Ebrahim Lab

Deep Learning for Microscopy Image Analysis Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?

20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026

✍️ Jan 15 2026 ✍️

🔁 pls!!

www.janelia.org/you-janelia/...

From earlier this week: This issue’s Cover: @ebrahim-lab.bsky.social @dominikrobak.bsky.social & team report on the septin cytoskeleton at apical junctions of intestinal epithelial cells, whereby it maintains barrier integrity & protects from inflammation: insight.jci.org/articles/vie...

Thanks, Helge!!

Very excited to share the latest work from our lab in @insight.jci.org, highlighting a role for the #septin #cytoskeleton in protecting against "leaky gut", by recruiting non-muscle myosin II and stabilizing the tight junction.

Credit to @dominikrobak.bsky.social for the stunning cover image!

Check out our new preprint on the discovery of a molecular switch in NAC that mediates nascent chain sorting on the ribosome and prevents mitochondrial protein mistargeting by SRP. A great collaboration with the Shan Lab @Caltech and the Qi Lab @UVA: www.biorxiv.org/content/10.1...

Having seen your bingo card, we had to make it happen 😉!

Thank you for highlighting our work @hankgreen.bsky.social ! 🙏🏽

Thank you, Ilya! :)

Proposed mechanism of MVB formation

Early for #MicroscopyMonday: #Hemifusomes- Newly discovered ESCRT-independent intermediates of intraluminal vesicle and multivesicular body formation! In collaboration with the Kachar Lab at the NIH and out today in @natcomms.nature.com : rdcu.be/emtQu

#cryoET #trafficking #organelle #hemifusion

😞

"Stereocilia"- actin-based skyscrapers that adorn sensory cells of our inner ear and covert vibrations into electrical signals—the first step in hearing and balance. #FluorescenceFriday

🎉🎉We’re on the cover of Nature Physics! @natphys.nature.com

Here is the original paper www.nature.com/articles/s41...

From stem cell to structure-
This human colonoid shows the self-organization of intestinal epithelial cells in 3D—nuclei in magenta, actin in green. A living miniature gut for your #FluorescenceFriday.

Expansion microscopy micrograph of the choanoflagellate Choanoeca flexa, vaguely evocative of a cactus. Red = tubulin, green = actin, blue = DNA

Same with yellow = lipids (BODIPY)

A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!

Only 29 slots left out of 200--register now!

🧫 A gentle reminder that your gut is an actual work of art.
#FluorescenceFriday #BeneathTheScope

Two months left for FASEB Conference - Septins: Spatial regulators of cell biology
Register now:
events.faseb.org/event/septin...
Come find out what these filaments do at the interface of the actin and microtubule cytoskeletons and cell membranes. You'll be hooked for life.

Is liver zonation conserved from mice to humans? And how does fibrosis affect zonation in patients? Now, these questions are answered using scDVP. Some collaborations are meant to be! @carolineweiss.bsky.social@frosenberger.bsky.social @mannlab.bsky.social@mlsb-borgwardt.bsky.social

#MicroscopyMonday | Colon-scoping turned coral reef

Was imaging the colon when I accidentally stumbled into this glowing patch of vascularized white adipose tissue.

🔵 mT/mG mouse (mT-only) → red membranes shown in cyan

Accidental imaging hits different.

#IntravitalImaging #LiveImaging

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

#3DThursday | Intestinal villi in all their folded glory

These self-renewing, nutrient-absorbing structures are beautiful and functional.

🔴 Phalloidin
🔵 DAPI
🟢 Clvd cas-3 (extrusion in action!)

Fixed tissue 3D imaging = big insight, tiny resolution.
#Microscopy #3DImaging #biophysics #intestine

Have cutting-edge cell biology research to share? Submit to Molecular Biology of the Cell (MBoC)- dedicated to advancing discovery and fostering collaboration.

Proud to be part of the editorial team supporting groundbreaking science. molbiolcell.org

#CellBiology #MBoC #Research