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: 👇

Welcome to blusky PhD student extraordinaire Laura Xénard @lxenard.bsky.social ! 🐙🪲

Just over two weeks left to apply for our bespoke 'Managing a core facility' workshop. It will run 8 – 10 December 2025 at @ebi.embl.org in Hinxton. Apply by 17 August: www.ebi.ac.uk/training/eve... #corefacility #bioinformatics #operationalmanagement #impactpathways #teamleader #STEMmanager 🧬🖥️🥼

🚨 Deadline extended! You now have until August 8 to apply for the Light-Sheet Image Analysis Workshop (Jan 5–9, 2026) at Universidad Mayor in Santiago de Chile with the support of CZI @cziscience.bsky.social and @lisium-chile.bsky.social 1/3

Opening for a professorship in multimodal imaging in the context of our cluster of excellence #3DMM2O. Here is the full advertisement with all details: tinyurl.com/2ksy2b2s

Looking for an opportunity to work on cutting super-resolution microscopy and AI? There's still time to apply to the two positions!

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)! More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

happy to finally share what we've been cooking 🍳

Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer www.fmi.ch/education-ca...

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀! Scalable #RDM solutions in the ome-zarr-verse, here we come!

Day 2 of #Zidas2025 is happening! After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !

And we're ON! #Zidas2025 has officially started at the @biozentrum.unibas.ch, and the first day is introduction to image formation by Arne Seitz, Fiji by Joana Delgado Martins and Fiji scripting by me !

Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.

Thank you for speaking with me about my research @iamshef.bsky.social! #newPI #metabodev #MetabolismMondays Please check out Shefali’s weekly interviews with different ECRs about metabolism and development @the-node.bsky.social! What a great initiative 👏 thenode.biologists.com/author/shefa...

Come and Join our Dpt in Beautiful #Geneva ! We are looking for a #Microscopy & #Image #Analysis expert to help all of us at the Dpt.

🙌 We’re excited to have @matthewfeickert.com, John Kirkham, and Ruben Arts teaching us "Reproducible Machine Learning Workflows for Scientists with pixi" at #SciPy2025! 🔥 Learn how to create fast and reproducible ML environments using pixi, the next-gen package manager for scientific workflows.

Just made it to beautiful Manchester for #MMC2025 Feels like la mecca of Microscopy Find me if you want to chat image analysis in this land if microscopes

The DB Unit Summer School, "Transitions in Developing Systems," kicked off with an incredible talk by Thibaut Brunet @thibautbrunet.bsky.social from the Pasteur Institute @pasteur.fr on the fascinating transition from unicellularity to multicellularity in choanoflagellates #EMBLDevBio

Our neighbours are looking for a light microscopy expert. Check out the job advertisement. www.novartis.com/careers/care...

And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be: www.youtube.com/watch?v=8t8R...

⌛ Only one week left! The application deadline for our open positions as Remote Web Developer, Remote Software Developer and Project Coordinator is just 7 days away. Don't miss your chance to apply! Check out all job openings on our careers page⬇️