Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!

OCTRON stands on the shoulders of giants. We make use of #SAM2 (meta), #YOLO11 (ultralytics) and some of THE best multi-object trackers out there #BoxMOT. For rapid data access we use python-zarr (>3.1). We couldn’t have done it without the super supportive community surrounding @napari.org.

Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate

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...

Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff: Paper: doi.org/10.1242/jcs.... Code: github.com/pertzlab/arc... Plugin: github.com/pertzlab/arc...

We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K. opencollective.com/napari/donate

🦠🔬🤖🧑‍💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out 💻: github.com/HenriquesLab... 📄: www.biorxiv.org/content/10.1...

And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly

I wrote my first proper post on LinkedIn today. It was cheesy, bit of a weird thing to do. Bottom line is I'm still buzzing from spending two days playing with napari sourounded by kind microscopy nerds at the #CBIAS2025 Napari Workshop.

Happy to finally share micromorph with everyone! If you are interested in performing morphological measurements of bacteria, and like using Python and Napari then this is for you! You can read about it in our preprint, and find the code on our Github repo, PyPi or directly from the napari hub!

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...

It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!

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

Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa... Survey: napari.typeform.com/sustainability If you use napari at all we would be super grateful if you filled it in! 🙏

Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa... Survey: napari.typeform.com/sustainability If you use napari at all we would be super grateful if you filled it in! 🙏

Hi Fans of Feedback Microscopy, what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org? Btw, it works as well in Fiji&ImageJ :-) Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.

I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way. quantixed.org/2025/11/04/a...

Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K. There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data. Applications open Dec 1st. More details: neuroinformatics.dev/open-softwar...

Happy Halloween from the napari team!

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!

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!

Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!

Do you use napari and love @xarray.bsky.social? Or use Xarray but cry when napari ignores the axis names? Read how we will improve this in the future! 🤝 napari.org/island-dispa... Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!

Filling out the attached survey and reading this blog will really help bring you up to speed with our progress as a team. Most importantly, we want to guide this project in the direction that sustainably supports the community -- and that's why we'd like your help!

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...

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!

napari 0.6.6 is out! 🚀 This is a bugfix release following up 0.6.5: if something in your napari workflow unexplicably broke, you might want to update ;) Also, with the new bundle you can now "open files with > napari"! Check out the full release notes on the website: napari.org/stable/relea...

We are incredibly proud to receieve this award, especially as it recognises the hard work of the entire BrainGlobe community. Thank you to everyone who has contributed to BrainGlobe over the years!

Join the new plugin sustainability initiative! Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK... Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann... The first zoom meeting will be this coming week: napari.org/stable/commu...

napari 0.6.5 is out! 🚀 Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...

Check out the cool new “release highlights history” page @timmonko.bsky.social cooked up for us! 😍 napari.org/stable/relea... Best of all: it’s automatically generated from release notes so it’ll always stay up to date.

the @napari.org crew came to town! 🥰

Jumping 🕴️ now into "Practical session 4: Behavior Modeling" with @kevinyamauchi.bsky.social online! First things first, students are getting to know how to do #bioimage visualization in Python 🖥️🐍 using @napari.org👇

Lovely talk by Open Software Week participant @ishratz25.bsky.social on the challenges of using @brainglobe.info tools to identify very small regions, in very large images.

Thrilled to share the first story from my postdoc! 🎉 A wonderful experiment + simulations collaboration. In the Drosophila wing, we find that 3D cell shapes affect signalling range and fine-tune developmental patterning www.biorxiv.org/content/10.1... Thread below ⬇️

In our next guest blog, GSoC participant Saarah Hussain talks about her summer working on @brainglobe.info. neuroinformatics.dev/blog/gsoc_20...

💻 You can directly try out CLEM-Reg for yourself with our @napari.org plugin where we also include a sample benchmark dataset. Installation instructions are here 👉 github.com/krentzd/napa... (8/9) www.youtube.com/watch?v=ud3z...

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊 Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

u-Probe now can be run without a MATLAB license, and exports detection and tracking results in a format that can immediately be visualized with @napari.org! github.com/DanuserLab/u...

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

Each experiment gets a jupyter notebook, so experiments are reproducible and easy to run, even for users with little coding experience. Image processing pipeline is modular, easily adjusted to different cell lines or experiments. Using @napari.org as GUI. Code: github.com/pertzlab/rtm...

I finally managed to upload the first version of the napari-czitools plugin (still in alpha - expect issues...) - open complete CZI images or subsets - read CZI metadata pypi.org/project/napa... or github.com/sebi06/napar...

🚀 napari 0.6.4 is out! Highlights from this bite-sized release: launching scripts from the command line with `napari <path-to-script>` and making the console auto-focus when opened. We’ll be announcing all future napari releases here, so stay tuned! 🔗 Release notes: napari.org/stable/relea...

🚀 napari 0.6.4 is out! Highlights from this bite-sized release: launching scripts from the command line with `napari <path-to-script>` and making the console auto-focus when opened. We’ll be announcing all future napari releases here, so stay tuned! 🔗 Release notes: napari.org/stable/relea...

The BrainGlobe track started with an introduction to image analysis with @napari.org, and then tutorials on how to use @brainglobe.info to register data to atlases, and how to detect cells in whole-brain microscopy images. All our tutorials are online: brainglobe.info/tutorials #niu_osw

📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social From conda to plugins to Jupyter, practicals on real data with expert guidance. For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025

Excited to share the final version of the STRESS software paper 🎉 Do you want to measure cell or tissue stresses using deformable beads or droplets, please check this paper: nature.com/articles/s41... Full access: rdcu.be/ezlGj and the preprint thread below ⬇️ x.com/CampasLab/st...

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