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Kevin Yamauchi

@kevinyamauchi.bsky.social
722 followers 253 following 1 posts

building open source image analysis software for science 🔬 co-founder and member of @image.coop 🏝️ core developer @napari.org kevinyamauchi.github.io

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Reposted by Kevin Yamauchi
Sebi @sebi06.bsky.social · 30/09/2026
Hi all, prototype of a napari-zenapi-streaming plugin is working using @zeiss-microscopy.bsky.social and @napari.org. - stream pixels from ZEN into multi-dim array and display live - stream pixels from ZEN directly into OME-ZARR (see video) For viewing I used: find-nuclei.github.io
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John Bogovic @bogovicj.bsky.social · 01/10/2026
It's @perlman.bsky.social representing the @image.coop at #i2kbina2026!
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Marie Held @makaefer.bsky.social · 28/09/2026
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.uk
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Igalia @igalia.com · 21/09/2026
Today Igalia turns 25. Ten engineers started it in A Coruña in 2001 with no investors and no managers. There are now close to 200 of us, and everything we build still goes upstream. igalia.com/2026/09/21/T...
Igalia's 25th anniversary banner. Three figures from the Igalia logo form the Roman numerals XXV, beside the words YEARS OPEN and a multicoloured circle marked 25th on a timeline arc.
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Aafke Gros @aafkegros.bsky.social · 24/08/2026
Split and animate separate subregions of your microscopy volumes with Microscopy Nodes! www.youtube.com/watch?v=7K-i... You can make your 3D cells sort to their classified locations, explode/reassemble your segmented tissue - and everything in full volumetric space! 🔬🎉
youtube.com
Split & Animate Microscopy Volumes in Blender | Microscopy Nodes 3.1.2
YouTube video by Aafke Gros
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Elisha Krieg @elishakrieg.bsky.social · 06/08/2026
How can we record the mechanical activity of cells in three dimensions? Our DNA force-history probes convert transient piconewton forces into persistent fluorescent signals, revealing spheroid activity, cellular protrusions, and migration tracks in a 3D matrix. www.biorxiv.org/content/10.6...
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Joel Lüthi @joelluethi.bsky.social · 14/08/2026
We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)
2025 OME-Zarr hackathon
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Dagmar Iber & CoBi @iberd.bsky.social · 13/08/2026
🎉 Our paper is out in Cell Systems @cp-cellsystems.bsky.social ! How does an embryo build an energy-efficient fractal lung before the first breath? 📄 doi.org/10.1016/j.ce... 🧵 bsky.app/profile/iberd.bsky.social/post/3lfrdth6k4c22 @maltemederacke.bsky.social @kevinyamauchi.bsky.social
doi.org
Redirecting
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John Bogovic @bogovicj.bsky.social · 17/07/2026
It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...
forum.image.sc
Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)
Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...
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Kathiravan Ezhilan @kathiravan-ezhilan.bsky.social · 16/07/2026
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/07/2026
Congratulations to superstar and awesome colleague Gaëlle Letort @gaellel.bsky.social, bioimage analyst extraordinaire for THE CRYSTAL MEDAL OF THE CNRS 2026!!! 🥳🎉🕺🦄🥳 We work with amazing people www.insb.cnrs.fr/fr/personne/...
insb.cnrs.fr
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Jakob Schnabl-Baumgartner @jakobschnabl.bsky.social · 07/07/2026
www.cell.com/molecular-ce... I'm happy to see our work published! If you are interested in transposons, transcriptional regulation and Pol III come and check it out 👀 🧫 🧬
cell.com
ChAHP silences SINE retrotransposons by inhibiting TFIIIB recruitment
SINEs are short transposable elements that make up large fractions of mammalian genomes. Known to be transcribed by RNA polymerase III, their regulation has remained largely unexplored. Schnabl-Baumga...
