napari

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: 👇

@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

Cell 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.

The 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 ...

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org

This 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!

The plugin listing is updated four times a day, so you shouldn't have to wait long to see your new plugin🧩. And (it goes without saying), it's open-source! If you notice any errors with your plugin's information, please open an issue on the GitHub repo: github.com/napari/hub-lite.

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🔥!

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.

🚀 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

Copying selected elements of a layer in napari into a new layer

#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

Btw, 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...

What 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

🚀The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari!

🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...

🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...

Excited and honored to speak at the @royalmicrosoc.bsky.social meeting tomorrow where I'll talk about our latest AI tools. Meanwhile, check out Vijay&Arlo's Napari "bootstrapper" plugin for massively accelerated segmentation of multidimensional imaging datasets

Github: github.com/ucsdmanorlab...

I'll be at the Learning Zone at #MMC2025 tomorrow afternoon with @martinjones.bsky.social, @lankylaste.bsky.social & Sara Salgueiro Torres, talking about how you can get started using #OpenSource software like #FIJI, @jupyter.org and @napari.org for #ImageAnalysis

rms-daim.github.io/DAIM-MMC2025/

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging

Let's have a look 👇🧪💻🔬

We developed Spotiflow with the mindset of making it useful and usable, and as such it comes in different flavors: one can use it as a Python API, as a CLI or with a GUI using our @napari.org plugin! Hopefully more integrations will come soon ;)
(7/N)

Career - German BioImaging Job offers Feel free to contact us, if you want to publish your job offer here. Project Coordinator (m/f/d, 50-100%, fully remote) at GerBI-GMB e.V. June 2025 We are looking

🚨 We’re hiring TWO new colleagues!

🧠 Structured Metadata Expert – Design data models, standards & annotations for #OMEZarr
🌐 Web Developer / Prototyper – Build interactive tools & demos for the community

Both fully remote. Both open science.
🔗 gerbi-gmb.de/resources/ca... #RSE #OpenScience

Bioimage Analysis Conference 2025 in Kobe GloBIAS Bioimage Analysis Conference 2025 Oct 26, 2025 - Oct 31, 2025 | Kobe, Japan Venue: RIKEN BDR, Kobe, Japan Registration via Google Forms here: https://tinyurl.com/3dtajhh6 General informatio...

Reminder: the @globias.bsky.social 2025 symposium is happening Oct 26-31 in Kobe, Japan, and, on top of many other cool bioimage analysis events, several members of the napari core team will be leading a napari hackathon. 🧑‍💻👩‍💻👨‍💻 Registration deadline is Jun 15!
www.globias.org/activities/b...

It's been a while since I was legitimately blown away by something but nnInteractive is, I swear, some kind of dark segmentation magic.

Every time I think "it can't possibly get this", somehow it does.

github.com/MIC-DKFZ/nap...

screenshot of the napari github repo page. The issues tab shows 999 open issues.

Ok guys **nobody open any more issues** 😂

DNA channel fluorescence intensity with overlaid object segmentation labels of chromosomes / cell nuclei in a zebrafish embryo. Acquired by Süheyla Eroglu-Kayikci on @visitech.bsky.social iSIM, labeled by student assistant Philip Kohle and rendered by PhD student Nils Friederich using @napari.org

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0!
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...

This is accompanied by a new set of tutorials showing exactly how you can start making beautiful microscopy visualizations in @blender.org!
Following along is also easy with the example OME-Zarr @openmicroscopy.org datasets 😄
Find the tutorials here: www.youtube.com/playlist?lis...

#GloBIAS conference 2025 Kobe, Deadline extended to June 15th! This includes the training school, two hackathons, and taggathon registration, not only the symposium (... but sorry, the travel grant for the training school has closed)

napari Americas/Africa/Europe community meetings - HackMD

It will be Wednesday the 21st at 5:30PM CET | 8:30am PST. Here are the details:
Agenda: hackmd.io/BXWDZ3i8Q6OA...
Zoom link: numfocus-org.zoom.us/j/8404893043...

Oh yeah and there will be an update to multichannel grid mode too!

Contributing to open source can be scary, but don't worry! We ourselves often write code where the initial implementation is not the best, but we are here to help simplify life. Want to know more about contributing or have anything else napari you want to discuss come join our community meeting!

We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!

Deadlines extended - you can still register for the GloBIAS conference! We have extended most deadlines. Please check our webpage: tinyurl.com/mr3kx5a5! Looking forward to welcoming you to Kobe, for training, developing and discussing a broad range of BIA topics!