Marcel Issler

Waiting for Sam to tell us that GPT-6 will be Nobel level of intelligence and that it can see more colours than a mantis shrimp

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?

In my experience the default zarr already scores quite efficiency on disk, but thats for data that has lots of zeros. In terms of czi conversion i would use the bioio package. However i don't know if you can maintain the compression. Otherwise native zarr supports zipstore, which might help.

Nice! Indeed nuclei are pancakes when they are not inside a 3D matrix, since glass or hard plastic is incredibly charged, pulling all towards the interface. Regarding the big files, i suggest to use zarr and dask, seems like the whole field is moving there.

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

🚀 Big news! The napari hub has been reimplemented and is now community-run! :tada: It's still the go-to place for finding and sharing napari plugins, but the website is now snappier and lighter-weight. Check it out 👉 www.napari-hub.org

Have you ever thought about inflating tissues?
Or maybe quickly deflating those inflated tissues?

New #EpithelialMechanics pre-print: doi.org/10.1101/2025...
🧵 with pressure control, multiscale buckling, controlled wrinkling

Morphodynamics of human early brain organoid development - Nature Human brain morphodynamics are explored using organoids.

Very happy to share it’s online! If you read the preprint, updates include tracking cells and tissue flow, Histo4i timecourse (69 Abs) comparing spatial patterning emergence and a new WLS KO ipsc line establishing mechanosensing via YAP-WLS/WNT caudalizes organoids www.nature.com/articles/s41...

The 2025 VIB.AI International PhD Call closes June 22nd.

We’re offering 4 fully funded PhD positions across labs tackling big questions in biology with AI and machine learning, covering protein design, computational neuroscience, gene regulation, and more.
👉 https://tinyurl.com/53nc9vnd

Unfortunately, we need to cancel the upcoming #GloBIAS seminar. Please check our webpage: www.globias.org/activities/b... for updates/ new date for this session.

Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST!

Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...

🧠 Interested in extending #Zarr?

Let us know what you think about ZEP10 "Generic extensions". Current plan is for voting on the proposal mid-June. 📅

github.com/zarr-develop...

Direct measurements of active forces and material properties unveil the active mechanics of early embryogenesis Despite progress in probing tissue mechanics, direct long-term measurements in live embryonic epithelia are lacking. This limits our understanding of amniote embryonic morphogenesis, which takes place...

🚨📣 New preprint alert!
Excited to share my new postdoc work on direct force and mechanical properties measurements in live embryos!
A great team effort with A. Chamolly (theory), under the supervision of F. Corson and @jeromegros.bsky.social
📄 www.biorxiv.org/content/10.1...
#devbio #mechanics

Thanks to Hanjin Liu, napari now has a command palette! 🎨 This thing is really nice to use — the core team can no longer live without it — and it even works with plugin commands! 🤩

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀

Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich.

🔗 Read the preprint: osf.io/preprints/bi...

🧵 (1/15)

An eppendorf centrifuge in that specific nicotine-yellow color from the 80s. It's the exact color as the old fridge in your garage that you keep sodas in that your parents replaced in 1997, and which has outlived a half-dozen of its replacements.

"Why don't you buy a new centrifuge"

Because everyone knows that any appliances in that shade of yellow will outlive you and your entire family, look at it

Fun group retreat in the Austrian alps with @priscaliberali.bsky.social! And perfect time to celebrate our new joint paper (from Shi-Lei Xue & Qiutan Yang) out on how mechanochemical bistability confers robustness to intestinal organoids! www.nature.com/articles/s41... - see 🧵! (1/n)

Excellent talk at today's #VirtualPub by Chiara Stringiari, France BioImaging, exploring the technical possibilities & limitations of #FLIM and providing a fantastic overview of recent applications. Want to try it out? Available in #openaccess via France BioImaging & other EuroBioImaging Nodes!

Want to engage with the #mechanobiology community? Why not join this group? Just drop me a DM and I´ll add you.
go.bsky.app/G5cQqYT

#BPS2025 is approaching! ✨🔬🧪

I will be presenting a poster on some TPE metabolic imaging and on a little bit of Phasor FLIM analysis. All recent and unpublished data.

Sun Feb 16th - B548

Find me if you are there and interested and want to chat about NADH, FPs, FLIM, or FCS (always up for that).

Abstracts When submitting your abstract, please indicate which topic(s) from the list best suit(s) your submission. This is to assist with the review process and the creation of the conference program itself.

Have you thought which topic suits your abstract🤔??

🫀 Tissue organization&Developmental mechanics
👩‍💻 Modeling
😷 Cancer&Disease
⚙️ Mechanotransduction
〰️ ECM Biomechanics
🔬 Organelle&Nucleus
🧫Cytoskeleton
🤖 Bioengineering&Emerging Technologies

📢 Submissions are now open for the CellMap Segmentation Challenge.

Build the best method for segmenting cellular organelles in vEM using our 289 annotated volumes, 40 organelle classes, and 22 diverse cell and tissue types.

🔗 hhmi.news/410evJQ

YouTube video by GloBIAS GloBIAS: Global BioImage Analysts' society - the idea

The people behind the project globias.bsky.social share a common vision: To bring together data scientists working in microscopy and share their knowledge.
scadsai.bsky.social researcher haesleinhuepf.bsky.social and his colleagues about the idea of the project:
👉 www.youtube.com/watch?v=LPJE...

At the #VirtualPub this Friday, we welcome Hellen Ishikawa-Ankerhold, LMU Klinikum-Munich, for a talk entitled, "Bringing Immunity to Light: The Power of Intravital Microscopy in Inflammation, Infection, and Cancer." All are welcome!
Register 🔽
www.eurobioimaging.eu/events/persp...

Killing Cancer Patients (Once the Payments Clear)

'Speeds things up, you know. Move fast and break things, amIright?
Problem is, in biomedicine some of the things you break are human beings.'
@dereklowe.bsky.social
www.science.org/content/blog...