Lucien Hinderling

Proteins dance.

Molecular dynamics animate life, but their analysis is limited by the capabilities of current measurement technologies.

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.

Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...

You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

eLife Science Digests Cutting jargon and putting research in context, digests showcase some of the latest articles published in eLife.

eLife digest:
elifesciences.org/digests

GitHub - QI2lab/opm-processing-v2: Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data. Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data. - QI2lab/opm-processing-v2

Tensorstore is much faster for read/write than vanilla zarr. Tools are here: github.com/QI2lab/opm-p...

Currently we only support our custom pymmcore-plus OPM format and ASI’s OPM format. Happy to work with you to support CZI LLSM files if you open an issue and provide some example data.

whats the advantage of tensor store over zarr? are the tools public? would love to have a completely python based solution running on our cluster, sound great!

I have this demo which is doing lazy tiled (multigpu) deconvolution of skewed dataset (to put all buzzwords): github.com/NicoKiaru/ij... + some background info in the pdf of this zenodo repo if you find it interesting: zenodo.org/records/1450...

for MCF10A also seems to be dependent a lot on density! looks very different compared to this (over)confluent epithelia i imaged some time ago on confocal. +1 for zarr+dask, has been working great for us with on data 👌 any tricks on how to convert .czi to .zarr without loosing compression?

"ZeissQuickStartCZIReader is an alternative to the default ZeissCZIReader [...] aiming at increasing the speed of the reader initialisation, which was too slow for files that contains a lot of planes, typically lattice light-sheet dataset." 😍
imagej.net/plugins/zeis...

oh perfect!! works with .czi? lazy loading?

most expensive office printer 😅

look how flat they are??? 🥞 nuclear marker is H2B

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org

pYtags - our in vivo biosensors for receptor tyrosine kinases - in all their beauty on the cover of Cell Reports! Read more here: www.cell.com/cell-reports...

We have used many microwells to confine biochemical reactions in our recent studies. We wanted to share the protocol for preparing and characterizing microwells; this protocol is now published here : www.frontiersin.org/journals/cel...

@manuelthery.bsky.social @lblanchoin.bsky.social

Are you using or interested in using ML to study cytoskeletal dynamics, cell migration and mitosis?

Join us at our upcoming workshop, Machine Learning of Cytoskeletal Machines (Cell Migration and Mitosis)! Applications are open now!

www.nitmb.org/cytoskeletal...

Copying selected elements of a layer in napari into a new layer

#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social

pay us £1500 for the privilege of doing our graphic design work for free

🚨 Second preprint of the week!

We uncover the multiscale dynamics of active viscoelastic buckling in epithelia.

We harness these mechanical instabilities for synthetic morphogenesis.

Led by @onenimesa.bsky.social 🙌. Theory by Marino Arroyo etal. @ibecbarcelona.eu

www.biorxiv.org/content/10.1...

Loved the preprint, congrats on the paper!

Screenshot of figure showing exposure calibration experiments for two different spin-coating speeds.

Updated paper has new QC experiments (check the supplementary figures), small corrections to the methods and discussion section.

Screenshot of table showing reagents required for protocol.

We use off-the-shelf 3D printing resin and microscope slides, replacing expensive SU-8 and silicon wafers. No clean-room required. See the preprint thread above for application examples & link to github repo.

PAPER OUT ✨ What if you could use your microscope as a 3D printer? Prototype microfluidics in-house, <5$ in material costs per chip. From idea to experiment within a day. Now published in Lab-on-a-Chip (open-access): doi.org/10.1039/D5LC...

YouTube video by LIBRE hub Open microscopy in the life sciences: Sharing is caring

A few weeks ago, I gave a talk on our (and other's) efforts towards open microscopy: www.youtube.com/watch?v=Yixv.... Thanks for the invite @makertobey.bsky.social and LibreHub!

YouTube video by LIBRE hub Open Hardware Microfluidics

A few weeks ago, I gave an overview talk on our efforts in making Open Hardware Microfluidics.
The talk is now online here:
www.youtube.com/watch?v=DP6L...

Thanks to @makertobey.bsky.social @ LibreHub for the invitation :)

🚨 #ExM meets #eSRRF 🔬🏄🌊 the full protocol now in ‪@natprot.nature.com‬: doi.org/10.1038/s415...

🔬👨‍💻📰 #SReD is out!
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.

Check: www.nature.com/articles/s41...

"Augmentation deskills us in the name of efficiency, while enhancement upskills us, fostering a richer interaction with the world. This determines whether we become mere passive operators or creative artisans."
mondediplo.com/2024/08/07ai...

Making waves with my trainee Marie Albinet and my colleague Alexei Grichine... Curves are cool

so cool! what printer/resolution? any issues with cell toxicity from the resin?

New adventure in 3D printing, Stampwell inspired @gaellerecher.bsky.social ; @idylle-labs.bsky.social
Next step, testing the molding
#Making waves with Marie Albinet