John Bogovic

It's fall, which means it's bioimage analysis conference season! @erinweisbart.bsky.social and @bethcimini.bsky.social had SUCH fun at the @bioimagingna.bsky.social/I2K #I2kxBINA2026meeting last month. We HAD to take advantage of being in person together to film on-site with our friends! (1/2)

I'll be speaking at the Open Bioimaging Practices meetup tomorrow - join us if you're curious about (3D) multiplexed protein image analysis! 🔬

#HappyFluorescenceFriday #microscopycommunity - Congrats to the winner of the Wayne S. Rasband Open Source Imaging Award! Wayne S. Rasband Open Source Imaging Award – Curtis Rueden Learn more: buff.ly/hwKCCwU

Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2027 course!

I was lucky to visit the @chazenartuw.bsky.social museum recently, and decided to have some fun with a photo I took of "Whorl" chazen.wisc.edu/collection/8... by Gillian Jagger. More details for #OMEZarr nerds here: forum.image.sc/t/ngff-weekl...

We are hiring an AI@HHMI Program Manager to help run HHMI's $500M AI initiative: projects, budgets, staffing, recruiting, events, outreach. Advanced degree, program management experience, fluent with AI tools and effective without them 😉. Work with me! hhmi.wd1.myworkdayjobs.com/en-US/Extern...

Image corrections might not be the answer to EVERYTHING, but in Ep 42, we discuss how they might be the answer to "improving your measurements enough to measure the thing you care about". @bethcimini.bsky.social and @erinweisbart.bsky.social discuss what, when, and why!

The Transmitter @thetransmitter.bsky.social just published a piece on this: www.thetransmitter.org/connectome/b...

Struggle with sharing data? @bogovicj.bsky.social shows us better options than emailing data #I2KxBINA

It's @perlman.bsky.social representing the @image.coop at #i2kbina2026!

ICYMI: OME-Zarr 0.6 is out! 🎉 This is big, years in the making. @bogovicj.bsky.social & @jo-soltwedel.bsky.social perseverance brought transformations into this next major step on the road to OME-Zarr 1.0. 👏👏👏 Huge congratulations to the Johns — and to everyone who helped get us here! 🥳🙌

Now I can say: last week we received Notice of Award from NSF on a Midscale Research Infrastructure Design proposal for a National Connectomics and Ultrastructure Volume Observatory (NCUVO) www.uvm.edu/uvmnews/news...

🚨New release: NGFF specification 0.6 🚨 Last week, we formally released the latest version of the NGFF specification: 0️⃣.6️⃣( ngff.openmicroscopy.org/specificatio...) Let's take a small tour through the things possible with #ome-zarr 0.6 now that this is out! 👇

Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...

Beautiful #topography images from the USGS 3DEP as Art Series: www.usgs.gov/3d-elevation...

Hear from the people building this: Stefan Hahmann, @bogovicj.bsky.social, @tischi.bsky.social, Eugene Katrukha, Vladimír Ulman & Will Moore. Learn more here: www.biovisioncenter.uzh.ch/en/events/Up... (🧵 4/10)

We wanted another video to highlight the #Drosophila MCNS connectome, and Alexandra Fragniere suggested showing the spatial distributions of male-specific and dimorphic neurons. @stuartberg.bsky.social suggested adding the synapses. The result turned out well. www.janelia.org/project-team...

We're thrilled with the publication of the Male CNS Connectome! www.cell.com/cell/fulltex... Also check out this (growing) collection of companion papers: www.cell.com/consortium/m...

Join the Open Bioimaging Practices Meetup all about OME-Zarr viewers on Monday, August 24th, 4pm CEST. Learn about ViZarr, napari & VolE & hear user stories on how they handle OME-Zarrs. More info here: www.biovisioncenter.uzh.ch/en/events/Up...

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

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 🧵)

zarr-python v3.3.0: zarr.readthedocs.io/en/stable/bl...

Do you want to learn more about OME-Zarr viewers, where they stand today and what's being developed at the moment? On August 24th at 4pm CEST, we will hear about 3 different OME-Zarr viewers and user stories for each. www.biovisioncenter.uzh.ch/en/events/Up... (1/5 🧵)

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...

