Martin Jones

Woody Guthrie inspired sticker with a microscope - and photo of Woody Guthrie with his guitar that famously was decorated with the words "this machine kills fascists".

Make your own sticker against #Fascism

Woody Guthrie used his music to fight in the 1940ies. Let his guitar be a reminder to us that we all have tools available to stand up.
As biologists, we are trained to See, Understand, Document, and Report - let's apply these today!

doi.org/10.6084/m9.f...

This article suggests the possibility of training AI on pre-existing proposals and their review reports, scores and related decisions. I.e. training them on a system which is known to preferentially award larger amounts of money to white men. What could possibly go wrong?

YouTube video by CellMorphoJSero Introduction to CellProfiler - by a biologist, for biologists!

If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I

Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...

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-...

Happy to share the first paper from my journey at @psich.bsky.social towards X-ray connectomics, now out in @natmethods.nature.com: www.nature.com/articles/s41...

Organisers of the Crick BioImage Analysis Symposium 2025

Organising symposia is a whole lot less work and more fun when you've got an enthusiastic group of fellow organisers to help out.

But #CBIAS2025 was my 6th and I think it's now time to step back a little.

So from next year, @lankylaste.bsky.social will be taking the lead.

Roll on #CBIAS2026!

From aerospace to neuroscience: new imaging tech captures the brain’s intricate connections Inspired by technologies used in aerospace engineering, scientists have developed a way to capture the brain’s intricate structures using X-rays without destroying the samples.

Researchers at the Crick, @psich.bsky.social and @esrf.fr have developed a new way to look deeper into brain cell connections by using a particle accelerator and a kind of resin borrowed from the aerospace industry.
www.crick.ac.uk/news/2025-11...

Want to automatically analyse your microscopy images but have no idea where to start?

👇

Get your #bioimageanalysis journey started with this workshop!

📍Cardiff, UK
🗓️18-20/05/2026

Introduction to Image Analysis 2026

Applications for the next @royalmicrosoc.bsky.social “Introduction to image analysis” workshop are now open!

Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org

www.rms.org.uk/rms-event-ca...

THANK YOU ALL for making another edition of CBIAS so special! Stay tuned for next year’s dates, we look forward to seeing you all again soon

#CBIAS2025

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

An immense thank you again to @cbias.bsky.social committee, sponsors and fellow imaging friends for this fantastic symposium!
It's is not the end but the beginning of tons of papers to read, colleagues to contact, new collaborations to form. And most importantly, it's a 'see you soon' #CBIAS2026 🔬🥰

Another brilliant #CBIAS2025. Now I know the rest of my week will be testing out all those cool new analysis tools!

Congratulations to @aafkegros.bsky.social for winning the Best Poster Award at #CBIAS2025! 🎉 Their Microscopy Nodes Blender plugin not only makes visualisation easier, but also shines as a brilliant link between computer vision, mathematics, and biology.

Had such a blast at #CBIAS2025 — a meeting full of image-analysis nerds (what more could you want?).
If you’d like to learn more about movement, the Python package I presented, my slides are live at neuroinformatics.dev/slides-movem...

It was brilliant having the opportunity to chair this session at #CBIAS2025. Thank you to all the wonderful speakers discussing new tools for morphological analysis and event detection in microscopy 🔬

Second #CBIAS2025 panel discussion on Interdisciplinary collaboration in bioimage analysis chaired by @virginieuhlmann.bsky.social panellists are @candiceroufosse.bsky.social from @imperialcollegeldn.bsky.social Andy French from @uniofnottingham.bsky.social and Amir Patel from @ucl.ac.uk

Last but not least: Samantha Ahern from the Society of Research Software #CBIAS2025

The TrackMate helper is there to do just that. #CBIAS2025

Lots of new features in TrackMate but with that comes increased uncertainty: which one is the right one? #CBIAS2025

Second speaker is @jytinevez.bsky.social from @institutpasteur.bsky.social introducing TrackMate 8 #CBIAS2025

Jean-Yves @jytinevez.bsky.social showcases the new #Trackmate version and the breadth of image analysis done at @pasteur.fr

#CBIAS2025

Some more information and background reading #CBIAS2025

On to session six of #CBIAS2025 chaired by @olatznv.bsky.social from @imperialcollegeldn.bsky.social first speaker is Kimberly Meechan from @ucl.ac.uk introducing the HEFTIE project: tools and training for getting started with OME-ZARR

BIOIMAGE ANALYSTS ASSEMBLE!!!

#CBIAS2025

Overcoming Nyquist-Shannon limitation with deep learning #CBIAS2025

#CBIAS2025 Checklists to improve figures for publications derived from community consensus www.nature.com/articles/s41...

Last speaker of the session Ilaria Testa of @scilifelab.se from @kthuniversity.bsky.social on imaging very small things with high dynamics. #CBIAS2025

TrackMate v8 - segmentation editor and Python CLI integration TrackMate v8: 2D Segmentation Editor & Python CLI Integration Hi everyone, I am excited to announce TrackMate v8, a major update introducing key improvements for both end-users and developers. Mai...

New release of the TrackMate single particle tracking plugin for ImageJ by @jytinevez.bsky.social looks amazing! forum.image.sc/t/trackmate-...
Loads of new features, most excitingly to me deep learning segmentation algorithms including Omnipose (for cells), and Spotiflow (for spots) #bioimaging