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Ben Barad @baradlab.com · 27/06/2026
Just in time for the weekend, the 2nd beta for our Surface Morphometrics 2.0 release: github.com/GrotjahnLab/.... Beyond the major API change from the first beta (which used for the michigan class!), this one includes a major overhaul of the dual gaussian fitting for thickness and refinement.
github.com
Release 2.0.0b2 · GrotjahnLab/surface_morphometrics
A quality and robustness release on top of 2.0.0b1, focused on the density-profile bilayer fitting (mesh refinement and thickness measurement), a forgiving centralized config system, and packaging ...
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Johannes Soltwedel @jo-soltwedel.bsky.social · 25/06/2026
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...)
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Caitie McCafferty @computingcaitie.bsky.social · 22/06/2026
Happy to finally share that I will be starting my independent group at the @fmiscience.bsky.social in Feb 2027 in a vibrant new environment. We will use integrative in situ structural cell biology methods to investigate ciliary structure and dynamics in several model (and non-model 👀) systems!!
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napari @napari.org · 17/06/2026
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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Johannes Soltwedel @jo-soltwedel.bsky.social · 17/06/2026
🚨New release 🚨 We just released ome-zarr-py 0.18 (pypi.org/project/ome-...), which brings an all new, shiny API for reading and writing #OME-ZARR data. Check out the documentation 📚 for more hints: ome-zarr.readthedocs.io/en/stable/ @openmicroscopy.org @will-j-moore.bsky.social
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Helena Lucia Crowell @helucro.bsky.social · 17/06/2026
Little blog post, preprint included, re: spatial/image Bioc hackathon on a little Venetian island — Thank you @wkhuber.bsky.social and especially @davi1893.bsky.social (and Elena!) for organizing and securing this 🤩 location 🤩 — Let’s do it again!
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Crystal Fleming is on sabbatical @alwaystheself.bsky.social · 17/06/2026
He kept coming back, repeatedly (in the way AI often loops) to this idea of AI (specifically Claude) representing "a position without an address", and it became increasingly clear to me that there was some odd mystification happening. Of course LLM products have an address. It's a corporate address.
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Ben Barad @baradlab.com · 13/06/2026
I had such a fun time teaching at the U Michigan Cryo-ET Course this week! I taught quantitative ultrastructure analysis and we made cool figures like these! My course materials are at baradlab.com/michigan_tutorial for anyone to try. Workflow include mesh refinement and thickness measurement!
ChimeraX/ArtiaX visualization showing mitochondria-associated ribosomes connecting drives reduced IMM-OMM spacing in yeast.Surforama depiction of mitochondrial outer membrane shows membrane-associated ribosomes.
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Kevin Yamauchi @kevinyamauchi.bsky.social · 09/06/2026
An egg-cellent meeting. Thanks, @erickratamero.com !
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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 07/06/2026
"2nd SpatialData Hackathon: Frameworks, Formats and Interoperability" doi.org/10.37044/osf.io/s6bph_v1 "The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of […] [Original post on fediscience.org]
Figure 1: Comparison of Zarr, bioimaging and single-cell/spatial omics packages across scverse and Bioconductor ecosystems that interface with SpatialData objects on disk (“Database-icon” by Zahra Ibrahem is licensed under CC BY-SA 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-sa/4.0/?ref=openverse.)
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Dagmar Iber & CoBi @iberd.bsky.social · 08/06/2026
Thrilled to see our #DCM paper out in @cp-newton.bsky.social! 🎉 How do cells self-organize into complex patterns so quickly during development? We show that #directed #cell #migration — chemotaxis, durotaxis, differential adhesion — is a surprisingly fast & versatile patterning engine. 🧵👇
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SciPy Conference 2026 @scipyconf.bsky.social · 03/06/2026
🔬 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
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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026
📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...
jobs.uzh.ch
UZH: Bioimage Analyst
The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...