At the next #NGFFCafe, Marvin Albert (ETH Zurich) will present 𝗺𝘂𝗹𝘁𝗶𝘃𝗶𝗲𝘄-𝘀𝘁𝗶𝘁𝗰𝗵𝗲𝗿, a Python package for scalable stitching/alignment/fusion of multi-view, tiled & multimodal image acquisitions. Join us! 🗓️ Thursday, July 30 🕚️ 11 am CEST 📍 Online Register⤵️ us02web.zoom.us/meeting/regi...

Tired of AI-generated figures? I asked our talented scientific illustrator Manon Zuurmond to draw some of the instruments and lab equipment we missed in NIH's otherwise fantastic BioArt resource. First batch now available as CC BY. Free for everyone to use in publications: github.com/Center-for-P...

🚨Just out: #NGFF specification 0.6 (rc0): ngff.openmicroscopy.org/specificatio... What's new, what's what? Short thread 🧵👇

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...)

In March, CCP-volumeEM hosted an OME-NGFF hackathon, bringing the community together to collaborate, share ideas and advance tools for volume electron microscopy. 🔬💻 Read about what we worked on and hear directly from two attendees about their experiences: www.ccp-volumeem.ac.uk/hackathons/h...

Agentic coding is genuinely useful now, and there are some impressive reports of AI agents doing science. But how well and how reliably can they handle tasks scientists actually want to hand off, ones that bottleneck progress? How do we even measure that?? New paper🧵 arxiv.org/abs/2606.07718 1/10

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...

🚨🧠 Our paper is out! We introduce a simple computational model that generates macroscopic, long-timescale dynamics as seen in large-scale neural recordings. #neuroscience #dynamics @marius10p.bsky.social @zhong-lin.bsky.social @hhmijanelia.bsky.social Link: go.nature.com/4tRNjIu

Story time friends... Ring attractor networks rely on fine-tuned symmetric connectivity. The fly head direction network has ring attractor dynamics but heterogeneous connectivity. How is this possible? 1/🧵 Link: www.biorxiv.org/content/10.6...

What's new in Ome-Zarr 0.6? Ome-Zarr is a cloud-optimised next-generation file format #NGFF for bioimaging, aiming to increase #FAIR access and remove barriers in the scientific process. The latest version offers numerous improvements and features. 👉 Find out more on Zenodo: doi.org/10.5281/zeno...

@davisvbennett.bsky.social gave a great talk on the present and future of #zarr, including extending the core github.com/zarr-develop... and #metadata.

🚨ngff-spec release candidate out🚨 Just out: ngff specification version 0.6.dev4 (github.com/ome/ngff-spe...), which will be the last dev version (!) and mark the beginning of the 🚧spec-phase🚧 (see also forum.image.sc/t/ngff-weekl...) This means: let's develop some implementations 👷‍♀️👷‍♂️ #OME2026 👋

Want to present a poster, talk, or workshop at this year's Images 2 Knowledge (I2K) meeting - Sep 27 - October 2nd in Madison, WI? Please fill out the form by Thursday - we really want to highlight your contributions! airtable.com/appPes56Tahc...

My first post here, we have a new preprint out from @aicjanelia.bsky.social! Upright LSFM is fantastic for live imaging, but not amenable to all samples - especially those requiring an air-liquid interface. We worked with Tokai Hit to try to fix that. www.biorxiv.org/content/10.6...

🔬 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...

🚨Gearing up for #NGFF 0.6! 🚨 Help us give this a final push over the finish line and join us in ironing out the last flaws on the way! More information here 👇 forum.image.sc/t/ngff-weekl...

We want to organize a learnathon to teach plugin development within #FIJI #scijava #imglib2 #BigDataViewer and other Big* parts of the Java ecosystem. Please spread the word, and if you know someone who can be interested, forward them the link below forum.image.sc/t/learnathon...

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

Graph neural networks recover interpretable circuit models from neural activity saalfeldlab.github.io/flyvis-gnn/ @HHMIJanelia @AllenInstitute to be presented at @CosyneMeeting

Calling all OME Community members, contributors, and lurkers! Please take a minute to answer the OME 2026 Community Survey (docs.google.com/forms/d/e/1F...) to help us prepare for discussing the future of OME governance during the OME 2026 Community Meeting at the end of April.

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.

Broad peer review is crucial for a healthy scientific literature, but neuroscientists turn down review requests too often. Simple math suggests that small groups of scientists can significantly bias the literature, writes @jvoigts.bsky.social. #neuroskyence www.thetransmitter.org/publishing/l...