We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...

Some impressions from last time (We had a good time, and aim for it again.) Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.

Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer! Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM? Stay tuned, Pasteur offers access to THREE courses, this June. 👇🎓

Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)

Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx Part of sfb1690.uni-goettingen.de to study hearing, vision, and more. Plus, you can create pretty pictures as the one below :).

Are you a neuroscientist with great coding skills, or a software engineer interested in the brain? We are recruiting for a research software engineer to help us build pipelines to process weeks of neural and behavioural recordings from freely moving animals. More details: bit.ly/rse-2026a

Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer

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...

AMAZING JOB OPPORTUNITY ALERT!!! @calm-stp.bsky.social is hiring a Data & Systems Steward! 🧬 🔹Manage #bioimage data & #OMERO admin 🔹Automate via #Python/#Bash 🔹Support #FAIR principles 🔹Work closely with @crick-ia-team.bsky.social ⏰ Deadline: 08 Feb 2026 Apply: www.crick.ac.uk/careers-stud...

#teamtomo gets another quantitative cell biology tool! We extend our Surface Morphometrics pipeline to measure membrane thickness. Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Our research scientist Núria Ros-Rocher won the 1st prize @zeiss-microscopy.bsky.social microscopy contest with this beautiful choano colony www.zeiss.fr/microscopie/... 🥳 C. flexa might not yet be a genetic model, but it is now at least a calendar model, which counts for something. I think.

The #CBIAS2025 poster collection is now available, along with associated DOIs for further dissemination. Take a look! crick.figshare.com/collections/...

🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...

I will be recruiting two postdocs early next year. - One image analyst - one biologist interested in working on lymphatics! Reach out if you are interested 👍

Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff: Paper: doi.org/10.1242/jcs.... Code: github.com/pertzlab/arc... Plugin: github.com/pertzlab/arc...

I was invited by @focalplane.bsky.social to write a short description about it: focalplane.biologists.com/2025/12/12/a...

🚨 Je cherche des chercheur-ses de toutes disciplines pour un doc radio pour parler de leur sujet de recherche mais aussi de leur quotidien (une journée type au labo). Contrainte supplémentaire, le labo doit être hors de Paris. Plus d'infos : forms.gle/hw9wH2p5UH4A...

Paris 13eme now.

BIOIMAGE ANALYSTS ASSEMBLE!!! #CBIAS2025

TrackMate now integrates even more cutting-edge detection, segmentation and tracking methods and makes them fun and easy to use!

MASSIVE thank you to everyone involved in this year's I2K meeting - 32 SUPER sessions from our volunteer presenters, and so many super-engaged participants. HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard! See you in the recordings and at next year's!

For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing. I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow. jacobtomlinson.dev/posts/2025/p...

Thrilled to have presented @globias.bsky.social at the @latambioimaging.bsky.social Meeting last week! 🇦🇷🔬 I really enjoyed sharing our mission in both a lightning talk and with a poster. It was fantastic to connect with so many passionate bioimaging scientists! Let's keep building this community!

If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr research.pasteur.fr/fr/job/open-...

We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.

Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I... Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...

I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us! The slides are online #openaccess 🧑‍🏫🔓 zenodo.org/records/1742...

I'm happy to release into the wild my new professional and personal website marcodallavecchia.gitlab.io/web/ I finally found some time to reorganize ideas and redo the framework with @quarto.org You can read my first blog post on the website here! marcodallavecchia.gitlab.io/web/blog/web...

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)? Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.

And we'll round off 2025 on November 26th at 4pm with guest presentations by Giliane Rochat about lightsheet processing for OME-Zarrs & Flurin Sturzenegger about the ZMB Fractal task collection. (5/6)

We'll start the season next week on September 24th at 4pm with a guest presentation by @csoneson.bsky.social & @silviabarbiero.bsky.social about the ez_zarr library (see github.com/fmicompbio/e...) (3/6)

We'll have the second meeting on October 28th at 4pm with a guest presentation by @m-albert.bsky.social about multiview-stitcher (github.com/multiview-st...) & dask-image (image.dask.org/en/latest/) (4/6)

Are you working with OME-Zarrs in Switzerland? We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)

🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮 www.scilifelab.se/news/ready-t...

Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

New short paper from our lab @currentbiology.bsky.social, in which we discover of a new mode of cell motility for choanoflagellates: flagellar gliding. www.cell.com/current-biol... - A 🧵

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊 Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects! My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally. Check out my portfolio and contact: acorbat.github.io

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

I'll be there! Giving a talk! and hacking on _something_ for a few days!

📣We have opened our official User Forum: forum.image.sc/tag/mesospim In this forum you can connect with 🔬developers and the image analysis experts. Ask your burning questions about the #mesoSPIM hardware, software, and image processing, or help the beginners to get started! Tip: use project tags!

A really nice interview with Juan. Important messages: - "I think that universities are missing a trick in not investing more in this type of work [open source software development]" - "Never code alone."

A few months ago @eurobioimaging.bsky.social organized the 'Image Data Community Days 2025' during which I could present our work within @france-bioimaging.bsky.social, creating a nationwide, remotely operating core facility for Bioimage Analysis. youtu.be/xtLHiio8RF0?...

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