Martin Weigert

Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social

🚨🚨🚨 DEADLINE EXTENSION ALERT! 🚨🚨🚨 Great news 🧬💻 The submission deadline for the BioImage Computing (BIC) Workshop at @eccv.bsky.social is now July 20, 2026! We can't wait to see your latest research! 🔬👩‍💻👨‍💻 🚪 Submit: openreview.net/group?id=the... 🌐 Info: www.bioimagecomputing.com

Heading to #CVPR2026 in Denver, where we'll present our highlighted poster: "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" enabling joint processing of local/global views. youtu.be/apFzMgmUUnM Friday 5th, 4pm Poster session 2 #602 Led by @albertdm.bsky.social

The paper is now published in Current Protocols!! 🎉🥳 currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1... Some personal story below 👇 , and technical details in the linked post that featured the preprint 👉

Want to build some of the most advanced light-sheet microscopes in the world to watch life assemble itself cell by cell? The Royer Lab @ Biohub is hiring an Optical Engineer (Advanced Light Sheet Microscopy). 🧪🔬💻🔧 #Hardware + #Python + Advanced #Optics job-boards.greenhouse.io/biohub/jobs/...

📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...

Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...

Join us again for the Bioimage Computing workshop at ECCV 2026! Paper deadline July 13th 🔥

💥 🚀 New preprint! 🎉🥳 How do hundreds of organelles organize themselves into near-perfect patterns inside a cell, without a blueprint? We dive deep into how basal bodies (BBs) self-organize in MCCs - and how actin actively tunes their dynamics into order 🍪 🧵👇 (1/17)

Apply by May 20th to do research @mpi-cbg.de or @biohub.org. For example, my lab is open to your #ideas that loosely align with the theme of the #evolution of #morphogenesis. The name of the game is #freedom. Join us to develop an independent research line. I provide support, mentoring & technology

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

BIG UPDATES! OCTRON now supports the new SAM3 models (alongside SAM2)! We’ve also added a global switch for Detection vs. Segmentation: Use the same annotations to train either lightweight detection or full segmentation models. Plus, we’ve added support for the new YOLO26 models. ⤵️ 1/12

Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx Part of sfb1690.uni-goettingen.de to study hearing, vision, and more. Plus, you can create pretty pictures as the one below :).

We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇). My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue. Apply by March 26.

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps. ascona2026.sciencesconf.org

Very happy that MuViT, our (CVPR 2026!) work on learning across spatial scales in microscopy w transformers, is out! Check Martin's thread for a nice walkthrough :) Big thanks to my advisors @maweigert.bsky.social @gioelelamanno.bsky.social! 🖥️: github.com/weigertlab/muvit 📜: arxiv.org/abs/2602.24222

#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you. www.biorxiv.org/content/10.6...

Method of the Year 2025: In his Comment, @janfunkey.bsky.social discusses current challenges in connectomics, which is time-consuming and labor-intensive. He focuses on proofreading and discusses how automated models might be further developed to embrace uncertainty. www.nature.com/articles/s41...

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...

Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues. The paper: arxiv.org/abs/2503.19545 1/🧵

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

(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...

Thanks Misha for the shout-out! It has been a truly mind-opening journey. WHOLISTIC is one step towards whole-organism neuroscience and a true physiological observatory - with extensions on the way! I am continually amazed by what the data reveals - so much remains to be discovered and mined.

Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy. Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)

How is this possible? This ant can lay eggs of two different species, birthed by the same mother

Thrilled to share 🎉 I’m starting my lab at University of Zurich, DMLS as Assistant Professor (tenure track) from Jan 2026! The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬

Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social ‬ & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...

EPFL, ETH Zurich & CSCS just released Apertus, Switzerland’s first fully open-source large language model. Trained on 15T tokens in 1,000+ languages, it’s built for transparency, responsibility & the public good. Read more: actu.epfl.ch/news/apertus...

Happy to share our work on uMAIA, a framework for building metabolomic atlases from mass spectrometry imaging. With uMAIA, we mapped the lipidome of zebrafish development, uncovering spatially organized metabolic programs . www.nature.com/articles/s41... #developmentalbiology #MSI #lipidtime

Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism. www.nature.com/articles/s41...

📢We're #hiring Group Leaders! Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning. 🔹5-year renewable appointment 🔹Pioneer new tools & approaches 🔹Collaborate across disciplines Apply by Nov. 4👉 https://janelia.link/groupleader

Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: community models beat expert tools. Read more in the @natmethods.nature.com article that just came out: 🔗 doi.org/10.1038/s415...

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

The Friday second try: After intense work, especially in the last year, this work is finally ready to be seen by the public. Led by @apramos.bsky.social and great collaboration with @carldmodes.bsky.social group especially @liormoneta.bsky.social : www.biorxiv.org/content/10.1...

Our beautiful Hydra made the cover!!! 😍😍😍 An experiment performed by Pavel Mejstrik with a HCR protocol by @giuliaserafini.bsky.social, @paveltomancak.bsky.social lab @mpi-cbg.de Actin fibers in blue, nuclei in orange.

A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3) forum.image.sc/t/qupath-ext...

We are today kicking off the two-week @embo.org practical course on #Lightsheet # Microscopy at @mpi-cbg.de in #Dresden. This is the fifth iteration of the course. Hashtag #LISH2025 meetings.embo.org/event/25-lsm

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr

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 2nd AI4Life Challenge is live! Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail. 📦 Paired noisy/clean datasets 📈 Ground-truth evaluation 🧠 DL focus Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/

Nature research paper: Morphodynamics of human early brain organoid development https://go.nature.com/4l7fDmc

Finally here! Our preprint on the MOSAIC, a multimodal adaptive optical microscope enabling non‑invasive in‑vivo imaging from molecules to organisms, is out. MOSAIC captures everything from subcellular dynamics to neural activity in live mice. www.biorxiv.org/content/10.1...

Get to know Spotiflow, an AI method that improves large-scale transcript localization by combining deep learning with a novel geometric detection approach. Learn more: 👉 scads.ai/transcript-d... Find the publication in Nature Methods: 👉 www.nature.com/articles/s41...

If you in need of a quick walkthrough @albertdm.bsky.social has you covered: