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Nicolas Chiaruttini

@nkiaru.bsky.social

960 followers 890 following 190 posts

Microscopist and Bio-Image Analyst for the BioImaging and Optics Platform https://biop.epfl.ch/ at EPFL https://nicolas.chiaruttini.org

biop.epfl.ch

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Nicolas Chiaruttini @nkiaru.bsky.social · 23h

#QuPath + Imglib2 and #BDV ❤️

Promising start!

(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)

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Nicolas Chiaruttini @nkiaru.bsky.social · 1d

And new little icons!

Nicolas Chiaruttini @nkiaru.bsky.social · 1d

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

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Nicolas Chiaruttini @nkiaru.bsky.social · 6d

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

Nicolas Chiaruttini @nkiaru.bsky.social · 7d

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

Nicolas Chiaruttini @nkiaru.bsky.social · 7d

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.

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Reposted by Nicolas Chiaruttini

Journal of Cell Biology @jcb.org · 21d

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...

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Nicolas Chiaruttini @nkiaru.bsky.social · 23d

Bright and beautiful! But the floor is tilted 😉

Nicolas Chiaruttini @nkiaru.bsky.social · 23d

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

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Nicolas Chiaruttini @nkiaru.bsky.social · 27d

New achievement unlocked in forum.image.sc!

Reposted by Nicolas Chiaruttini

François Fleuret @francois.fleuret.org · 28d

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Nicolas Chiaruttini @nkiaru.bsky.social · 28d

Ahahahaha! Wth ?

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Nicolas Chiaruttini @nkiaru.bsky.social · 28d

Close enough!

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Nicolas Chiaruttini @nkiaru.bsky.social · Sep 6

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.

Nicolas Chiaruttini @nkiaru.bsky.social · Sep 5

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)

Nicolas Chiaruttini @nkiaru.bsky.social · Sep 5

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

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Nicolas Chiaruttini @nkiaru.bsky.social · Sep 4

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

Nicolas Chiaruttini @nkiaru.bsky.social · Sep 3

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.

Nicolas Chiaruttini @nkiaru.bsky.social · Sep 3

(and bsky video quality is not great)

Nicolas Chiaruttini @nkiaru.bsky.social · Sep 3

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

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Nicolas Chiaruttini @nkiaru.bsky.social · Sep 2

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

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Nicolas Chiaruttini @nkiaru.bsky.social · Aug 29

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

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Nicolas Chiaruttini @nkiaru.bsky.social · Aug 25

Maybe you have a nice astigmatic psf for 3d smlm ?

In other news, we had almost the same issue, and it took a year for the repair (but they were very careful in the shipment😅: bsky.app/profile/nkia...)

Nicolas Chiaruttini @nkiaru.bsky.social · Aug 21

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

A small objective within boxes within boxes within boxes

Reposted by Nicolas Chiaruttini

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · Aug 25

🧬🔬🧪 🎉 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...

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Nicolas Chiaruttini @nkiaru.bsky.social · Aug 21

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

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