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John Bogovic

@bogovicj.bsky.social
250 followers 253 following 16 posts
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Reposted by John Bogovic
Josh Moore @joshmoore.bsky.social · 25/09/2026
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! 🥳🙌
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Reposted by John Bogovic
Davi Bock @dddavi.bsky.social · 24/09/2026
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...
uvm.edu
UVM Launches $19 Million National Observatory to Unlock…
| The University of Vermont
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John Bogovic @bogovicj.bsky.social · 24/09/2026
Here's a whimsical example of what you can achieve with #bigwarp and the brand new #ome-zarr 0.6!
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Reposted by John Bogovic
Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026
🚨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! 👇
ngff.openmicroscopy.org
Version 0.6 — NGFF documentation
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Feliciano Lab @feliciano-lab.bsky.social · 22/09/2026
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
science.org
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues
Cell-state diversity drives tissue adaptability, repair, and disease resilience, but capturing this complexity is a challenge. Current approaches rely on transcriptional profiling and overlook organel...
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Reposted by John Bogovic
Philip Hubbard @philiphubbard.bsky.social · 21/09/2026
Beautiful #topography images from the USGS 3DEP as Art Series: www.usgs.gov/3d-elevation...
usgs.gov
3DEP as Art Series
Experience the topographic beauty of the United States through the 3DEP as Art Series. A modern illustration of each state's landscape uses 3DEP data to showcase subtle beauty in their elevation diffe...
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Reposted by John Bogovic
Joel Lüthi @joelluethi.bsky.social · 21/09/2026
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)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup, September 2026
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Reposted by John Bogovic
Philip Hubbard @philiphubbard.bsky.social · 08/09/2026
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...
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Reposted by John Bogovic
Janelia FlyEM @janelia-flyem.bsky.social · 04/09/2026
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...
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Joel Lüthi @joelluethi.bsky.social · 19/08/2026
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...
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Reposted by John Bogovic
Johannes Soltwedel @jo-soltwedel.bsky.social · 17/08/2026
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
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Reposted by John Bogovic
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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Davis Bennett @davisvbennett.bsky.social · 30/07/2026
zarr-python v3.3.0: zarr.readthedocs.io/en/stable/bl...
zarr.readthedocs.io
Zarr-Python 3.3.0 - zarr-python
An implementation of chunked, compressed, N-dimensional arrays for Python.
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Joel Lüthi @joelluethi.bsky.social · 24/07/2026
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 🧵)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup August 2026
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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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Reposted by John Bogovic
eurobioimaging.bsky.social @eurobioimaging.bsky.social · 15/07/2026
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...
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Magnus Palmblad @magnuspalmblad.bsky.social · 07/07/2026
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...
Drawings of various laboratory equipment (liquid chromatography system, mass spectrometers and a centrifuge).
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Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026
🚨Just out: #NGFF specification 0.6 (rc0): ngff.openmicroscopy.org/specificatio... What's new, what's what? Short thread 🧵👇
ngff.openmicroscopy.org
Version 0.6rc0 — NGFF documentation
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Reposted by John Bogovic
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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CCP-volumeEM @ccp-volumeem.bsky.social · 17/06/2026
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...
ccp-volumeem.ac.uk
OME-NGFF Hackathon March 2026 — CCP in vEM
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Reposted by John Bogovic
Kristin Branson @kristinmbranson.bsky.social · 10/06/2026
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
arxiv.org
A case study of evaluating AI agents on a neuroscience data-to-discovery pipeline
Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where...
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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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Carsen Stringer @computingnature.bsky.social · 22/05/2026
🚨🧠 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
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Brad Hulse @bradkhulse.bsky.social · 21/05/2026
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...
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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 06/05/2026
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...
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John Bogovic @bogovicj.bsky.social · 30/04/2026
@davisvbennett.bsky.social gave a great talk on the present and future of #zarr, including extending the core github.com/zarr-develop... and #metadata.
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Reposted by John Bogovic
Johannes Soltwedel @jo-soltwedel.bsky.social · 28/04/2026
🚨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 👋
github.com
Release 0.6.dev4 · ome/ngff-spec
What's Changed fix: avoid non-unicode characters (dev) by @jo-mueller in #121 specification: Tie down possible output for coordinate transformation… by @jo-mueller in #109 Improve readability of m...
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Reposted by John Bogovic
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 19/04/2026
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...
A cow behind some buildings overlooking a lake - top banner says "I2KxBINA 2026 Community Congress", while bottom banner says "Cultivating the Multiscale Imaging Frontier"
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Reposted by John Bogovic
Chad Hobson @cmhobson.bsky.social · 20/04/2026
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...
