Unexpected artistic image.

Smashing console logs (which are not errors) -> very dumb bottleneck 😅.

Claude code flexing: ---- For your case with uniform TIFFs on network storage, lazy validation would transform a multi-hour init into seconds. The validation cost is amortized across actual reads. ---- Let's see if that's true!

Is there a way to sync claude code with git: if I switch branch or checkout an older commit then the discussions revert to their states at these previous points / branch ?

📢 Open faculty position – Origins of Life We have an opening in our section at the University of Geneva! 🧬🚀 SPREAD THE WORD Apply here: jobs.unige.ch/www/wd_porta...

"Resist the empire building" Too late! Here's the dependency graph of packages developed at the BIOP for ABBA (go.epfl.ch/abba) (except clij and labkit)

A bit late to the party but 🤯 by Claude code.

Are there any rankings of LLM capabilities by language? My intuition is: more verbose and grammatically strict languages would perform better.

Cadeau :

Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2) forum.image.sc/t/bigvolumeb...

We are happy to share our latest work, 4Pi-SIMFLUX, which combines structured illumination with interferometric detection to achieve near-isotropic 3D localization precision of 2–3 nm and resolve sub-10 nm structural features across whole mammalian cells. www.nature.com/articles/s41... rdcu.be/eQVxt

Diving into video editing to update ABBA's tutorial. CapCut's free version is pretty great! (Now I will need to make peace with the sound of my own voice). Here's a preview:

Our new paper is published in the Journal of Chemical Biology! 🏮 We share StayRose, a red version of StayGold 🏮 StayRose has an unnatural amino acid-based chromophore, and has the same immense photobleach-resistance as StayGold 💡

For those who like cooking and microscopy, www.pnas.org/doi/10.1073/... Thanks for the link @anjaliesch.bsky.social

Had an amazing time at the ZEISS Smart Microscopy Workshop! Huge thanks to @romainguiet.bsky.social and the entire @zeiss-microscopy.bsky.social team for their dedication and fantastic organization. #Microscopy #ZEISS

LUT color mapping for spots/particles rendering in #bigvolumeviewer is almost finished. The speed is mapped by color (middle) and color + spot size (right).

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

I managed to make #ABBA work with a white background and dark mode! #FijiSc #BDV. Useless for the moment, but I like it.

Pythonists & bio-image analysts: Any recommendations for a library to add simple metadata (axes names, dimensions, physical units) to a NumPy array? Bonus if it handles slicing gracefully. For instance img[::2, :] updates the output pixel size automatically.

Delage, Guilbert, and @frankyates.bsky.social provide a primer on light sheet fluorescence #microscopy to guide biologists through the specific challenges of this 3D imaging technique. rupress.org/jcb/article/... 📕 In #Reproducibility and Best Practices in Cell Biology: rupress.org/jcb/collecti...

In case you want to retrieve gifs or images from gdrive presentations: 1. File > Download > .pptx 2. Unzip .pptx file 3. Navigate to ppt/media folder 4. Profit Filename are generic, but I did not find anything more convenient

New achievement unlocked in forum.image.sc!

Close enough!

@mistralai.bsky.social’s Le Chat > @anthropic.com's Claude for Nextflow this week 👀

pip, pip3, conda, mamba, poetry, uv, pixi... welcome to python's easy world!

Same cell division as posted below, rendered with bene51.github.io/3Dscript/

Nice cell division observed on Zeiss LLS7 yesterday! Sample: @romainguiet.bsky.social

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

- I need to ship this objective - How many boxes do you need ? - Yes.

Has anybody ever mounted an ethyl cinnamate-cleared mouse embryo (E10 - so about 5 mm) into a light sheet system? Any tips appreciated!

We've updated our BIOP extensions to QuPath 0.6! 🎉 forum.image.sc/t/qupath-bio... One-click extension installs are her! ABBA, Warpy, Cellpose, and the last one? chef's kiss 👌(1/3)

I played a bit with llms and physics sketch generation, it's not a well defined benchmark, but out of Model =[gemini, chatgpt, mistral, claude] x OutputFormat=[Undefined, svg, tikz, geogebra], Claude + Geogebra is the current winner. My prompt - without output format, is posted below

Does anybody know if there's a working way to generate vector graphics for education (ideally editable) by a llm? Typically "draw a trajectory of a free falling object, with a vector g and a labeled coordinate system". I'm not sure what the proper output format should/could be. svg ? geogebra ?

Our Live cell actin probe SPY650-FastAct efficiently labels primary keratinocytes isolated from mice.

Jumping on the bandwagon after being advised by @tibuch.bsky.social and @imagejan.bsky.social, I started using @nextflow.io. I should have listened sooner!

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

One protein, two opposing roles: This ‘compelling’ study shows how the same signalling molecule can drive either protrusion or retraction in migrating cells depending on its concentration and activation dynamics. buff.ly/qy3M8s5

Italian 🇮🇹 scientists! Our open call for image analysis support through the @humantechnopole.bsky.social national facilities is currently accepting applications!

Synthetic ecosystems that autonomously and continuously evolve in silico 👾 An Alifer dream we pursue with Flow-Lenia, a mass-conservative continuous CA ! If you are interested in complex systems with (1) emergent creatures and (2) intrinsic evolutionary dynamics, go check our new paper ! A 🧵

Some rough edges, but it works! #Fiji MCP server (+ Claude desktop) can do things in Fiji (get some info about the current state of the app, execute groovy scripts...).

First step into this MCP server thing with #Fiji (through pyimagej) and Claude Desktop. Ain't much but yep, it's rather easy to do.

I've put some BigDataViewer demos in #Fiji 's PTBIOP update site. Check them out ! forum.image.sc/t/new-bigdat...

🎀✨Recording now available ✨🎀 youtu.be/jtDunWK8g1o?...

This reminded me of @sergedmi.bsky.social 's github.com/SergeDmi/Con...

Who would have thought inverting colors would be so tricky ? jordan.yoonbuck.com/post/contras...

Hehe, finally had time to revamp a bit Warpy. It's now possible to concatenate a series of transformed sections in a 3D stack for #QuPath. Computed on the fly and with reasonable performance (image and transform field caching).

Currently playing with blender - with scripting capabilities and llms, it is really super powerful. Also crazy: I copy pasted a screenshot of a material (image) - and I ask the llm to convert it to an equivalent piece of code. It worked!

Thanks @truenorth-ia.bsky.social ! And if you want quickly want to test whether tiled GPU deconv works on your machine, there's a self-contained demo (look for 'CLIJ 3D Deconvolution Demo' in #FijiSc 's search bar).

I tested a llm with langchain + function calling in #FijiSc. This is crazy. "Here's this tool to execute a script", "here's this tool to look for the source code", "here's this tool to ask for my advice about an error". And it all works. (I'm staying at the ImageJ 'blobs' level for the moment)