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

Passive morphogenesis of the gut: work by @zhaoshh.bsky.social @lepuslapis.bsky.social @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social and collaborators at Princeton University, @flatironinstitute.org now #published @pnas.org: doi.org/10.1073/pnas.2505160122

The final version of our "Thrifty" paper is up now: elifesciences.org/articles/10... . We were motivated to fit wide-context mutation models based on previous analyses showing "mesoscale" effects and a position-specific effect. But, how to avoid exploding the number of parameters? 🧵

🌟 Launch your own lab at Janelia 🌟 Advance our understanding of biology through theory, computational modeling & machine learning. 🔹 No teaching requirements 🔹 100% internally funded 🔹 Collaborate with expert support teams 📅 Apply by Nov. 4 👉 https://janelia.link/groupleader

We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social hhmi.wd1.myworkdayjobs.com/en-US/Extern...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Come join us at University of Toronto. We're hiring a Professor of computational cognitive neuroscience. #neuroAI #compneuro jobs.utoronto.ca/job/Toronto-...

🪰 How do dozens of tiny fly muscles cooperate to move a leg? We’re excited to share the first 3D, data-driven musculoskeletal model of Drosophila legs based on Hill-type muscles, running in OpenSim and MuJoCo simulation environments. Preprint: arxiv.org/abs/2509.06426

ModernBERT goes MULTILINGUAL! One of the most requested models I've seen, @jhuclsp.bsky.social has trained state-of-the-art massively multilingual encoders using the ModernBERT architecture: mmBERT. Stronger than an existing models at their sizes, while also much faster! Details in 🧵

Become a Theory Fellow at Janelia. 🔍 Use computation & theory to tackle biological problems. 🖥️ Leverage state-of-the-art computational infrastructure 🤝 Collaborate across scientific disciplines Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram

Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo. www.biorxiv.org/content/10.1...

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)

🥳Congrats! Exciting to see the similarities and differences between hunger-modulation from our findings in the brain and the VNC. Internal state configures olfactory behavior and early sensory processing in Drosophila larvae | Science Advances www.science.org/doi/10.1126/...

We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)

UMA: A Family of Universal Models for Atoms www.compchemhighlights.org/2025/08/uma-... #compchem

github.com/allierc/MPM_pytorch @HHMIJanelia pytorch version of github.com/yuanming-hu/...

On the Theoretical Limitations of Embedding-Based Retrieval Google DeepMind demonstrates that vector embeddings have fundamental limitations in representing all possible document combinations. 📝 arxiv.org/abs/2508.21038 👨🏽‍💻 github.com/google-deepm...

Research team @nadlerlab.bsky.social, A. Honigmann @biotec-tud.bsky.social, B.Drobot @hzdr.bsky.social, M. Hof @heyrovskeho-ustav.bsky.social develops approach to visualize lipids in cells & uncovers the main transport mechanism for lipids within the cell. @nature.com www.mpi-cbg.de/news-outreac...

📢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

FlyBase needs your help! Visit the link below for more information, and please consider donating to help save this amazing resource. wiki.flybase.org/wiki/FlyBase...

How do you quantify cell structures which are deformed between different observations? Our preprint shows how to perform Simultaneous QUAntification of Structure and Structural Heterogeneity (SQUASSH) on 3D fluorescence microscopy data. (1/5) www.biorxiv.org/content/10.1...

Happy to contribute to this new work from @micoxscopy.bsky.social et al, helping apply SSQUASH to analyse the shape of spectrin rings along axons. Data analysis is the next frontier in SMLM, and I'm always up for chatting, sharing data and see how we can push things further!

✨ We’re #hiring Theory Fellows!✨ Janelia is recruiting early-career scientists to join our collaborative research environment and use #computation & #theory to tackle bold questions in #biology. 🔗 Apply by Nov. 3 👉 janelia.link/theoryfellow... @hhmi.org

How is the nervous system organized to coordinate behavior? To approach this massive question, a team led by @asbates.bsky.social, @jasper-tms.bsky.social, @mindyisminsu.bsky.social, & Helen Yang present the BANC: a Brain and Nerve Cord connectome. Preprint: doi.org/10.1101/2025... 🧪#Neuroskyence

With @megyounger.bsky.social's lab, et al., we present the first connectomics work in the disease-vector mosquito Aedes aegypti, revealing how its brain is wired to detect host cues. Preprint: doi.org/10.1101/2025... #Neuroscience #Connectomics #vEM #VectorBiology 🧪

THIS IS HUGE! The FIRST 100% effective HIV PrEP drug, Lenacapavir, is APPROVED AND GOING GLOBAL. The makers are providing AFFORDABLE access to the drug in the United States AND beyond, signing ROYALTY-FREE licensing agreements with SIX generic manufacturers to produce AND supply it. 🧪🧵⬇️

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:

Physik studieren? Oder ein anderes Fach? In Göttingen geht jetzt beides, mit dem "Bachelor Interdisziplinär", der Physik mit spannenden Disziplinen Eurer Wahl, wie z.B. Künstlicher Intelligenz, Philosophie, Neurowissenschaften, ... kombiniert. www.uni-goettingen.de/de/studium/6...