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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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Johannes Soltwedel @jo-soltwedel.bsky.social · 09/01/2026
🚨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...
forum.image.sc
NGFF weekly dev update thread
🏁 Sprint to 0.6 🏁 Dear NGFF-community, it's been some time since the last release of a mjor version of the NGFF-specification. Since then, many of you engaged with the community which resulted in a lo...
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 20/03/2026
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...
forum.image.sc
Learnathon/hackathon on the development of ImgLib2/BigDataViewer based Fiji tools for dealing with large image data (survey)
Hello all, There is an increasing number of new tools to work with image data. But for many life scientists, Fiji remains a very important platform when it comes to interactively working with image d...
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Image Cooperative @image.coop · 16/03/2026
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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Cedric Allier @allierced.bsky.social · 10/03/2026
Graph neural networks recover interpretable circuit models from neural activity saalfeldlab.github.io/flyvis-gnn/ @HHMIJanelia @AllenInstitute to be presented at @CosyneMeeting
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Erick Ratamero @erickratamero.com · 10/03/2026
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.
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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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The Transmitter @thetransmitter.bsky.social · 02/03/2026
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...
thetransmitter.org
Lack of reviewers threatens robustness of neuroscience literature
Simple math suggests that small groups of scientists can significantly bias peer review.
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Laura Grima @lauragrima.bsky.social · 24/02/2026
Excited to be co-organising a #cosyne2026 workshop with Alison Comrie on 'algorithms for learning from scratch'! With a great line-up of speakers, we'll be tackling the question of what processes enable naive biological & artificial agents to adapt to new situations. Info here: tinyurl.com/4u8enf7k
sites.google.com
learningfromscratch
march 16th, workshop day 1 @ cosyne 2026
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Nicolas Chiaruttini @nkiaru.bsky.social · 17/10/2024
Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer
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Carsen Stringer @computingnature.bsky.social · 18/02/2026
Are you working at the interface of #neuroscience and ML/AI? Share your research at Janelia in Nov! 🧠 🤖 janelia.news/NAI26
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Stephan Saalfeld @herrsaalfeld.bsky.social · 17/02/2026
This is work that we presented at last year's #Cosyne workshop on #GNN s sites.google.com/bu.edu/gnnwo.... Better late than never. You can reproduce everything with the associated notebooks. I think it's a good start to learn how to use GNNs to infer something about NNs. arxiv.org/abs/2602.13325
arxiv.org
Graph neural networks uncover structure and functions underlying the activity of simulated neural assemblies
Graph neural networks trained to predict observable dynamics can be used to decompose the temporal activity of complex heterogeneous systems into simple, interpretable representations. Here we apply t...
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Erick Ratamero @erickratamero.com · 06/02/2026
I am joining @joss-openjournals.bsky.social as an editor! I wrote a little bit about how much I hate academic publishing and why this felt like the right thing to dedicate some volunteer time to. pages.erickratamero.com/personal-web...
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Davi Bock @dddavi.bsky.social · 04/02/2026
beautiful protist ExM images here from @dudinlab.bsky.social and @gautamdey.bsky.social
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Luca Marconato @lucamarconato.bsky.social · 02/02/2026
We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework. We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
embl.wd103.myworkdayjobs.com
Research Software Engineer - Spatial-omics
The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...
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Erin Weisbart @erinweisbart.bsky.social · 26/01/2026
@bethcimini.bsky.social and I talk about the Cell Painting Assay a LOT, especially on our podcast Ask Erin/Dear Beth, so we figured it was about time to talk about what it actually is! youtu.be/9-d6DoHtgUY h/t @drannecarpenter.bsky.social #science #biology #cellpainting #microscopy #imageanalysis
youtu.be
Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23
YouTube video by Ask Erin, Dear Beth
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Erick Ratamero @erickratamero.com · 22/01/2026
The OME meeting has followed me from New England to Germany! consistently my favorite scientific meeting of the year, with the nicest community anywhere. Join us there!
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Davi Bock @dddavi.bsky.social · 20/01/2026
This course looks great. Amazing organisms + friendly and highly expert instructors, several of whom I have had the privilege of getting to know during my time so far here in Heidelberg. Strong recommend!
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Erick Ratamero @erickratamero.com · 14/01/2026
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
embl.wd103.myworkdayjobs.com
Scientific Workflows Developer
The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Hannah Haberkern @hannah-haberkern.bsky.social · 23/12/2025
📢 Join us, the Haberkern lab, @uni-wuerzburg.de for a postdoc studying neural circuit mechanisms of navigation. You’ll spearheading neurophysiology experiments on our brand new 2P! ⏳ Apply by 28th February 2026 Details: www.haberkernlab.de/docs/ENPostd... #neuroscience #academicjobs #postdoc
On the left, the image shows a schematic of a fly head, ring neurons and EPG neurons together with some calcium imaging frames. On the right is a photo of a fly on a ball in virtual reality and another schematic of a VR system.
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