Videos are now available from the 2025 QuPath Training Course, from @iamichaelnelson.bsky.social, @zmikulski.bsky.social, and myself. Watch for multiplex tutorials! For image analysis inspiration! Or just watch to hear me speak like an overcaffeinated squirrel! www.youtube.com/playlist?lis...

📣 We are accepting applications for the 2026 Boston Bioimage Analysis Course (BoBiAC): bobiac.github.io! Join us this July at Harvard Medical School for a 6-day intensive hands-on course to learn bioimage analysis with Python! Apply by May 18th! No prior Python experience required! 🧫->🔬->💻->📊

Unleashing live-cell imaging for the masses! Adapting the OpenFlexure Microscope for Affordable Live-Cell Imaging www.biorxiv.org/content/10.6... Fits into existing incubators for time-lapse experiments & feeds into existing bioimaging analysis pipelines. Thanks @wellcometrust.bsky.social funding

We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework. We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

Recruitment for the EMBL International PhD Programme is officially open! 🔊 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us! 🔎 Read more here: tinyurl.com/4jdt2ra5

The OME meeting has followed me from New England to Germany! consistently my favorite scientific meeting of the year, with the nicest community anywhere. Join us there!

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

BOOOOOOO

GO BILLS!

Won best thesis award with this video! 4 years of research and play in 3 minutes :') youtu.be/so0fPlK1-LM

Kind of flew under the radar, BUT we released napari-omero 0.6 recently 🥳 @openmicroscopy.org You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :) Thanks @psobolewskiphd.bsky.social and other maintainers!

Very pleased to announce the release of #OMERO.figure 7.3.0 including ROI Labels, Colorbars and lots of bug fixes. Thanks to contributors: Rémy Dornier, @tom-bssnnt.bsky.social, Jens Wendt, Niraj Kandpal. www.youtube.com/watch?v=cUy5...

#Bills red helmets! 😍

It's new annual conference budget time! I've updated the public, filterable Chemistry Conference Database with hundreds of new conferences. There are currently 564 conferences in the list. supersciencegrl.co.uk/conferences #chemsky #chemchat

🚨 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 :)