Want to use the massive MICrONS dataset for your own research? We understand the challenges and we are here to support you. Submit your proposals for our Proofreading and Annotation program: Virtual Observatory of the Cortex (VORTEX) by August 15. microns-explorer.org/vortex

Key numbers in cell biology Having a sense of scale helps to think more rigorously and realistically about biological systems.

🚨 SAVE THE DATE 🚨 Inaugural CCP-volumeEM Community Meeting, 3rd November 2025 at @crick.ac.uk in London "Towards a collaborative computational community for volume EM" Timings: 12pm - 5.30pm, followed by networking reception #volumeEM #BioImageAnalysis #VEM #CCPvolumeEM #CoSeC

Linear recurrent models such as Mamba can process extremely long sequences compared to transformer models, but..... they struggle to generalize beyond the sequence lengths they were trained on. This wouldn’t be a major issue—except that training on longer sequences is extremely difficult.

- A postdoc to work on cancer extravasation (4-year project). - A postdoc help in completing Filopodia-related lab projects (2-year). - Multiple Marie Curie postdoc positions that will open in the fall. - We will open a 5-year position to cover my teaching (70% research and 30% teaching).

Novel Research in Biological Artificial Intelligence: Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence @mpi-cbg.de and @csbdresden.bsky.social. More information: www.mpi-cbg.de/news-outreac...

New paper hot off the press www.nature.com/articles/s41... We analysed over 40,000 computer vision papers from CVPR (the longest standing CV conf) & associated patents tracing pathways from research to application. We found that 90% of papers & 86% of downstream patents power surveillance 1/

From June 23 to June 29, 2025, Freie Universität Berlin will be cutting out the letter e from its communication. Why? Because the university itself is facing cuts: around 37 million euros this year alone. Additional cuts are also planned for 2026 and 2027. (1/3)

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social www.nature.com/articles/s41... rdcu.be/epIB7

Wouldn't it be great if we could not only image large connectomic volumes but also completely reconstruct them? And if a whole mouse brain project didn't cost billions? With the PATHFINDER preprint (www.biorxiv.org/content/10.1...), we preview a future where it doesn't have to.

The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more! www.biorxiv.org/content/10.1...

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0! This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more! Preprint at doi.org/10.1101/2025...

An important addition to the Nature paper, beyond what was shown in the 2024 preprint, is 12 rounds of iterative imaging and sectioning of a LICONN volume, achieving 205 microns in axial extent (native scale) with manual tracing of axons: www.nature.com/articles/s41...

Some early attempts to show 3D SMLM data in #bigvolumebrowser : 4M points from @shuangfu-shawn.bsky.social re-analysis of our LLS-paint data (see recent retweet). It can be overlaid with any volumetric data input. @christlet.bsky.social are you still interested in Fiji SMLM renderer?

Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching. A collaboration with @mh123.bsky.social 🚀 github.com/danionella/w...

Thanks to a dose of activation energy from @dpshepherd.bsky.social, I've finally cleaned up my Biggs–Andrews accelerated version of our automatic parameter-free deconvolution code and made it available at beryl.mrc-lmb.cam.ac.uk/rlgcba_noteb.... This is ~2.75× faster than the previous version. 1/4

Nature research paper: Light-microscopy-based connectomic reconstruction of mammalian brain tissue https://go.nature.com/3YCLkuZ

🚨🔬💗Whether investigating cell organelles or mapping proteins, together with Victor Puelles's lab we lay a roadmap for selecting optimal #ExM and #SuperResolution #microscopy combinations. Daria Aristova and Dominik Kylies review with amazing co-authors pubs.aip.org/aip/apr/arti...

New era for brain mapping, latest from Johann Danzl lab in @nature.com. Light-microscopy connectomics is at single-synapse resolution. Engineered hydrogel embedding + expansion, deep learning-based segmentation, and molecularly resolved reconstructions: axons, spines, connectivity, all visible.

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n

Excited to share my PhD paper is out! We studied how motion vision is processed beyond the optic lobes to help flies walk straight. It has been a wonderful collaboration with @michaelreiser.bsky.social, @dddavi.bsky.social and many others not in bluesky! Paper + digest here: bsky.app/profile/cham...

Media sites: A tip If you can use an AI image for an article header The article didn't need a picture So just don't Thanks, bye