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Erick Ratamero @erickratamero.com · 29/05/2026
ok this one made me laugh
a crop from one of the images in the parent post, of section "standardisation" containing items "standardisation" and "standardization"
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Jean-Yves Tinevez @jytinevez.bsky.social · 25/05/2026
Do you support people on the forum.image.sc or the forum itself? Do you want to feel good? forum.image.sc/t/i-finally-...
forum.image.sc
I finally got my PhD, thank you image.sc!
Hi everyone, I would like to make a small positive post. I finally got my PhD! The viva was actually on April 27th, but due to university paperwork, it only became official last Friday. A large par...
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Image Cooperative @image.coop · 22/05/2026
We want to hear from you about your experience using the OME-Zarr ecosystem and how we can improve it! We are joining the upcoming OME-NGFF community call to introduce ourselves to the community and to collect your feedback (May 26, 9AM and 5PM CET). See you there! forum.image.sc/t/join-us-fo...
forum.image.sc
Join us for the next OME-NGFF Community Call on Tuesday May 26, 2026 9:00 CET and 17:00 CET!
Dear all, We are delighted to announce our Q2 OME-NGFF Community Call to be held on Tuesday May 26! As usual, we will repeat the agenda over two time slots to welcome participants from everywhere aro...
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Nico Stuurman @nicostuurman.bsky.social · 21/05/2026
I'll be writing a few posts about new features in Micro-Manager. If you are interested in those, please follow @micro-manager.bsky.social.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 21/05/2026
New release of #BigVolumeBrowser (0.1.1) adds support for (multiscale) OME-Zarr (thanks to libraries from @bogovicj.bsky.social, Stefan Hahmann, Vladimir Ulman). And midi gizmo navigation (from @herrsaalfeld.bsky.social ), shown below.
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David Gaboriau @dgaboriau.bsky.social · 07/05/2026
Random thanks to the image.sc forum, for such a treasure trove of information on bioimage analysis. It's always a great read!
image.sc
Image.sc Forum
Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).
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Simon F. Nørrelykke @simonfn.bsky.social · 06/05/2026
The SwissBIAS Annual Meeting is taking place on June 3rd in Bern. Registration deadline: Friday, May 15th, so make sure to secure your spot now! We look forward to seeing you all there for a fantastic day of science, networking, and inspiration. @swissbias.bsky.social tinyurl.com/SwissBIAS2026
eventbrite.com
SwissBIAS annual meeting 2026
It is the time of the year to make veterans meet new members, discuss to foster feedback on existing activities and promote new initiatives.
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Arfon Smith @arfon.bsky.social · 05/05/2026
After 10 years, I'm stepping down as Editor-in-Chief of @joss-openjournals.bsky.social. A few thoughts on the decade: www.arfon.org/stepping-dow... The EiC call: blog.joss.theoj.org/2026/05/call... #opensource #openscience
arfon.org
Stepping down as Editor-in-Chief of JOSS | Arfon Smith
After 10 years, reflecting on launching the Journal of Open Source Software and what comes next.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 03/05/2026
If you missed this because, like me, you were busy at #OME2026, please check it out! @kevinyamauchi.bsky.social and I wrote a thing on how we can all do our part to enable the next generation of microscopy-data-driven biological discoveries. Enjoy the read!
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Hanjin Liu @liu-hanjin.bsky.social · 22/02/2026
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
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Guillaume Witz @guiwitz.bsky.social · 02/04/2026
I’m trying to figure out (like everyone else) how to reasonably use LLMs both for my work and teaching. This is fantastically written and clearly articulates a lot of ideas and concerns I had vaguely in mind. I’m considering suggesting this as a read to participants in my scientific coding courses.
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Martin Panknin @mpanknin.bsky.social · 27/03/2026
Kiln also has experimental OME-Zarr support. This is the Beechnut — a 3 GB micro-CT scan streamed directly from a public OME-Zarr store into the browser. No preprocessing, no conversion. github.com/MPanknin/kil... #WebGPU #OMEZarr #VolumeRendering
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Martin Panknin @mpanknin.bsky.social · 27/03/2026
Meet Kilian. A 2 GB CT scan of a chameleon — rendering in the browser in a few hundred milliseconds. Built with Kiln: a WebGPU-native out-of-core volume renderer. Bricked volume storage, GPU memory virtualization, LRU streaming, compute shader ray marching. Open source: github.com/MPanknin/kil...
