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John Bogovic

@bogovicj.bsky.social

10 Posts237 Follower236 Folgt
John Bogovic@bogovicj.bsky.social · 3w ago

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...

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...

forum.image.sc

Kristin Branson @kristinmbranson.bsky.social · 2mo ago

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

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...

arxiv.org

Image Cooperative@image.coop · 3mo ago

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...

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...

forum.image.sc

Johannes Soltwedel@jo-soltwedel.bsky.social · 3mo ago

🚨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 👋

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...

github.com

Johannes Soltwedel@jo-soltwedel.bsky.social · 7mo ago

🚨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...

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...

forum.image.sc

Eugene Katrukha 🇺🇦@ekatrukha.bsky.social · 5mo ago

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...

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...

forum.image.sc

Jan Funke@janfunkey.bsky.social · 5mo ago

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.

Human Technopole@humantechnopole.bsky.social · 5mo ago

🎓 How can #AI and #datascience unlock new insights into human health? 📊 We’re offering 4 #PhD positions through Polimi’s DADS Programme in the groups of Emanuele Di Angelantonio, Francesca Ieva, @janfunkey.bsky.social and Fernanda Pinheiro. Apply by 26 March 👉 humantechnopole.it/en/news/4-ph...

The Transmitter @thetransmitter.bsky.social · 5mo ago

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...

Lack of reviewers threatens robustness of neuroscience literature

Simple math suggests that small groups of scientists can significantly bias peer review.

thetransmitter.org

Carsen Stringer@computingnature.bsky.social · 6mo ago

Are you working at the interface of #neuroscience and ML/AI? Share your research at Janelia in Nov! 🧠 🤖 janelia.news/NAI26

Janelia Conferences@janeliaconf.bsky.social · 6mo ago

📢 Applications are open! This meeting brings together scientists using data-driven #AI to analyze + model neural circuits and uncover how the brain performs complex computations. 🧠 Apply by May 28 ➡️ janelia.news/NAI26 @computingnature.bsky.social @sinzlab.bsky.social @srinituraga.bsky.social

Stephan Saalfeld@herrsaalfeld.bsky.social · 6mo ago

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

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...

arxiv.org