🚨 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/...

Someone making some copycat #chemistry accounts: mastodon.social/@matthartingss And mastodon.social/@fraserstoddar #ChemSky

New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...

🚀⭐️ Trackastra update 🚀⭐️ We just released a new model that uses pre-trained image features from Meta’s SAM2 model. This improves performance on many datasets, most notably for bacteria tracking. To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...

💻 🧬 How does #CompSci power biomedical research? Celebrate Computer Science Education Week with @jacksonlab.bsky.social's Beginner's Guide to Genomic Databases, a 🆓 self-paced course on genomic data structures, annotation & sequence alignment: education.learning.jax.org/genomic-data... #CSEdWeek

Thanks to an up to $30M contract award from ARPA-H, JAX aims to revolutionize drug safety testing with the #CARDIOVERSE—a new project that combines #AI, #stemcells, and #genetic variation to predict #drugsafety before human trials. 💊 🧪 🔬 🤖 go.jax.org/cardioverse

Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]

DDMF

DDMF #GoDuke #NextPlay

📅 We're excited to share @jacksonlab.bsky.social's 2026 Courses & Workshops lineup and invite you to join us! Our programs in Maine and Conn., along with virtual options for many events, will accelerate your development and support your success in #BiomedicalResearch: www.jax.org/education-an...

OMG Black Thought doing a Biggie impression on the new #TheRoots DYWM anniversary live album is amazing. The whole album is really great.

The EMBO Practical Course "Hack your microscope" in Oeiras, PT, 20–25 Apr 2026 aims to innovate, democratize advanced #imaging technologies and shape the future of open-source #microscopy – Apply now! Deadline: 12 Dec https://meetings.embo.org/event/26-microscope#imaging#microscopy#EMBOmicroscope #EMBOevents 🧪

Wow! What a game! #GoDuke #NextPlay

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...

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

DDMF

Trackastra is part of the brand-new TrackMate v8. It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm. Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖

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...

Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration: www.i2kconference.org/workshops

I did it again. @globias.bsky.social #GloBIAS2025 Here's hoping I get a chance again next year.

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

2025 PitchingNinja "Mound Impressionist" Award. 🤣🏆 Winner: Miguel Rojas

uh oh

Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)

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.

Been busy in Zürich für the last 24h or so. Talks have been great so far, and I have a talk too. Still find it weird to see my name on a poster.

Talking about impostor syndrome..... I'll be a teacher in the EMBO "Hack your Microscope" together with some of the very best researchers in the field. 5.5 days of hacking and microscope/fluidics shenanigans in Portugal. You can apply here: meetings.embo.org/event/26-mic... #EMBOmicroscope

Not pretty, but a W is a W! #GoDuke #NextPlay

I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment. Those interested in talking about and contributing to napari, let’s join the regular community meeting together!

It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!

Another #OME-Zarr RFC, another implementation! Started a basic display of OME-Zarr Collections (RFC-8) in ome-ngff-validator at github.com/ome/ome-ngff...

This is shaping up to be a banger!! Don’t miss it!! (Love seeing three familiar faces!)

🚀 Exciting news! The SciPy 2025 Proceedings are officially published: 👉 proceedings.scipy.org/2025 Huge thanks to the Proceedings Committee, @curvenote.com, Jim Weiss, all the authors, and reviewers who made this happen. 🙌

No matter how advanced you become in bioengineering, the rake awaits us all. The most important thing to do in this godforsaken field is to learn deeply from failure, maintain intellectual humility, and speak up about your struggles. You never know who is out there ready to help.

More than 10 years ago, I designed my first course, Sensors and Devices, in which I teach Arduino and 3D printing to life science and biotech students. This year is the last year of this course. That was a fantastic run, and I will see how this will transform into a new course next year. #Chemsky

microfabricated stamps, fresh off the printer :)

If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on image.sc about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later. forum.image.sc/t/ome-transi...

Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎

For my Year 1 lecture course this year, I used AI to produce an audio podcast to support student learning. I was amazed how listenable it was, and how broadly accurate it turned out to be. In this thread, I talk through the process I used to make the podcast. www.youtube.com/watch?v=gK36...

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!

As part of our monthly meeting, we do a run-down of all* the new #bioimageanalysis tools that have been published in the last couple of weeks on BioRxiv**, so I thought I'd start sharing here as well. *I will miss some, apologies if I miss your paper

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!

Unreal. Of all the ways… Crushed. Brutal.

#bioimageanalysis wouldn't be the same without all the great RSEs who make our tools and keep them working! Great paper on this from a couple of years ago linked below - if there's a tool that makes your life easier, think about taking a few minutes today to thank the person or people who make it!

My former team at JAX sent two people to SciPy this year and they teamed up to teach a workshop on scaling-up deep learning inference to large-scale bioimage data - it's finally on youtube! if you need an intro to the dask/zarr world, this is a great starting point. www.youtube.com/watch?v=QCWu...

finally hit πthon

Apparently it’s possible to make “non-screen printed” electrodes using a CO2 laser. And guess who has a laser cutter? :) #chemsky

Want to hear a mid-career PI pontificate about science, career and cooking? Today's your lucky day thanks to The Microscopists podcast! Thanks Peter @yorkbioimaging.bsky.social for having me 🎙️🎧 themicroscopists.bitesizebio.com/episodes/chr...

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

For last 10 years - we have worked with thousands of organizations around the world helping support them in integrating foldscope programs. To bring in a new cohort of organizations - we are re-launching “fast and curious” 2025 edition - apply and get a Foldscope trainer and Foldscopes for free!