napari needs your help! Has napari helped you make cool and groundbreaking discoveries? We'd love to highlight that in our docs. Please tell us about it! You can fill in this survey:
napari.typeform.com/to/vTCKeTKv
and/or, as ever, drop by our chat room or meetings:
napari.org/dev/community/
🙏
BIG UPDATES!
OCTRON now supports the new SAM3 models (alongside SAM2)!
We’ve also added a global switch for Detection vs. Segmentation: Use the same annotations to train either lightweight detection or full segmentation models. Plus, we’ve added support for the new YOLO26 models. ⤵️
1/12
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:
- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports
github.com/imaging-form...
v0.0.rc1 on PyPI
I'll never get tired of lazily browsing elastix-coregistered #WSI data in @napari.org using the upcoming @openmicroscopy.org ome-zarr @zarr.dev format version that allows to specify and read transformations directly from the image data itself.
Data source: rodare.hzdr.de/record/3131
smart microscopy postdoc position in Montpellier, France. Could definitely do worse. With @glyg
https://forum.image.sc/t/up-to-4-year-postdoc-position-in-montpellier-smart-microscopy/119201
#FOSS #Microscopy #GetFediHired
1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:
📣 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!
🧫->🔬->💻->📊
Our updated @napari.org video plugin includes a small widget to play videos with sound. github.com/danionella/n...
Time is running out to apply for this year's @royalmicrosoc.bsky.social Intro to Image Analysis course in Cardiff - deadline is tomorrow!
Spread the word!
Great team effort, with @retof.bsky.social and more! Most imaging performed with with a snouty equipped Oblique Plane Microscope. Rendering done in @napari.org.
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!
Thanks to everyone who has donated already, and thanks to @aganders3.bsky.social for the animation! 😍
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...
the napari logo (a two-lobed island) modified to look like a snowman, with Christmas (red/green) colors
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...
OME-Zarr is the answer. The question was: How do we enable interactive visualisation, FAIR sharing & image analysis at the TB scale?
Lorenzo Cerrone demoing visualizing HCS plates stored as OME-Zarr
Joel presenting Fractal
CytoData 2025 audience
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...
The schedule of the open source summer school, showing the four tracks of Animals in Motion, Large array data, BrainGlobe & Extracellular Electrophysiology
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...
