This example has 11.7K neurons, one for each cell type in the #HHMIJanelia male #Drosophila CNS connectome.
www.janelia.org/project-team/flyem/male-cns-connectome
02.02.2026 15:44
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This example has 11.7K neurons, one for each cell type in the #HHMIJanelia male #Drosophila CNS connectome.
www.janelia.org/project-team/flyem/male-cns-connectome
11.7K neurons, one for each cell type in the male Drosophila CNS connectome.
For #Neuroscience videos in #Blender3D, importing lots of neurons from separate OBJ files is slow. It's faster to import subsets into temporary scenes in parallel with `subprocess.Popen`, then add them to the final scene with `bpy.data.libraries.load`. It's 10x as fast for this example (16 cores).
When #HHMIJanelia released the #Drosophila hemibrain in 2020, rendering all cell types at once with full shading/shadows was too hard, so the video showed them region by region. Technology has since advanced, and I went back and rendered them all together. I like how it shows the internal structure.
On this day 10 years ago, #Tableau released Vizable for the iPad. It gave a way to explore data with gestures: pinch/unpinch to aggregate/disaggregate, swipe to filter out, etc. The development effort, led by Robin Stewart and Dave Story, was great fun. #DataViz #DataVis
vimeo.com/142648727
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” 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!
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!
