Guillaume Jacquemet

We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows.

Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis.

(1 / 10🧵)

www.biorxiv.org/content/10.6...

Accessible minimal requirements for reproducible light microscopy. This viewpoint presents a community-endorsed checklist defining minimal light microscopy metadata to improve rigor, reproducibility, and transparency in research. rupress.org/jcb/article/...

@quarep-limi.bsky.social

Last 3 days to register for 𝐈𝐌𝐒𝟐𝟎𝟐𝟔 symposium organized by
@itqbnova.bsky.social.
DON´T miss these amazing researchers on 19/03: @seamusholden.bsky.social, @guijacquemet.bsky.social, @silvapereiralab.bsky.social, @pinholab.bsky.social, @henriqueslab.bsky.social.

🔗: ims2026.itqbnovacommunity.org

I'm really looking forward to this meeting 😁. See you in Lisbon 🔬

Assistant Professor (Tenure Track) of Computational Immunology

We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!

You still have 3 days to apply to the postdoc positions available in my lab 😀
🔬Come and work with us 🔬

Restoring the tumour mechanophenotype of vocal fold cancer reverts its malignant properties - Nature Materials Vocal fold cancer tumours lose some of their malignant traits when mechanically stimulated by physiological stretch or vibrations, mimicking the opening and closing of vocal folds and phonation.

What music should we play to our cells? This was the start of an amazing journey from @ivaskalab.bsky.social at @turkubioscience.bsky.social with Jasmin Kaivola and collaborators @sarawickstrom.bsky.social and others to explore larynx cancer mechanosensitivity!

www.nature.com/articles/s41...

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:

- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports

github.com/imaging-form...
v0.0.rc1 on PyPI

Spatial transcriptomics (ST) should be conductive to anyone who has done microscopy in their lives, but it's not! Resolution vs coverage tradeoffs, static workflows, heavy data analysis still plague it...
IT'S TIME TO CHANGE THIS!!
INTRODUCING NaVis
www.biorxiv.org/content/10.6...

GitHub - Izzilab/NaVis: A virtual microscopy experience for spatial transcriptomics A virtual microscopy experience for spatial transcriptomics - Izzilab/NaVis

Try it for yourselves and let us know what you think!!! Oh, and if you don't have ST data don't worry, we have curated them for you too! Check our git:
github.com/Izzilab/NaVis

Awesome, congrats!!!

Closing date is 19th Feb so why not go for it to enjoy the rain in London!

Delighted to share our latest preprint "Filopodia-mediated trans-endocytosis"

www.biorxiv.org/content/10.6...

Work driven by many people including Hanna, Marcela, Sujan, Marie-Catherine, Anna and Monika. Fantastic collaboration with Johanna Englund, Emilia Peuhu, and Eija Jokitalo

💡 Interested in mechano-immunology (or biology of adult B-ALL) ?

💥 We have an #MSCA postdoctoral fellowship offer for you
@ec.europa.eu

🖥️ : euraxess.ec.europa.eu/jobs/hosting...

🏙️ Where ? In beautiful #Strasbourg #CRBS @inserm.fr @unistra.fr

🥼 Interested ?
📧 jacky.goetz@inserm.fr

Neat 😊

Thanks Stephen 🙏

Thanks 🙏

Any questions and comments welcome 😀
We still really poorly understand the mechanics of this

Only a few spots left for this amazing meeting! Just sign up and join us to discuss all #cellbio #imaging things!

Thanks 🙏

The abstract submission deadline for our upcoming 'Imaging Cell Dynamics' meeting is this Friday. We still have a few places remaining so apply now to secure your spot!

Find out more at:
www.biologists.com/meetings/jcs...

#imaging #microscopy #cellbiology

As always preprint formated using the #RxivMaker engine created together with @henriqueslab.bsky.social
github.com/HenriquesLab...

Delighted to share our latest preprint "Filopodia-mediated trans-endocytosis"

www.biorxiv.org/content/10.6...

Work driven by many people including Hanna, Marcela, Sujan, Marie-Catherine, Anna and Monika. Fantastic collaboration with Johanna Englund, Emilia Peuhu, and Eija Jokitalo

Same👍

Thanks a lot

1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:

Our solution is to rely on an idea we had in a previous collaboration with @guijacquemet.bsky.social . We automatically configure tracking parameters by optimization.

Awesome!! Congrats to the whole team

New preprint alert!

We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin).
www.biorxiv.org/content/10.6...

👇🧵

🚀