Every 3D tissue is a map waiting to be drawn. Flatten a curved tissue, follow how it deforms, find its hidden axis, or measure its shape to explain how it moves: it's all cartography!

Last call! This is a great opportunity for those interested in learning and applying SOTA ML/DL models to microscopy data with the leading experts in the field. Personally super excited to be a lead TA along with the amazing @afoix.bsky.social and @edhirata.bsky.social! Hope to see you there :)

Jan Funke@janfunkey.bsky.social · 9mo ago

We moved the AI@MBL course "Deep Learning for Microscopy Image Analysis" to HHMI Janelia (@hhmijanelia.bsky.social). Join us for two weeks of intense lectures, exercise, and hands-on project work! Course dates: June 4-18 2026 Application by: January 15 2026 www.janelia.org/you-janelia/...

🚨 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/...

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.,

janelia.org

This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!

Anna Foix@afoix.bsky.social · 9mo ago

📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee 📍 Janelia Research Campus, VA 🗓️ Apply by Jan 15, 2026 🔗 shorturl.at/j4sgY

We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...

New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains 1/ doi.org/10.1101/2025...

(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging Let's have a look 👇🧪💻🔬

Check out our "In Preprints" @dev-journal.bsky.social w/ Yonit Maroudas-Sacks & Marc Trani Bustos @mpi-cbg.de @poldresden.bsky.social, putting recent #gastruloid work from @viktri08.bsky.social @thomasgregor.bsky.social @amartinezarias.bsky.social labs in broader perspective: doi.org/10.1242/dev....

In preprints: exploring developmental robustness and timing with gastruloids

How developmental processes are coordinated in time and space to ensure the robust formation of complex, functional patterns during embryogenesis remains an outstanding question. Investigating this in...

doi.org

Thoughtful preview article by María Rodríguez Colman & @sonnenlab.bsky.social on recent papers from our lab and @jesseveenvliet.bsky.social lab! Grateful for their in-depth analysis of the papers and their big-picture perspective on the role of metabolism in development. doi.org/10.1016/j.st...

Signaling switches: Metabolism regulates gastruloid self-organization

Metabolic regulation of embryonic development is increasingly recognized. Villaronga-Luque et al. and Stopornwongkul et al. show that metabolic activity influences gastruloid formation from mouse embr...

cell.com

This my first big project during my PhD and I couldn’t be happier about it being out! Please give it a read if you’re interested in embryo models, data fusion, machine learning, image analysis, metabolism, scSeq…. because a lot of great people made this project possible! 🚀

Jesse Veenvliet@jesseveenvliet.bsky.social · last yr.

😱 A very hungry #PacManoid ate the original post 🍬🍬🍬 Here’s the 🧵 on our latest in @cp-cellstemcell.bsky.social again! Gastruloids w/ a sweet tooth better model natural embryos: doi.org/10.1016/j.st... Spearheaded by @cryaaa.bsky.social & Alba Villaronga-Luque @mpi-cbg.de @poldresden.bsky.social

📢 Fresh off the press and featuring new exciting experiments! 🧪 We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊 doi.org/10.1016/j.st... B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩

Festive times with @mpi-cbg.de predocs Ryan Savill @cryaaa.bsky.social & Alba Villaronga Luque! What were we celebrating? More tomorrow! Supported by @sumoconsortium.bsky.social, part of @ec.europa.eu European Innovation Council Engineered Living Materials Portfolio #EUeic #EICPathfinder #ELMs

Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀 github.com/BiAPoL/napar...