026

This was a fun effort from our lab retreat (!) to recreate a "arms-length" benchmark (i.e., one that someone else created) using our Omnibenchmark framework. We all learned a lot in the process ..

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Bioconductor @bioconductor.bsky.social · 30/04/2026

🚀 We’re excited to share the release of Bioconductor 3.23, featuring: ✅2418 software packages (94 new) ✅437 experiment data packages (5 new) ✅928 annotation packages ✅8 books (2 new) ✅28 workflows 🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...

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Helena Lucia Crowell @helucro.bsky.social · 28/04/2026

Moments like these... -> R'll be there for you.

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Reposted by Helena Lucia Crowell

Luke Zappia @lazappi.bsky.social · 23/04/2026

Last week I attended a SpatialData hackathon with members of the @scverse.bsky.social, @bioconductor.bsky.social and @openmicroscopy.org communities in Padua, Italy. Here is a short blog post about the experience www.data-intuitive.com/insights/blo....

data-intuitive.com

2nd SpatialData Hackathon – Data Intuitive

Frameworks, formats and Interoperability

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Wolfgang Huber @wkhuber.bsky.social · 21/04/2026

Bioconductor Spatial Omics Hackathon in Venice, 19-22 April 2026.

A flock of scientists standing on San Servolo island, with a view of Venice

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Bioconductor @bioconductor.bsky.social · 08/04/2026

🚨 Bioconductor and R-universe are joining forces to modernize infrastructure for bioinformatics tools while preserving the strong governance and review processes that have made Bioconductor a trusted resource for over 20 years. 🔗 Learn more: blog.bioconductor.org/posts/2026-0...

blog.bioconductor.org

Collaborating between Bioconductor and R-universe on Development of Common Infrastructure – Bioconductor community blog

R-consortium ISC top-level project R-universe is working with Bioconductor to help gradually modernize parts of its infrastructure, while accommodating the project’s scale, governance, and…

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Bioconductor @bioconductor.bsky.social · 19/03/2026

📣 Call to Host EuroBioC2027! Interested in bringing the European Bioconductor Conference to your region? Applications are now open to host EuroBioC2027 or to join the planning committee to gain experience for future editions. 👉 Apply here by 20 April 2026: docs.google.com/forms/d/e/1F...

Bioconductor promotional graphic announcing a “Call to Host EuroBioC2027.” The image features a green speech bubble with text inviting applications to host the European Bioconductor Conference in 2027 or join the planning committee, with a deadline of April 20, 2026. A megaphone illustration appears in the lower left.

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Reposted by Helena Lucia Crowell

CNAG @cnag-eu.bsky.social · 04/03/2026

🚀 𝗡𝗲𝘄 𝗽𝗮𝗽𝗲𝗿 𝗼𝘂𝘁 𝗶𝗻 𝘁𝗵𝗲 𝗘𝘂𝗿𝗼𝗽𝗲𝗮𝗻 𝗝𝗼𝘂𝗿𝗻𝗮𝗹 𝗼𝗳 𝗜𝗺𝗺𝘂𝗻𝗼𝗹𝗼𝗴𝘆! A Spatial Transcriptomics Map of the Human Tonsil Reveals New Dimensions Beyond the Cellular Atlas, offering new insights into immune responses By @pascual-reguant.bsky.social & @helucro.bsky.social (1st author) 📎 www.cnag.eu/news/spatial...

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Bioconductor @bioconductor.bsky.social · 13/02/2026

🚀 Join the Bioconductor Hackathon on Spatial Omics & Image-Derived Data in San Servolo, Italy (Venice) from 19–23 April 2026. Developers in this field are invited to participate. 💡 Limited travel support is available for junior developers 📝 Apply by 20 February: forms.gle/Gv8EdpxV7XK7...

forms.gle

Bioconductor-centric hackathon on spatial omics and image-derived data analysis methods

We’re planning a 4-day Bioconductor-centric hackathon on spatial omics and image-derived data analysis methods, 19-23 April 2026 in San Servolo, Italy (an island in front of Venice's San Marco…

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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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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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Davide Risso @davi1893.bsky.social · 23/12/2025

This year's CSAMA Biological Data Science Summer School in Brixen takes place 24-29 May 2026. Topics: single-cell and spatial omics, statistics, multi-omics, ML/AI, all very hands-on using R / Bioconductor! More info: csama2026.bioconductor.eu Registration: 1 Feb 2026! @bioconductor.bsky.social

csama2026.bioconductor.eu

CSAMA 2026 Biological Data Science – CSAMA 2026 Biological Data Science

22nd Edition Bressanone-Brixen, Italy 24-29 May 2026

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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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Helena Lucia Crowell @helucro.bsky.social · 03/12/2025

A little feisty this, dear Spotify, preluded by “Age is just a number. So don’t take this personally”, but on point as always, and point well taken 🙂‍↕️

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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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Bioconductor @bioconductor.bsky.social · 14/11/2025

📣 Calling Bioconductor users and developers! 🧬 ✨ Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!

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Bioconductor @bioconductor.bsky.social · 31/10/2025

🚀 Bioconductor 3.22 is released! Thanks to all developers and community members for contributing to the project! 🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...

bioconductor.org

Bioconductor - Bioconductor 3.22 Released

The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and…

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Reposted by Helena Lucia Crowell

Bioconductor @bioconductor.bsky.social · 29/10/2025

🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026! Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology. 👉 More details soon at eurobioc2026.bioconductor.org

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Bioconductor @bioconductor.bsky.social · 24/10/2025

Thank you to all our amazing sponsors, organizers, speakers, and attendees for making #EuroBioC2025 in Barcelona such a success! Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1... And, see you next year at #EuroBioC2026! 🎉 #Bioconductor #Community #Conference

blog.bioconductor.org

EuroBioC2025 conference recap – Bioconductor community blog

Highlights from the 2025 European Bioconductor Conference in Barcelona

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Samuel Gunz @samuelgunz.bsky.social · 14/10/2025

I'm very excited to share our latest preprint! We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells. We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...

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Anna Pascual Reguant @pascual-reguant.bsky.social · 15/09/2025

🚀 Spatial Transcriptomics (Imaging) + Spatial-centric analyses by @helucro.bsky.social : the way to truly interrogate tissues!!! 📖 Read our pre-print on human tonsil architecture (full of tonsiLove ♥️) here: doi.org/10.1101/2025...

doi.org

A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts

The tonsil is a highly compartmentalized organ in which different microanatomical structures orchestrate designated (immune) functions. We use this already well-studied tissue to survey spatial molecu...

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Bioconductor @bioconductor.bsky.social · 26/08/2025

🌟 One Week Left to Nominate for Bioconductor’s 2025 Advisory Boards! 🌟 Help shape the future of open science and bioinformatics by joining the Community or Technical Advisory Board. 🗓️ Deadline: August 31 📥 Apply or nominate: CAB 👉 forms.gle/8NYxRGhprfuN... TAB 👉 forms.gle/eqef9ThpUypc...

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Wolfgang Huber @wkhuber.bsky.social · 24/08/2025

In July we had the 3rd edition of the Ukrainian Biological Data Science Summer School. Now a regular, it has created a sense of community: young people eager to learn new topics, network across the country&world. Seeing how science is a positive&optimistic force. www.huber.embl.de/group/posts/...

huber.embl.de

Ukrainian Biological Data Science Summer School 2025 – Huber Group @ EMBL

Uzhhorod, 19 July - 1 August 2025: the third edition

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Bioconductor @bioconductor.bsky.social · 21/08/2025

⏳ One week left to register! Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics. 🗓️ Registration closes August 28 — don’t miss out! 🔗 eurobioc2025.bioconductor.org #EuroBioC2025 #RStats

eurobioc2025.bioconductor.org

European Bioconductor Conference 2025 – EuroBioC2025

The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…

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Bioconductor @bioconductor.bsky.social · 17/07/2025

🌟 Bioconductor 2025 CAB & TAB nominations are open! Join our advisory boards to support community growth or guide technical strategy. 📅 Apply by Aug 31 CAB: forms.gle/8NYxRGhprfuN... TAB: forms.gle/eqef9ThpUypc... #Bioconductor #RStats

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Bioconductor @bioconductor.bsky.social · 15/07/2025

🎨 Calling all Bioconductor package developers! We’re building a Sticker Hexwall for #EuroBioC2025 Submit your package sticker by July 22 to be featured: 🔗 eurobioc2025.bioconductor.org/pages/hexwal... Know a package that’s missing a sticker? Encourage them to join in! #Bioconductor #RStats

A musical note composed of small hexagonal package stickers, arranged in a gradient from dark to vibrant colors. The overall shape resembles a quaver (eighth note), forming a colorful, pixelated mosaic.

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Reposted by Helena Lucia Crowell

Sergio Marco Salas @sergiomarcosalas.bsky.social · 08/07/2025

Did you know you can infer CNVs using image-based spatial transcriptomics? Check it out in our latest preprint.

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

📝 New blog post: Bioconductor and ggplot2 4.0.0 - What’s Changing and How to Prepare A major ggplot2 update is coming and may impact Bioconductor packages. What’s changing, how to test, and where to get help 👉 blog.bioconductor.org/posts/2025-0... #Bioconductor #RStats

blog.bioconductor.org

Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog

Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/07/2025

In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics www.biorxiv.org/content/10.1101/202…

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Bioconductor @bioconductor.bsky.social · 27/05/2025

📝 New Bioconductor Blog Post! We’ve just launched the first in a new series by Vince Carey, founding contributor to Bioconductor and core developer, exploring the evolving complexity and value of the Bioconductor ecosystem. Check it out 👉 blog.bioconductor.org/posts/2025-0... #Bioconductor #RStats

blog.bioconductor.org

Ask and you shall receive – Bioconductor community blog

Discussion of evolving complexity and value of the Bioconductor ecosystem.

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Helena Lucia Crowell @helucro.bsky.social · 19/05/2025

EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊

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