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)

Thierry, our microscopy wizard, still as excited as day one about scopes… but now, he’s also geeking his new van for retirement! 🚐 And you know what that means? 🚨 Whoop, whoop! We’re hiring! 🚨 Come join us at the BIOP at EPFL: careers.epfl.ch/job/Lausanne...

Long time without a small BDV video! Here's an instant lazy loaded warped 1000000x750000 image. A million pixels along x. Code here: github.com/BIOP/bigdata...

These code models are so good, they can even deal with my crappy API 😅

Is it possible for a FP to bleach much faster in point scanning confocal microscopy than in spinning-disc confocal ? To the extent that it's barely usable in point scanning but works fine in SDC? A user seems to have observed this with an RFP variant - (and I tested 3 point scanners...).

New EPFL Mastodon instance (actu.epfl.ch/news/the-epf...), but: "We decided not to join Bluesky for now because this social network doesn’t seem suited for helping us reach the general public and the groups we target." No offense, but good luck reaching the general public on mastodon.

Now playing with mistral.ai. If you're ok with them looking at requests, you can get a free API token and get your hands on a solid code model. Gave it a go with LangChain and Fiji's plugin API... That documentation is finally writing itself! Next step: a plugin-aware agent. So far, this is crazy

I just tried the free version of chat.mistral.ai - it's incredibly fast! I tested if it could write a script for my niche ABBA software. Both ChatGPT and Le Chat failed similarly, so I guess they're on par?

Pleasure of coding on mac: looking for a { character anywhere, ctrl+c, ctrl+v, ah no! mac+c, mac+v. Looking for a } character. Inverted mouse 😠 Looking for @, finding it on the keyboard, wouhou! Trying all combinations, not managing to get the @. Falling back to a copying @, ctrl+c, ah NO AGAIN!

Finally, a new release for Aligning Big Brains and Atlases! A preprint 🎉 + plenty of small improvements, have a look at the forum thread for details! forum.image.sc/t/abba-align...

Achieving optical transparency in live animals with absorbing molecules | Science www.science.org/doi/10.1126/... Has anyone tried it with live C. Elegans? How did it go?

There's a new wave of discussion to improve the clarity of Fiji's original menus and plugins. If you have opinions or suggestions to make, don't hesitate to participate on the forum! forum.image.sc/t/houseclean... #microscopy #imagej #fiji

Why do so many packages store massive files (models, atlases, etc.) per user? The same 70GB for 10 users = massive waste. We need a cross-platform standard for downloading and system-wide caching of immutable files from URLs. Imagine: immut://zenodo.org/records/12345/stuff.h5. Does this exist?

Great example of how #WebAssembly is going to revolutionize scientific computing with no installation required.

It's not quite the Java 'null' billion-dollar mistake, but the OS-dependent string representation for File, URI, or URL is definitely up there in the ball-breaking rankings.

If you were to choose an AI subscription for work in a microscopy facility, would you pick ChatGPT, Claude, or something else?

2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year ! 2025.zidas.org

Surprisingly accurate 3D model of the #EPFL campus! Can you guess which video game it’s from?

Finally had a bit of time to play with multi-GPU deconvolution. Using @truenorth-ia.bsky.social and @haesleinhuepf.bsky.social previous work. Here it is in action in #BigDataViewer using async and lazy processing. Look at the two poor laptop GPUs going as fast as they can:

Quantitative Imaging From Acquisition to Analysis applications are due Jan 31! 2 weeks of total microscopy & image analysis immersion with me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott! See comments... (1/5) meetings.cshl.edu/courses.aspx...