Martin Jones
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martinjones.bsky.social
Martin Jones
@martinjones.bsky.social
2.5K followers 1.9K following 43 posts
Ex-physicist in a biology institute, working on image analysis and building new hardware at the Francis Crick Institute

ORCID: 0000-0003-0994-5652
Posts Replies Media Videos
Reposted by Martin Jones
hannah-superres.bsky.social
🚀 Exciting news for the imaging community!
The EMBO Practical Course – Hack Your Microscope is coming to ITQB NOVA (Oeiras, Portugal) on April 20–25, 2026 🧠🔬

👉 Course details & registration: meetings.embo.org/event/26-mic...

#Microscopy #OpenScience #Bioimaging #EMBOmicroscope
November 10, 2025 at 9:10 AM
Reposted by Martin Jones
bethcimini.bsky.social
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!
A flyer for the Bioimage Analysis Beginnings Bootcamp - blue and white with a picture of cells on the top. It says "Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels." It also says it will be held a the Broad Institute, 415 Main Street, Cambridge MA USA, on Monday to Friday January 12th-16, 2026, from 9-5pm. Registration is $750 academic, $1250 industry, and applications are open at broad.io/BAB3
October 14, 2025 at 9:31 PM
Reposted by Martin Jones
dstansby.bsky.social
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Reposted by Martin Jones
david-j-barry.bsky.social
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!

Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.

Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Provisional Program for day 1 of the Crick BioImage Analysis Symposium 2025 Provisional Program for day 2 of the Crick BioImage Analysis Symposium 2025
September 23, 2025 at 12:06 PM
Reposted by Martin Jones
crick-ia-team.bsky.social
A day in the dark side, from light to electron microscopy image analysis!

We're attending today the @ccp-volumeem.bsky.social meeting, discussing approaches to build a collaborative computational community for volume electron microscopy
November 3, 2025 at 12:58 PM
Reposted by Martin Jones
virginieuhlmann.bsky.social
If you ever used napari in your research, take a moment to read this.
Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it.
Now you get a chance to give back, don't miss it :)
napari.org napari @napari.org · 23d
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:

napari.org/island-dispa...
October 22, 2025 at 11:14 AM
Reposted by Martin Jones
bioimaginguk.bsky.social
🔬 THREAD: UK Bioimaging User Access Fund is OPEN!

Up to £5k for imaging experiments, £2k for image analysis

Access world-class facilities at Crick, ESRIC, KCL, Liverpool, Oxford Brookes & York

First deadline: 9 Dec 2025 📅

🧵👇
October 24, 2025 at 1:27 PM
Reposted by Martin Jones
crick-ia-team.bsky.social
And it’s a wrap! Thanks to all attendees for your hard work in analysing bioimages with open source software to make science more reproducible. Best of luck for your image analysis adventures!
October 28, 2025 at 9:24 PM
Reposted by Martin Jones
lankylaste.bsky.social
Very proud of the students for progressing very quickly over the course of the workshop! 🔬💻

And grateful to be working with an amazing team 🙏✨ @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, Sara and Cameron
crick-ia-team.bsky.social Crick Image Analysis Team @crick-ia-team.bsky.social · 15d
And it’s a wrap! Thanks to all attendees for your hard work in analysing bioimages with open source software to make science more reproducible. Best of luck for your image analysis adventures!
October 29, 2025 at 5:19 PM
Reposted by Martin Jones
david-j-barry.bsky.social
I'm in the photo, but I had very little to do with the successful delivery of this workshop - @lankylaste.bsky.social, Sara Salgueiro Torres, @martinjones.bsky.social, Cameron Shand and @k-meech.bsky.social did all the heavy lifting.
crick-ia-team.bsky.social Crick Image Analysis Team @crick-ia-team.bsky.social · 15d
And it’s a wrap! Thanks to all attendees for your hard work in analysing bioimages with open source software to make science more reproducible. Best of luck for your image analysis adventures!
October 29, 2025 at 8:47 AM
Reposted by Martin Jones
david-j-barry.bsky.social
Want to automate workflows in #FIJI?
Don't know where to start?
We (@lankylaste.bsky.social, Alicja Skórkowska and Sara Salgueiro Torres) have added a step-by-step tutorial to the wiki to get you started.

Thanks @ctrue.bsky.social for adding!

imagej.github.io/tutorials/ba...
Batch Processing with the ImageJ Macro Language
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.github.io
October 23, 2025 at 4:32 PM
Reposted by Martin Jones
crick-ia-team.bsky.social
All set up and ready to go for our 2-day Introduction to Image Analysis workshop for external attendees at @crick.ac.uk!

With Sara Salgueiro Torres, @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, @lankylaste.bsky.social and Cameron Shand
A seminar room with some people sitting at laptops and chatting
October 27, 2025 at 4:33 PM
Reposted by Martin Jones
crick.ac.uk
To mark World Menopause Day, Crick scientists Maxine Holder and Celine Bouchoux, as well as former Crick scientist Georgina Fletcher, appeared on The Microscopists podcast to talk about their experiences of perimenopause.

Listen now 👇
themicroscopists.bitesizebio.com/episodes/the...
The Microscopists | The Microscopists Discusses Menopause and Perimenopause
In this special episode of The Microscopists, we're joined by three passionate voices who share their personal experiences with perimenopause and menopause.They share personal stories of navigating...
themicroscopists.bitesizebio.com
October 20, 2025 at 12:58 PM
Reposted by Martin Jones
will-j-moore.bsky.social
The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!
October 20, 2025 at 1:00 PM
Reposted by Martin Jones
imgprague.bsky.social
🧬Get a feeling of electron microscopy in biomedicine in one week
🔬Learn principles of electron microscopy and become an independent user
👩‍🏫Highly experienced tutors – focus on hands-on training

Register now – spots are limited to 15 participants!
course.img.cas.cz/tem/
October 17, 2025 at 6:44 AM
Reposted by Martin Jones
cppape.bsky.social
Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published:
www.molbiolcell.org/doi/full/10....
SynapseNet is a deep learning based software tool that automates the segmentation of vesicles, mitochondria, synaptic compartments, and the active zone. This is visualized in three panels. On the left, a section of an electron tomogram with a synaptic compartment densely filled with vesicles, which appear as round structures with dark boundary and light body in the image, is shwon. The top right panel shows the segmentation result of vesicles, visualized by masks with an individual color per vesicle and outlines for the segmented compartment (red) and active zone (blue). The bottom right panels shows a 3D rendering of the segmentation with vesicles shown as yellow spheres.
October 17, 2025 at 11:09 AM
Reposted by Martin Jones
biorxivpreprint.bsky.social
Sexual dimorphism in the complete connectome of the Drosophila male central nervous system https://www.biorxiv.org/content/10.1101/2025.10.09.680999v1
October 9, 2025 at 5:15 PM
Reposted by Martin Jones
bethcimini.bsky.social
Now that I can say it publicly - huge congratulations to @michelleitano.bsky.social , winner of this year's @bioimagingna.bsky.social Michael W Davidson award for "Community contributions, in any of the areas of Engagement, Education, Mentorship, and Standardization". So well deserved! #GBIxBINA2025
A black slide with the Bioimaging North America colorful logo in the top left, with the text "2025 Award Recipient - Michelle Itano, University of North Carolina, Chapel Hill". It has a picture of Michelle, as well as white text in a box- "Michelle embodies the various attributes that Michael Davidson was known for, and she is a beloved member of the imaging community who never hesitates to support it, or contribute to its growth.”
October 9, 2025 at 3:09 PM
Reposted by Martin Jones
jytinevez.bsky.social
Job alert!

We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?

See also on the forum:
forum.image.sc/t/research-e...
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
forum.image.sc
October 7, 2025 at 12:39 PM
Reposted by Martin Jones
retof.bsky.social
We present multi-immersion Oblique Plane microscope (miOPM), a light-sheet platform that can be adapted to a wide range of applications, from sensitive live cell imaging to imaging organs and cleared tissues.
www.biorxiv.org/content/10.1...
October 6, 2025 at 5:52 PM
Reposted by Martin Jones
dlegland.bsky.social
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
jofmicroscopy.bsky.social jofmicroscopy.bsky.social @jofmicroscopy.bsky.social · Sep 29
"From cells to pixels: A decision tree for designing bioimage analysis pipelines" by Elnaz Fazeli, Robert Haase, Michael Doube, Kota Miura & David Legland is free-to-view here: doi.org/10.1111/jmi....
September 29, 2025 at 4:17 PM
Reposted by Martin Jones
david-j-barry.bsky.social
I forgot that I had this made. As a prototype that never went into full production, it's the only one in existence and, therefore, highly desirable.

Let's start the bidding at £1,809, £1 for every day since the very first CBIAS.

For an extra 50%, you can have it signed by @martinjones.bsky.social.
Crick BioImage Analysis Symposium 2024 Commemorative Mug
October 3, 2025 at 7:48 AM
Reposted by Martin Jones
bioimagearchive.bsky.social
🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
September 15, 2025 at 9:57 AM
Reposted by Martin Jones
bioimagingna.bsky.social
#HappyFluorescenceFriday!

#microscopycommunity-new to the field of bioimaging or just looking to brush up? Wed Sept 17, the I&E tools series will bring a talk on raw image data- don’t miss out on setting yourself up for success- join us!

More info: buff.ly/BIhYKtO
September 12, 2025 at 4:56 PM
Reposted by Martin Jones
florianjug.bsky.social
🚨 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...
Ready to shape the future of AI in life science?
The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...
www.scilifelab.se
September 12, 2025 at 1:46 PM