Volume Rendering - ChameleonVolume Rendering - ChameleonVolume Rendering - ChameleonVolume Rendering - Chameleon
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Joel Lüthi @joelluethi.bsky.social · 26/03/2026
🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET Hybrid: FMI Basel & Zoom Talk by @jo-soltwedel.bsky.social : Transforming OME-Zarr: What’s coming in v0.6 Plus short updates from the BVC & time for discussion www.biovisioncenter.uzh.ch/en/events/Up...
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup: March 2026
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napari @napari.org · 24/03/2026
napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/relea... We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant contributors 🤩 and the community for their support and feedback!
napari.org
napari 0.7.0
Mon, Mar 23, 2026 We’re happy to announce the release of napari 0.7.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing…
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napari @napari.org · 10/03/2026
napari needs your help! Has napari helped you make cool and groundbreaking discoveries? We'd love to highlight that in our docs. Please tell us about it! You can fill in this survey: napari.typeform.com/to/vTCKeTKv and/or, as ever, drop by our chat room or meetings: napari.org/dev/community/ 🙏
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Artur @arturruppel.bsky.social · 17/03/2026
First paper as first & corresponding author, out in PLOS Computational Biology! 🎉 napariTFM brings traction force & monolayer stress microscopy into napari, accessible via GUI; open-source, validated and no coding required. 😉 Check it out 👇
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BrainGlobe @brainglobe.info · 17/03/2026
BrainGlobe has a new roadmap! Somewhat overdue, the March 2026 roadmap summarises our recent progress, and our priorities for the coming year. Read more: brainglobe.info/community/ro...
An illustration of many of the atlases supported by BrainGlobe.
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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 13/03/2026
We have three neuroscience research software engineering jobs available at @sainsburywellcome.bsky.social, two joint with the Advanced Microscopy Facility. All positions start ASAP, funded until Sept 2028 in the first instance. Salary £54-64k. More details: neuroinformatics.dev/get-involved
neuroinformatics.dev
Get involved — NIU
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Josh Moore @joshmoore.bsky.social · 11/03/2026
Help shape the future of @openmicroscopy.org! 🔮 The OME 2026 community survey is open—tell us what’s working, what isn’t, and what you'd like to see next. Takes just a few minutes 👇 forum.image.sc/t/ome-2026-c...
forum.image.sc
OME 2026 Community Survey
Calling all OME Community members, contributors, and lurkers! This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final mee...
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Annika Nichols @annika-nichols.bsky.social · 10/03/2026
I'm thrilled to announce that I'll be starting my lab as a SNSF starting grant professor at the Center for Integrative Genomics in Lausanne! I'm looking for PhD students who are fascinated about the neuronal basis of behaviour across species @fbm-unil.bsky.social
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napari @napari.org · 11/03/2026
🔬 Registration is open for our pilot Introduction to napari Workshop! napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast. #napari #Python #ImageAnalysis #DataScience #OpenSource
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Joel Lüthi @joelluethi.bsky.social · 10/03/2026
We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...
biorxiv.org
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Jan Funke @janfunkey.bsky.social · 05/03/2026
We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇). My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue. Apply by March 26.
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Albert Dominguez Mantes @albertdm.bsky.social · 02/03/2026
Very happy that MuViT, our (CVPR 2026!) work on learning across spatial scales in microscopy w transformers, is out! Check Martin's thread for a nice walkthrough :) Big thanks to my advisors @maweigert.bsky.social @gioelelamanno.bsky.social! 🖥️: github.com/weigertlab/muvit 📜: arxiv.org/abs/2602.24222
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