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...

It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!

I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment. Those interested in talking about and contributing to napari, let’s join the regular community meeting together!

Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !

If you ever used napari in your research, take a moment to read this. Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it. Now you get a chance to give back, don't miss it :)

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...

The #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!

Huge congratulations to the @BrainGlobe.info team for winning the 2025 International Prize awarded by the @theneuro.bsky.social and Helga Cooper Foundation Open Science Prizes Selection Committee 🎉 www.sainsburywellcome.org/web/research...

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

#QuPath + Imglib2 and #BDV ❤️ Promising start! (Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)

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/...

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

We (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/

Excited to share my postdoc work from the Eggeling lab in Jena (@leibnizipht.bsky.social, #FSUJena, #KTHuniversity) on bringing smart microscopy to super-resolution MINFLUX: event-triggered MINFLUX microscopy.

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 🧵)

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

📢 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

Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!

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.

How can cells self-organize rapidly into complex patterns during development? Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM). Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025... 👇Thread 🧵(1/11)

ChimeraX 1.10.1 is available now, incorporating critical bugfixes since last month's release. www.cgl.ucsf.edu/chimerax/dow...

🚀 Big news! The napari hub has been reimplemented and is now community-run! :tada: 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

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)! More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

🚀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...

it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io) but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂 as a mild deutan myself, I appreciate it! 🙏

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 👇🧪💻🔬

Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!! jobs.ethz.ch/job/view/JOP... jobs.ethz.ch/job/view/JOP... x.com/DagmarIber/s...

🚀 We’re hiring again! Join @gerbi-gmb.de as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OME #Zarr 📣 Tell your #NGFF friends. Remote, full-time. Apply by 30 June 2025: All submissions via bit.ly/gerbi-jobs-2...

Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology! 🎉✌️ journals.plos.org/ploscompbiol... So happy about this paper and how the work turned out. A small thread 👇 #bioimageanalysis #corefacility

We’re kicking off the DinoSphere Online Seminar Series! Join us for our first session with Karel Mockaer (Heidelberg) & Yong Heng Phua (OIST) 📅 1 July 9AM CEST 🔗 tinyurl.com/4mjaverj Spread the word! @protistwtmostest.bsky.social @ehehenberger.bsky.social @chandnibhickta.bsky.social&Norico Yamada

E11 Bio is launching Volara: an open-source Python library for block-wise processing of large volumetric microscopy datasets! 🧪🔬 Volara features block-wise task abstractions, making scalable image processing more accessible, robust, and repeatable. Read more: e11.bio/blog/volara

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...

Image normalization: trivial enough to automate, impactful enough to quietly sabotage your results. Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome. 👇 haesleinhuepf.github.io/BioImageAnal...

We are proudly hosting 𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School): 𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦 When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time) Join us on Zoom! harvard.zoom.us/j/9762343464...

🦠🧠 MemBrain update! 🧠🦠 We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics. 🔗 Preprint: doi.org/10.1101/2024... 🔗 Code: github.com/CellArchLab/... 🧵(1/6) #TeamTomo

‼BREAKING‼ We’ve secured new funding for the Boston Bioimage Analysis Course (BoBiAC) this July at Harvard Med School! Course fees down 37%, with fee waivers for academic applicants, for an intensive hands-on intro to bioimage analysis with Python! Apply by June 1st! iac.hms.harvard.edu/bobiac/2025

We're excited to announce the Neuroinformatics Unit Open Source Week, August 11-15 2025 in London, UK. Bringing together researchers and developers of open-source software for training, community-building and hacking. No cost and travel stipends available. neuroinformatics.dev/open-softwar... 1/

Check out our new MINFLUX Simulator: www.biorxiv.org/content/10.1... with @zacsimile.bsky.social. Realistic simulation of optics, mechanics, fluorophore dynamics and estimators. @abberior.rocks users can directly simulate sequence files.

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

Great to see that many noise2void inspired denoising algorithms have been ported to @pytorch.org! Kudos to @florianjug.bsky.social and many others ... github.com/CAREamics/ca...

23andMe is going under. Californians have the right to delete their genetic data before it's turned over to next party buying the assets. If you have a 23andMe account, go log in to download whatever reports you want to save, then follow these instructions to delete your data.

Pavel Tomancak asks everyone who uses FIJI in the crowd to stand ... and dammit, 90% of the crowd stood. What a testament to the power of such tools. #DROS25

Amazing news on thr #Fiji front. The new launcher holds beautiful promises for better bioimage analysis tools, and not only for Fiji!! See this summary thread by Curtis forum.image.sc/t/fiji-2024-...

Happy to share that the final version of record for our ( @nanigrotjahn.bsky.social) #teamtomo mitochondrial cotranslation story is online at @jcb.org! We combined STA with surface morphometrics to learn how ribosomes bind to and alter mitochondrial membranes in yeast. rupress.org/jcb/article/...

dust off the cobwebs, #vizarr is getting support for OME-NGFF "labels" metadata soon. preview:

📣 EuroBioC2025: Abstract Submissions Open! Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24. ➡️ Submit https://buff.ly/3EN9w6P #EuroBioC2025 #Bioinformatics #RStats #DataScience

An image analyst position is available in our microscope facility. Please share!

📝 FeatureForest: the power of foundation models, the usability of random forests. Nomen est omen! We use features of the biggest models and train a handy random forest based pixel classifier with them. 👍 Hit bioRxiv recently… check it out! www.biorxiv.org/content/10.1...

GerBI is offering 3 travel grants for the OME2025 meeting at MBL, Woods Hole, US (28.4.-1.5.2025) – an amazing opportunity for networking and knowledge sharing on #RDM! Grants cover registration, travel, and accommodation. Open to GerBI members presenting at the conference. Any questions? Reach out!

Together with Christian Tischer, 3D rendering of multi-res microscopy data was added to MoBIE FIJI plugin using #BigVolumeViewer. Check any remote datasets (like @dudinlab.bsky.social maps of protists using ExM) in the highest quality. For full details read forum.image.sc/t/mobie-plus...