1/n: A new collaborative preprint from the lab to start the year: "A multi-ring shifter network computes head direction in zebrafish" together with Siyuan Mei, Martin Stemmler and Andreas Herz from the LMU, Munich.

Are you a bachelor or master student anywhere in the world, and would like to come to us to work full-time on a supervised research project? Applications for the 2026 MPIA Summer Internship are open now!

Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social Huge collaborative effort! So glad to see the community already using it to develop new resources & tools. Check it out here: shorturl.at/z4i4c #CryoEM #CryoET

New preprint showing how the membrane-associated periodic skeleton (MPS) restricts endocytosis in neurons: www.biorxiv.org/content/10.6... It nicely confirms our work from last year (science.org/doi/10.1126/science.ado2032) and extends it to other compartments in more mature neurons

Apply by Feb. 3 to become a Janelia Group Leader! Group Leaders drive breakthroughs & experimental approaches in imaging, molecular engineering, protein chemistry, mass spectrometry, & methods that don't yet exist. Learn more: janelia.org/groupleader 🧪

An awesome figure illustrating key aspects of hippocampal encoding and replay during continuous behavior ; from great work by Brian Lustig and co www.biorxiv.org/content/10.6...

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets https://www.biorxiv.org/content/10.64898/2025.12.10.693416v1

I am currently reading Innumeracy. We were warned about the dangers of a society incapable of doing basic math 37 years ago. How I wish elected officials, anti-vaxxers and conspiracy theorists would read that book😞.

New release of #BigVolumeBrowser. Many things were added: UI improvement (thanks to @kwolbachia.bsky.social feedback), pyramidization for BioFormats dataset, bug fixes. Now there is an isosurface rendering mode (1/4)

Devcontainers are great. But related, does anybody know of a good mechanism to bleep the secrets that ClaudeCode or OpenCode spill when they decide to ignore deny rules? Like a rule that replaceAll()s everything on the client before it goes out?

I had heard this was coming, but it’s still an amazing indication of how far we’ve come in the last decade or so!

Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too! preprint (with videos!) + thread 🧵 Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking www.biorxiv.org/content/10.6... 1/9

(1/2): Using cryo-electron tomography and an instrument like this one, HHMI Investigator Michael Rosen & team (not pictured) have captured the most detailed images to date of the molecules inside chromatin condensates. hhmi.news/4iFBIrV

Very excited to show off our latest data. Videos hot off the microscope! Come see what crazy things cells of al types are up to tomorrow!

I am very much in favor, we just put out a recent preprint thinking about learning to navigate from the perspective of generative models of trajectories www.biorxiv.org/content/10.1...

The era of coding agents is here. How do we approach this as scientists? Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science. www.youtube.com/watch?v=Rbhs...

Do you have 2D-to-3D image registration challenges? Let me know about them here forum.image.sc/t/toward-bet...

Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41... This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)

PhD position in my lab in #AI #RNA, in co-supervision with superstar @florianjug.bsky.social www.polimi.it/dottorato/fu...

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:

Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2) forum.image.sc/t/bigvolumeb...

Wow, huge work, congratulations to all!

1. New preprint resolving a conundrum in systems neuroscience with an AI scientist, and humans Reilly Tilbury, Dabin Kwon, @haydari.bsky.social, @jacobmratliff.bsky.social, @bio-emergent.bsky.social, @carandinilab.net, @kevinjmiller.bsky.social, @neurokim.bsky.social www.biorxiv.org/content/10.1...

We are looking for a scientific computing associate interested in data-driven equation discovery here at @hhmijanelia.bsky.social. This is an alternative to a postdoc that you can use to move into academic or software jobs. Please spread the word! hhmi.wd1.myworkdayjobs.com/en-US/Extern...

Curious about or committed to collective behavior? Please register and submit your abstract ASAP! We are hoping to have a big crowd in Heidelberg in February.

😳 mastodon.social/@glyph/11546...

The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1

A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...

The new @mpi-cbg.de research group leader Daniela Egas Santander is looking for a Postdoctoral Researcher (m/f/d) in Applied Topology for Biology. Apply until November 16th here: careers.mpi-cbg.de/jobs/6002777...

Join the team at Janelia to use #theory, computation, and modeling to tackle bold questions in #biology. Collaborate across scientific disciplines to drive discovery. Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram #computationalbiology #sciencecareers

Hello dear diary, today I've added some minor features, like highlighting boxes and canvas selecting objects + manual transform mode. Small update, mucho trabajo, but it should be helpful for user experience #bigvolumebrowser

The Shanahan Fellowship is a unique PostDoc opportunity at the intersection of Neuroscience and Data Science. If you are considering a PostDoc in this area, I encourage you to apply! Applications are open! And due by Dec 1st alleninstitute.org/shanahan-fou...

Very excited to be co-organizing this meeting. Hope to see you there!

Excited to share our new #biorxivpreprint: “Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1... We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10

The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social www.biorxiv.org/content/10.1...

Cell Physics community is missing Jochen Guck deeply.. He was a very kind and generous person, one of the most creative minds, and always ready to help everyone in the field.. He inspired many of us.. He will always be missed..

Great Job - Great Colleagues - Great Science👍 Help us pick the next generation of @hhmi.org Investigators, Freeman Hrabowski Scholars, Hanna Gray Fellows, Gilliam Fellows Relocation to DC is required, perfect for academic PIs looking for their next chapter hhmi.wd1.myworkdayjobs.com/External/job...

I love this piece! It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions. And it makes me feel good about having helped to generate the thing. :)

🔊 Listen to Senior Group Leader Hari Shroff discuss microscopy, biology and his path through science in the latest episode of Ashoka University's The Science of It podcast: https://www.youtube.com/watch?v=dyoP5HwAFAc&list=PLaTCrA79FLSx-NV34W0Ee2Ei8FgmBDEKn&index=16

#QuPath + Imglib2 and #BDV ❤️ Promising start! (Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)

I managed to make #ABBA work with a white background and dark mode! #FijiSc #BDV. Useless for the moment, but I like it.

Apply now!!! 🔥

We're very proud to be releasing the complete male fly CNS connectome! It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators. More soon... www.janelia.org/project-team...

“framing science as a debate to be won makes it easy to paint established scientists as opponents who must be overcome” An interesting thesis and suggestion of a solution www.nytimes.com/2025/10/03/o... 🎁

New blog post, where I review some recent interesting papers on the role of cell organelles for neuronal calcium signaling: gcamp6f.com/2025/08/11/i... Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. Read more: e11.bio/blog/prism

NEWS🎉 We’re excited to announce @hhmijanelia.bsky.social Investigator David Stern will join the Institute from Janelia Research Campus. His lab studies how aphids transform plants at the genetic level, uncovering secrets of #evolution & new strategies for pest control. @hhmi.org bit.ly/4np96Fb

We're announcing a new update to MTEB: RTEB It's a new multilingual text embedding retrieval benchmark with private (!) datasets, to ensure that we measure true generalization and avoid (accidental) overfitting. Details in our blogpost below 🧵

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Back to work on #bigvolumebrowser, I've added the import of point clouds that change over time. The test data generation was a pleasant detour into the world of attractors (Thomas' cyclically symmetric is shown).