napari
n-dimensional image viewer for Python
- Reposted by napari📣 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! 🧫->🔬->💻->📊
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- Reposted by napariTime 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!
- ✨New Year's resolutions involve learning something new?✨ Then apply for our “Introduction to Image Analysis” workshop in Cardiff in May 2026! Deadline for applications is January 16th. 🔗⬇️ www.rms.org.uk/rms-event-ca... @royalmicrosoc.bsky.social @david-j-barry.bsky.social @martinjones.bsky.social
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- Reposted by napariKind 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!
- 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
- Thanks to everyone who has donated already, and thanks to @aganders3.bsky.social for the animation! 😍
- Reposted by napariDo 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!
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View full threadReposted by napariOCTRON 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.
- Reposted by napariNew 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...
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- 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
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- Reposted by napariAnd 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
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- Reposted by napariApplications 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...
- Reposted by napariIt'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!
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- 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! 🙏
- 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...
- Reposted by napariHi 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.
- Reposted by napariI'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...
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- Happy Halloween from the napari team!
- Credit to @timmonko.bsky.social for our rounder, friendlier logo tweak (coming soon) and Lorenzo Gaifas for the Halloween Special Edition Logo.
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- 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!
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- 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...
- … or just skip straight to filling out our survey! 📋 napari.typeform.com/sustainability
- Reposted by napariThe #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...
- Reposted by napariWe 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!
- 🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025! 🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative. #OpenScience #Neuroscience
- 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...
- Current goals: 1. Centralizing community resources to foster collaborative development. 2. Create an initiative to encourage best practices and highlight plugins. 3. Improve the plugin development infrastructure. 4. Create tooling to evaluate plugin health and support sustainable maintenance.
- This initiative is born out of an URSSI Early-Career Fellowship awarded to @timmonko.bsky.social, and we thank them for their support! urssi.us/blog/2025/09...
- 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.
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- Reposted by napariThrilled 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 ⬇️
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- Reposted by napariWe (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/
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- Reposted by napariOnce 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 🧵)
- Reposted by napariWe'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 🧵)
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- Reposted by napariI 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...
- Reposted by napariThe 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
- Reposted by napari📢 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
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- Reposted by napariIt'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: 👇
- @napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software. Learn more: youtu.be/0g_MkTa_NwQ #EurekaPrizes
- Reposted by napari@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software. Learn more: youtu.be/0g_MkTa_NwQ #EurekaPrizes
- Reposted by napariCell tracking is never perfect, and it's important to understand the types of errors your solution contains. Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d... You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
- Reposted by napariThe 1st working version of my little @napari.org plugin (napari-czitools) is almost ready. It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read. Still quite some things to improve ...
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- 🚀 Big news! The napari hub has been reimplemented and is now community-run! 🎉 It's still the go-to place for finding and sharing napari plugins, but the website is now snappier and lighter-weight. Check it out 👉 www.napari-hub.org
- We’ve taken over development and maintenance, using the visual design of the original -- thank you to the CZI team for building and maintaining the hub over the last four years, and to Yunha Lee for creating the prototype of the new site.
- The hub is now deployed statically via gh-pages, using data stored and served via npe2api🧑💻🌐. Not only is this a simpler and more lightweight implementation to maintain, but it's significantly faster too🔥!
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View full threadThis marks a huge milestone towards long-term sustainability for napari and its plugin ecosystem — and we’re just getting started. Over the next few months we'll be updating the visual design, adding more searching and filtering options, re-enabling Zulip updates, and so much more!
- Reposted by napari#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis @mazoc.bsky.social
- Reposted by napariBtw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️ 🌍 www.fabriziomusacchio.com/teaching/tea...
- Reposted by napariWhat I really like about @napari.org is how well it integrates modern #Python tools. Great to have such a flexible, evolving #opensource platform for #bioimage analysis! 👌 #Napari #imageanalysis #neuroscience
