❤️: gitlab.pasteur.fr/iah-public/l...

Converted my old elastix + transformix Java wrapper to use the appose.org approach with Opus. Total cost? $12. Worth it.

I retried this given the claimed new capabilities of Claude for (interactive) sketches. Better, but we're not there yet (look at the v0 tangent:

👏 and so happy to see the task progress bar being used!

Appose processing hackathon with @jytinevez.bsky.social, @ctrue.bsky.social, @gaellel.bsky.social, @strigaud.bsky.social, Carlos and Thomas . Simple POC with Java calling python through Appose to flip blocks. Promising!

I need this.

YouTube's real genius: get companies to pay for ads so annoying that users end up paying Google directly to remove them. Brands fund their own irrelevance.

Very informative: ome.github.io/ome-ngff-too...

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.