Nicolas Chiaruttini

BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...

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...

4Pi-SIMFLUX: 4Pi single-molecule localization microscopy with structured illumination - Nature Methods 4Pi-SIMFLUX is a single-molecule localization microscopy approach that achieves a near-isotropic resolution below 10 nm in whole mammalian cells.

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:

Very cool! We tried this, and it worked beautifully! (We did not require the second film; maybe we were lucky! )

There's just one thing we did not achieve yet: the gel was moving quite a lot. How do you prevent that ? Does PLL treatment work with the FEP film ?

StayRose: A photostable StayGold derivative redshifted by genetic code expansion Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric GFP recently monomerized through sequence engineering, addresses thi...

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 💡

I really want to get some time to play with it!

Droplet outbursts from onion cutting | PNAS Cutting onions often leads to tear-inducing aerosol release, yet the underlying mechanics remain poorly understood. In this work, via high-speed ch...

For those who like cooking and microscopy,

www.pnas.org/doi/10.1073/...

Thanks for the link @anjaliesch.bsky.social

My favorite thingy: Direct data streaming and stage control from Java!

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)

And new little icons!

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

Nice! I see that you can somewhat work with indexing but there's a plan to do better: github.com/orgs/pydata/...

Automatic conversion looks great! But I guess it does not handle slicing (smth like subsampling -> increase in pixel size)

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...

Bright and beautiful! But the floor is tilted 😉

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!

Ahahahaha! Wth ?

Close enough!

Mistral pro and Claude pro. To be fair it could just be a glitch, but Claude had a lot of hallucination and mistral was a bit more down to earth in this particular case.

Blindspots happen. But mistral can be surprisingly good. Definitely useful to get another point of view when Gemini and Claude are sttruggling. (I'm quite disappointed by Claude recently)

@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!

It's tubulin-GFP (low contrast), histone mCherry and mitotracker. I think we should try sir-tubulin and replace mitotracker with maybe mitotracker green, if that exists. And yes, I concatenated the output of 4 3dscript runs.

(and bsky video quality is not great)

FOV captured multiple cells. Tubulin contrast came out weaker than what I hoped for - a labeled MAP might give us better signal in interphase.