napari

github.comGitHub - BiAPoL/napari-clusters-plotter: A napari plugin for clustering objects according to their properties.A napari plugin for clustering objects according to their properties. - BiAPoL/napari-clusters-plotter

Just released the napari-clusters-plotter 0.11.0 github.com/BiAPoL/napar..., a little passion-project of mine for interactive exploration of datasets and attached features in @napari.org Two cool things to take note of 👇

New blog post: a recap of our latest hackathon, naPLari in Krakow, Poland, this past July! Read why our hackathons are world famous! (With GloBIAS, we've had attendees from every continent except Antarctica!) And give us a follow to make sure you don't miss the next one! napari.org/island-dispa...

napari reposted

Marie Held

@makaefer.bsky.social

Want to enhance your image analysis skills with napari? We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data. 🕒 Applications close on 15 September. Learn more and apply 👇 www.crick.ac.uk/whats-on/cbi...

crick.ac.ukcrick.ac.uk

@clairedessalles.bsky.social

🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach ⏱️ Contract, 14–35 hrs/wk 🌍 Global 100% Remote Learn more and apply today: napari.org/island-dispa...

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Claire Dessalles

NeMo is finally out! 🐟 We present our new method to peel cellular layers and extract their nematics. If you're wondering what a fish has to do with curved nematics, check out the thread and the publication 👀👇🏼 arxiv.org/html/2609.12...

napari reposted

Replying to @jo-soltwedel.bsky.social

🟦🟦🟦 Less fancy, just as handy: Attaching simple translations to your image tiles allows the #stitching tool of your choice (here: github.com/multiview-st... at work in @napari.org) and just hit "Fuse". Dataset from github.com/JaneliaSciCo...

napari reposted

Replying to @jo-soltwedel.bsky.social

OME-Zarr 0.6 allows to compose multi-modal image data across dimensionalities into a joint dataset and ingest it into a supporting viewer of your choice. Combining image data across scales from µm 🧫 to cm 🧠 and beyond will be much easier now! Dataset source: rodare.hzdr.de/record/3131

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@henriqueslab.bsky.social

Replying to @jo-soltwedel.bsky.social

The main new things in 0.6 are ✨transformations ✨ - adding the "Where" directly to your image data. Some data (e.g., SCAPE microscopy) require a transform to display correctly. View your data correctly, data-duplication free with OME-Zarr 0.6! (UI is WIP, made for @napari.org x napari-ome-zarr)

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Ricardo Henriques

15 Sept

🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇 doi.org/10.1038/s44488-026-00022-y

napari reposted

SWC/GCNU Neuroinformatics Unit

@neuroinformatics.dev

21 Sept

Our Google Summer of Code participants have been writing up their projects. First up, Anna Teruel-Sanchis who built an interactive GUI in @napari.org for correcting pose estimation tracks directly within the movement framework. Read more in Anna's blog: neuroinformatics.dev/blog/gsoc_20...

napari.orgTriageThis guide describes how napari curates its issue trackers and pull requests. A healthy tracker makes the project easier to use and to contribute to: issues are clearly described, duplicates are linke...

Thanks for the shout out! 😍 Our goal in writing this blog was to share the (recent) overthinking we've done our typechecking journey to help others. Thank you Aniket for writing this up! Our new triage team truly shined 🌠 on this multi-week process: napari.org/stable/devel...

Pyrefly@pyrefly.org

@napari.org reports its Pyrefly check at ~0.7s warm / 0.9s cold, versus ~15–25s cold in its previous mypy setup. Fast checks change habits: run it locally, fix the thing, move on. Compute left for science. Thanks for the great write-up on your experience! napari.org/island-dispa...

napari.orgFrom Any to Certainty: A Typechecking Journey — napari blog documentation

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DrLachie

@drlachie.bsky.social

10 Sept

Proud to present the publication of napari-lattice – our solution to the immense computational requirements of Lattice Light Sheet and Oblique Plane Microscopy. onlinelibrary.wiley.com/doi/10.1111/... Before I get into the thread, the important part is on github: github.com/BioimageAnal... (1/n)

onlinelibrary.wiley.comnapari‐lattice: A user‐friendly image processing tool for lattice light‐sheet microscopy dataLattice light-sheet microscopy (LLSM) enables researchers to capture high-speed 3D videos of living cells with high definition and minimal damage. However, this technology generates terabytes of data....

napari reposted

Tamas Nagy

@tamasnagy.com

6 Sept

Even with all the advancements in automated cell tracking getting us to 90%+ accuracy...that's still a lot of broken tracks over long movies! Our brains are pretty good at this so I made Vizsla 🐕, a little @napari.org plugin, to help you fix your tracks manually. 👉 pypi.org/project/napa...

napari.orgnapari 0.9.0Tue, Aug 25, 2026 We’re happy to announce the release of napari 0.9.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing l...

🚨🚨🚨 napari 0.9.0 is out! 🚨🚨🚨 This is a huge release for us and for our community, with over 30 people contributing new features, improvements, and bug fixes in the 6 weeks since 0.8.0! Release notes here: napari.org/stable/relea... and some highlights in the thread below! 👇

Surface layers can now be sliced in 2D, including with thick slicing! This makes it possible to navigate surface data in the 2D view, and supports thick slicing and async slicing, allowing support for large surface layers.

