Philip Hubbard

Some fly neurons are “dimorphic”, existing in both males and females but connecting to different neighboring neurons. Neighbors may be “isomorphic”, the same in both male and female; or sex specific; or dimorphic themselves. Here's an example, the type AOTU012, present in left and right instances.

A connectome spanning the brain and nerve cord reveals interesting pathways. Visual-motor pathways connect visual neurons, which help the fly detect objects, to motor neurons, which help the fly move in response. Here's one such pathway, from R1-R6 visual neurons to the DNg13 motor neuron.

I used Cycles, with some custom Python to simplify setup common to videos of neuroscience and cell biology: github.com/connectome-n...

In the past I used the OTOY Octane renderer with Blender. But it has a commercial license, and these days I think Cycles produces good results with less effort.

Rendering this video was a nice test for #Blender3d, as the full set of bodies visible by the end involved almost 1.1 billion polygons. It all worked out well on our H200 cluster.

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A second AI Engineer position is now open, for work at the intersection of protein engineering, evolution, and machine learning:

hhmi.wd1.myworkdayjobs.com/en-US/Extern...

Larissa Heinrich's diffusion model:
github.com/saalfeldlab/...

Visualized with Gephi. I shrank each layer for visualization, yet there are 1.8 million nodes and 109 million edges, so layout with Gephi ForceAtlas2 takes some time.
gephi.org

Inspired by Matt Fyles:
www.hpcwire.com/2017/02/15/h...

Come to #HHMIJanelia to work on the frontiers of AI and biology. Apply now for an AI Engineer position working on protein biosensors:

hhmi.wd1.myworkdayjobs.com/en-US/Extern...

More openings coming soon. Interesting AI is widespread at Janelia, like this diffusion model from Larissa Heinrich.

Fly labs — Now is the time to show some solidarity and chip in support for this vital resource!

The Menagerie - Tui T. Sutherland From the New York Times bestselling author of the Wings of Fire series, Tui T. Sutherland, and her sister, Kari Sutherland, comes the Menagerie series, perfect for fans of Brandon Mull’s Fablehaven se...

“The Menagerie” series by Tui Sutherland: tuibooks.com/book/the-men...

The #HHMIJanelia FuncEWorm project is building the first cellular/molecular blueprint of an entire organism, the C. elegans nematode. Here's a video showing some of what's involved: light sheet fluorescence microscopy, electron microscopy, spatial transcriptomics.

www.janelia.org/project-team...

Larissa's U-net:
open.quiltdata.com/b/janelia-co...

Layer sizes reduced for visualization.

Layout with Gephi, using ForceAtlas2:
gephi.org

Inspired by Matt Fyles:
www.hpcwire.com/2017/02/15/h...

Thanks to Roman Vaxenburg, Konrad Rokicki, @preibischs.bsky.social, @herrsaalfeld.bsky.social

What does a neural network look like? Maybe like this view of Larissa Heinrich's U-net for organelle segmentation, with edges between layer inputs and outputs.

Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...

Interested in AI and scientific discovery? HHMI Janelia has openings for data engineers as part of a new AI initiative. Preference for senior candidates with experience developing pipelines for scientific data, especially in biology or medicine.

hhmi.wd1.myworkdayjobs.com/en-US/Extern...

#FediHire

Igor Siwanowicz created these images of the underside of the front foot of a male diving beetle. You can see suction cups that are used during mating, as well as a broad plate and exterior spines that aid in swimming.

This Juneteenth we're spotlighting the work of the first Black trained TV meteorologist, June Bacon-Bercey.

Two sets of connecting fly neurons with fine, wispy arbors.

A final found image, with blue LPsP neurons that input to the grey PFL1s.

Two sets of connecting fly neurons with fine, wispy arbors.

Here's another image I found, showing Delta7 neurons in gold providing more inputs to PFL1 neurons in grey. I like that the transparency makes the PFL1s look almost like glass.

Two sets of connecting fly neurons with fine, wispy arbors.

Cleaning up disk space, I found this image I made for someone not long after the release of the #HHMIJanelia #Drosophila hemibrain #connectome in 2020. It shows EPG neurons in pink providing inputs to PFL1 neurons in transparent grey. I'm not sure if the image was ever used.

How about #SciVis, #SciViz?

The video shows electron microscopy matched to light microscopy, perfect for #FluorescenceFriday. Takashi Kawase and Hideo Otsuna wrote the renderer, VVD Viewer, and I generated the animation with neuVid.

Happy to officially introduce FilaBuster - a strategy for rapid, light-mediated intermediate filament disassembly. Compatible with multiple IF types, modular in design, and precise enough to induce localized filament disassembly in live cells.

www.biorxiv.org/content/10.1...

🎉Congratulations to HHMI’s Beautiful Biology, winner of a 2025 Webby Award in the Science Websites and Mobile Sites category ➡️ hhmi.news/42KRBpI

💻Explore the site ➡️ www.hhmi.org/beautifulbio...

📷Igor Siwanowicz

Wanted to share some key takeaways from this meeting for the broader public. If you were there and I missed things, please add on to this thread!

Research Technician - Open Chemistry Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Summary: Open Chemistry is a collaborative research group whose missio...

We're looking for 1-2 enthusiastic early career chemists to join our Open Chemistry team at @hhmijanelia.bsky.social. Come help us create amazing dyes and share them with the world. Please share with the best recent/soon-to-be B.S. chemists you know! bit.ly/42w8C6N

If you are a scientist who is looking for joy in these times, I would strongly suggest signing up for @skypeascientist.bsky.social. I spent part of my afternoon talking to second graders who had AMAZING questions and asked me what advice I wanted from 2nd graders. Wholesome, joyful, science-y fun!

Connectome-driven neural inventory of a complete visual system - Nature A connectome of the right optic lobe from a male fruitfly is presented together with an extensive collection of genetic drivers matched to a comprehensive neuron-type catalogue.

I know there's a 𝒍𝒐𝒕 going on right now, but I couldn’t be prouder to share this long-incubated labor of love: the complete connectome of the male 𝐷𝑟𝑜𝑠𝑜𝑝ℎ𝑖𝑙𝑎 optic lobe 🧠🪰
🔗 www.nature.com/articles/s41...

When beauty and wonder seem elusive, try HHMI's Beautiful Biology site, for a reminder of what the scientific study of nature has to offer. Noah Green and the team update the collection every week and write accessible descriptions for everything.

www.hhmi.org/beautifulbiology

Excited to be presenting this work at #cosyne2025 this week - as a poster (session 3, no. 3-017) and as part of the “Reimagining RL in the Brain” workshop organised by Alison Comrie and @nathanieldaw.bsky.social. My first in-person cosyne, so looking forward to it!

Is anyone using #GodotEngine for #Drosophila #Neuroscience experiments in VR, as an open-source alternative to #Unity3D? Requirements include high frame rates (120+ Hz), support for multiple cameras and for processing of the final frame image (to stitch a panorama), or multiple output displays.