napari

Are you guys still here? 😅👋 Just dropping in to spruik our account on the other site: @napari" target="_blank" rel="nofollow noopener">fosstodon.org/@napari. Follow us there!

Hello naparistas! Core dev @Czaki_PL has been hard at work to improve the performance of Shapes layers. We've now released napari 0.5.6rc0 with the option to turn on C++ acceleration of Shapes layer creation. Check out our ✨brand new blog✨ for details! napari.org/island-dispatc…

New preprint: We have developed an integrated pipeline to i) image gastruloids in toto with dual-view 2-photon🔬, ii) quantitatify cell and tissue-scale patterns of gene expression and morphometric features, iii) interact with the data in @napari_imaging. biorxiv.org/content/10.110…

@aquicarattino @loicaroyer @jobragantini @napari_imaging Visualizing individual shots so I can make a selection before aligning and stacking them. Being able to navigate between shots in the stack is very convenient.

@loicaroyer @jobragantini @napari_imaging Napari is very cool. I use it in my Python toolchain for astrophotography.

Super stoked that @jobragantini 's @napari_imaging plugin for Meta's Segment Anything Model 2: napari-sam2, as well as our cell tracking software ultrack were showcased during Chris Cox's Keynote at Meta's Connect 2024. Jordao and I were in the audience; it was great fun! github.com/royerlab/napar… github.com/royerlab/ultra… biorxiv.org/content/10.110… @czbiohub

Sneak peek👀: Remember the @napari_imaging napari-clusters-plotter? We are scaling up⬆️! New plotting by @zoccolermarcelo along with other major upgrades makes cross-layer clustering possible. It’ll take a bit (0.9.0🪧), but we’re developing in the open: github.com/BiAPoL/napari-…

We are organizing with @giulia_paci and @MaKaefer the @The_CBIAS @napari_imaging Workshop 2024 at @TheCrick : 27-28 November 2024 Applications by: 15 September 2024 Introduction to conda environments, napari plugins, basic #bioimageanalysis with Jupyter Notebooks and napari

these dancing cells kill people! video done completely with open source software: stardist for segmentation, trackpy for tracking, @napari_imaging for visualisation, @Blender for video editing

🚨📢Our paper on imaging, segmenting, visualising and measuring patterns in gastruloids across spatial scales w/ @napari_imaging is out‼️ An project led by @_AliceGros, @JVanaret, @DunsingValentin et al.🤓 A collab. between @Equipe_lenne, @PhilippeRoudot's and our lab. ⬇️Link⬇️

It was a pleasure to have @zoccolermarcelo present and do hands-on on @napari_imaging on our workshop! If you missed his session, you can check his #OpenAccess resources on Zenodo.

We've just released the "brainmapper" widget allowing analysis of cellular distributions in whole-brain microscopy images entirely within @napari_imaging. Full details available on the blog: brainglobe.info/blog/brainmapp…

Automatic detection of calcium waves with two @napari_imaging plugins: conv-paint (segmentation) and ARCOS (collective events). Links below :)

New to napari? Now is a great time to learn how to contribute. Join @WVierdag for another #napariCodeCafe on Jul 16 at 7pm CET! See his announcement for details: forum.image.sc/t/napari-code-… The contribution from the first café is being released with 0.5.0!

Check out the release notes here: napari.org/dev/release/re… and try it out with `pip install --pre "napari[all]"`!

After a furious few weeks fixing bugs, we just pushed napari 0.5.0rc0! Barring any new bug reports, 0.5.0 will drop in ~24h just in time for @psobolewskiPhD to announce the release to @SciPyConf #SciPy2024 attendees in the SciPy Tools Plenary. 😃

In the absence of a whiteboard ⁦@jobragantini⁩ used a Labels layer to explain watershed segmentation during #skimage and ⁦@napari_imaging⁩ tutorial ⁦@SciPyConf⁩ 🤣

We'll have more highlights when the full release rolls around next week, but for now please test, chat with us on Zulip(1), and raise issues on GitHub(2)! 🙏 (1) release thread: #narrow/stream/212875-general/topic/napari.200.2E5.2E0.20alpha.200.20release!/near/447226692" target="_blank" rel="nofollow noopener">napari.zulipchat.com/#narrow/stream… (2) github.com/napari/napari/… /end 🧵

Here's a PR demonstrating this for affinder: github.com/jni/affinder/p… It's easy *and* it's backwards compatible with 0.4.19 so you can add and release updates to your plugins *today*!

The big new thing is contributable menus! 📋🍽️ Add your plugin's commands to napari menus with just a few extra lines in your napari.yaml. Now commands can be grouped together by function rather than mixed in a plugin salad! 🎉 Read all about it in NAP-6: napari.org/dev/naps/6-con…

We've tried pretty hard not to break anything that wasn't deprecated in 0.4.19* but yea, it's big, so please test. (As a reminder, many of the deprecations previously slated for 0.5.0 have been postponed until 0.6.0.) * #deprecations" target="_blank" rel="nofollow noopener">napari.org/dev/release/re…

🚨 Attention all naparistas! 🚨 Announcing napari 0.5.0a4 pre-release! 🚀 napari.org/dev/release/re… 🧵👇

This is a *huge* release, and the first in 18mo from the main branch of napari (don't ask) (or ask but you have to buy us a beer 🍺😜). We are aiming to release next week ahead of @SciPyConf, so if you can test ASAP we would be very grateful!