Be sure to check out the full release notes at top! A HUGE thanks to our contributors, including our SciPy and EuroSciPy sprint contributors, our naPLari 🇵🇱 hackathon contributors, and more! Want in on the action? As always, check out our community page! napari.org/stable/commu...

You can now take a guided tour of the viewer! This is a great way to get your colleagues started with using napari. Spread the word! 😉 Access the tour from the Help menu, or using the Command Palette (Ctrl/Cmd+Shift+P).

napari.orgPlugin contributionsThis page provides guides on many of the plugin contribution patterns. Each provides a general overview of the purpose of the contribution and an example implementation. For details on the type and me...

One for plugin authors: plugins can now contribute and query preferences from users! No more guessing whether a user wants to open a zarr as a NumPy array or using Dask: just point them to the setting! See the contribution guide here: napari.org/stable/plugi...

Using the same infrastructure, you can now just add @xarray.bsky.social DataArrays as images to napari and napari will read the axis labels, scale and translate, and units metadata automagically! This was issue number 14 in the napari repo. We get to stuff eventually! 😅

Another long-standing issue fixed: for all of napari's history, you could only change settings on a single layer. No more: common controls now show for any selection of layers, and you can then adjust them together! 🤯

First up: if you add axis_labels to your layers, they will automatically propagate to the viewer! This makes it easier to reason about high-dimensional data, as shown by our friendly FLIM ghost! (Source: www.ebi.ac.uk/biostudies/b...) Check it out yourself with: gist.github.com/jni/d188d977...

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Sebi

@sebi06.bsky.social

24 Aug

Hi all, I updated pypi.org/project/czit... (0.21.0) and pypi.org/project/napa... (0.12.1) again. Now in @napari.org also opening large CZI files should work much better when using the plugin. The image shown in the video is about 100 GB on disk.

20 Aug

Sizzling Summer Series 4 - global 🌍️ napari 0.9.0 is about ready to fly out the door! ✈️ We would be grateful if you tried out the pre-release: Install into an environment with `pip install "napari[all]>=0.9.0rc1"` or try with uv in a temp environment with `uvx "napari[all]>=0.9.0rc1"`.

napari.orgnapari 0.9.0⚠️ Note: these release notes are still in draft while 0.9.0rc1 is in prerelease testing. ⚠️ Thu, Aug 20, 2026 We’re happy to announce the release of napari 0.9.0! napari is a fast, interactive,…

20 Aug

We would especially like folks to test the layer controls section when multiple layers are selected (it now works!), inheritance of metadata when passing Xarrays, and the new contributable npe2 plugin settings! Read the full release notes, with highlights, here: napari.org/dev/release/...

20 Aug

This 0.9.0 release has the most contributors (30+) since napari 0.5.0 and all in barely a month since 0.8.0! 🤩 We are so grateful for our wonderful community of contributors and users, especially those that we met at SciPy, EuroPython, EuroSciPy, their sprints, and our own naPLari Hackathon. 👏

napari reposted

17 Aug

One cool feature in the latest #ome-zarr spec are "projectAxis" transforms 📽️: Projecting images into higher dims (i.e. 2D->3D) is absolutely transformative for some use cases! Now to do this with maaaany more slides 🔬 Dataset from rodare.hzdr.de/record/3131 cc @napari.org

13 Aug

Sizzling Summer Series 3 - naPLari Hackathon, Kraków 🇵🇱 A lucky crew of 13 got to spend 6 jam-packed sunny days inside pumping out a fantastical assortment of napari features 🖥️ It was a ☕️ caffeine-, string 🧀 cheese- and 🥟 pierogi-fuelled extravaganza 🎊

12 Aug

Sizzling Summer Series 2: Minneapolis -> Kraków ✈️ We talked, tutorialed and sprinted at EuroPython! The sprints WENT OFF -- 22 merged PRs don't lie 🤯 Then rinse repeat for EuroSciPy - our first conference as platinum sponsors! 💐THANK YOU💐 to those who joined us in Kraków!

12 Aug

July was a whirlwind 🌪️ Join us for a Sizzling Summer Series of posts highlighting the community's amazing work💪 First, @timmonko.bsky.social, @aganders3.bsky.social and @willingc.bsky.social took on Minneapolis for SciPy 2026 with a tutorial, talk and plenary update - bit.ly/napari-scipy26

napari.typeform.comnaPLari HackathonQuestionnaire for the napari hackathon in Krakow, Poland, July 24-29th, 2026.

31 July

And it's a wrap! The hackathon was a fantastic success! 🥳 You can look forward to a longer post about all we did, and one of our biggest releases yet in 0.9.0! Huge thanks to all the participants 🤩, and we hope to see you at the next one!

napari@napari.org

🎉 Announcing the naPLari hackathon in Kraków, Poland 🇵🇱, July 24–29 2026, after EuroSciPy! Hack on napari, join deep dives, meet the team. All experience levels welcome! 📝 Register by July 1: napari.typeform.com/naplari-hack #napari #ScientificPython #OpenSource #EuroSciPy #BioImageAnalysis

napari reposted

napari.orgnapari: a fast, interactive viewer for multi-dimensional images in Pythonview and explore 2D, 3D, and higher-dimensional arrays on a canvas;, overlay derived data such as points, polygons, segmentations, and more;, annotate and edit derived datasets, using standard data st...

