New preprint alert!

We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin).
www.biorxiv.org/content/10.6...

👇🧵

1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:

Sign it.

https://doi.org/10.5281/zenodo.14762435 https://bsky.app/profile/falk-illustrations.de

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...

Advanced fluorescence imaging techniques EMBL Course

Curious about Advanced fluorescence imaging techniques? 🔬 Check out this course organised in collaboration with @embl.org Node experts, taking place at EMBL Heidelberg from May 17-22.
🗓️ Apply by February 8 🔽
www.embl.org/about/info/c...

Tune in on 23. jan to hear about our work on smart microscopy:

📯👨‍🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab

arxiv.org/abs/2601.08859 #ScientificComputing

The new version of TrackMate, the v8.1 has just been released. It builds upon the recent v8, linked below, and offers two main improvements 👇

Very nice! Did you spray or dab the stencil ?

Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out

Customizable FDM-based zebrafish embryo mold for live imaging
www.biorxiv.org/content/10.1...

Work by Marcela and Jaakko in the lab

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.

Great visibility for #microscopy images from @france-bioimaging.bsky.social platform Montpellier Ressources Imagerie at European Researcher's Night!

Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...

#imageanalysis #bioimaging

Biscuits, someone has left oil on the 10x again…

Myself

B y the means of Telescopes, there is nothing so far distant but may be represented to our view; and by the help of Microscopes, there is nothing so small, as to escape our enquiry.

Robert Hooke

We see past time in a telescope and present time in a microscope. Hence the apparent enormities of the present.

Victor Hugo

La science est redevable au microscope et à l'art de s'en servir d'un grand nombre de découvertes.

Reply with cool microscopy quotes, Jules Girard, 1877, "les plantes étudiées au microscope"

YouTube video by Euro-BioImaging Communication Towards a nationwide core facility offering bioimage analysis services| Image Analysis session

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?...

YouTube video by Brian Northan Pixi and Napari-Easy-augment-Batch-DL

I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8

GloBIAS: strengthening the foundations of BioImage Analysis There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...

Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):

Optical Microscopy Support Specialist | John Innes Centre An exciting opportunity has arisen for an Optical Microscopy Support Specialist to join the Bioimaging Platform at the John Innes Centre.

VACANCY - We’re seeking an Optical Microscopy Support Specialist to join our Bioimaging Platform, to help train users on light microscopes, collaborate on imaging projects and provide technical support.

www.jic.ac.uk/vacancies/op...

Closing date - 11 August 2025
Contract - Full time, indefinite

Yes same LEDs that we had in Marseille! Looking forward 🤩

F-BIAS: Towards a distributed national core facility for bioimage analysis † Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...

Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️

journals.plos.org/ploscompbiol...

So happy about this paper and how the work turned out.
A small thread 👇

#bioimageanalysis #corefacility

Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. Where & When Broad Institute, 415 Main Street, Cambridge MA (in-person only) Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM About the Bootcamp Learn core bioimage analysis skills using open-source tools for light microscopy in this hands-on, in-person course. The Bootcamp covers annotation, segmentation, and deep learning fundamentals. Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit) For more information email ImagingAdmin@broadinstitute.org

BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...

The FIRST GloBIAS conference is happening in Kobe, Japan, and we launched the webpage and the registration form. Training school, Hackathon, Taggathon, and Symposium with talks, posters, open-source software lounge, call-4-help on stage!

#BioimageAnalysis
#GloBIAS

GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.

I tricked ChatGPT into helping me create an #ImageJ macro language extension to create/process data in the XML format. It's available here for anyone to use: github.com/mutterer/XML...

Thank you @gerbi-gmb.de for a wonderful week 💚🔬!

2 - New support for NGFF images (OME-Zarr, N5, remote or local)

The support for tracking remote images have been completely reworked, based on the N5-universe codebase by @herrsaalfeld.bsky.social lab, with a custom caching strategy.

Image analysis associate job description Image Analysis Associate Broad Institute of MIT and Harvard, Cambridge, MA Impact the discovery of new disease therapies in the Cimini laboratory at the Imaging Platform Join our vibrant, world-clas...

New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad!

First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)