23 July

Not going to be in Cracow for the big event so had to make do with a small impromptu @napari.org x @openmicroscopy.org #omezarr Hackathon in Bern 🔬🇨🇭 @m-albert.bsky.social @guiwitz.bsky.social

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Samuel Le Meur-Diebolt

@sdiebolt.bsky.social

17 July

napari is such an incredible piece of scientific software! 🚀 And it's not just for visualizing static data. I've been using it for the past 6 months to drive a @verasonicsinc.bsky.social ultrasound system for #fUSI, and get a nice GUI for sequence control and live visualization! 🤩

napari@napari.org

napari 0.8.0 is out now on PyPI, conda-forge, and as a standalone bundle! napari.org/stable/

napari reposted

SciPy Conference 2026

@scipyconf.bsky.social

16 July

📣 One of the best parts of #SciPy2026 is seeing the Scientific Python ecosystem evolve in real time. Today's Tools Plenary featured updates from the teams behind Zarr, Xarray, Tiled, Pangeo, scikit-image, Matplotlib, and napari, showcasing new features & future directions 🫶

16 July

napari 0.8.0 is out now on PyPI, conda-forge, and as a standalone bundle! napari.org/stable/

napari@napari.org

Struggling for something to do in a TWO DAY gap without ⚽? How about trying our pre-release of napari 0.8.0? napari.org/dev/release/... Of note, this release drops Py3.10 support and deprecates PyQt5 in favor of PyQt6. It also adds some neat new features and improvements! See below: 👇

numfocus.myspreadshop.comnapari | NumFOCUS Official Swag Shopnapari pocket logo light design? ⭐ napari hat and mug design ❗ napari (pocket logo)

16 July

Also! Do you love napari and want to show that off *and* support the project? Thanks to our fiscal sponsor @numfocus.bsky.social, we now have a swag shop! numfocus.myspreadshop.com/napari Help the project and look good doing it! 😎👍 20% off for next 2 days (add the discount at checkout!).

That's the highlights, but there's many more enhancements, performance improvements, and bug fixes. See the full release notes: napari.org/dev/release/... And, as always, we'd love to hear from you. You can get in touch a myriad ways; see our community page for more: napari.org/stable/commu...

12 July

If you've never tried a pre-release, you can install it with pip install "napari[all]>=0.8.0rc1"

Annotating blobs just got easier with auto-fill of labels when right-clicking! Right click, draw your shape, and the whole shape gets auto-filled. This should give much faster annotations for many workflows!

12 July

Speaking of annotation: if you've switched back and forth between annotating in 2D and checking your work in 3D, you know it can be disorienting! You can now sync the 2D and 3D cameras so that panning, zooming, and scrubbing around in 2D affects 3D view, and vice versa. Let us know if it helps you!

*Finally*, napari gets a built-in histogram! It's still a work in progress but already *very* cool if we do say so ourselves, with live update based on the canvas and progressive, background update when computing on large full data.

napari reposted

3 July

Replying to @jo-soltwedel.bsky.social

Still, what's new? My personal favorite: The scene 🎥 Thanks to a now standardized set of transformations, you can write out the spatial relationships between (multi-modal) images, which is super neat in image registration... (Dataset: rodare.hzdr.de/record/3131)

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Joel Lüthi

@joelluethi.bsky.social

30 June

Working with OME-Zarrs in @napari.org ? Check out the newest release of napari-ome-zarr-navigator to make your life easier & allow more interactive ways to write back to OME-Zarrs. Follow the thread for more (1/5 🧵)

napari.typeform.comnaPLari HackathonQuestionnaire for the napari hackathon in Krakow, Poland, July 24-29th, 2026.

26 June

Hack with over a dozen awesome folks in Poland! Just a month away! 🥳

napari@napari.org

napari reposted

25 June

Just the occasional this-thing-is-really-easy-in-ome-zarr-0.6 kind of post: Stitching in napari @napari.org with napari-stitcher (@m-albert.bsky.social) and napari-ome-zarr (@will-j-moore.bsky.social) (WIP) : (Sample data from the awesome big-stitcher tool github.com/JaneliaSciCo...)

17 June

napari 0.7.1 is now available!! 🚀 🎉 Read the full release notes here: napari.org/stable/relea... Highlights: the scale bar inherits units from layers, colorbars for points layers, locking layers, and a signed Windows bundle! We thank especially our 9 new brilliant contributors 🤩

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SciPy Conference 2026

@scipyconf.bsky.social

3 June

🔬 Tutorial Spotlight: Build custom image analysis tools without starting from scratch. Tim shows you napari's power for microscopy, satellite data, and everything between 🛰️ Extend, visualize, annotate like a pro! #SciPy2026 🔗 scipy2026.scipy.org