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
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#HHMIJanelia
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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.
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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.
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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...
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We encourage applications from early-career scientists, including soon-to-be PhDs, with strong backgrounds in mathematics, physics, computer science, or engineering.
👉 Apply by Nov. 3: janelia.link/theoryfellow...
#HHMIJanelia #ScienceCareers #ComputationalBiology
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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.
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Dense arbors from neurons on one side of a fruit fly's head.
Here's a #MicroscopyMonday segmentation of some neurons from the optic lobe, or visual processing area of the #Drosophila fruit fly's brain. The #connectome for the full optic lobe was released in 2024 by #HHMIJanelia, Google, and the University of Cambridge, with support from the Wellcome Trust.
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Dense arbors from neurons on a fruit fly's nerve cord.
This segmentation of #MicroscopyMonday data reconstructs neurons of the "MANC", or male adult nerve cord, from the #Drosophila fruit fly. The nerve cord is like a spinal cord and connects the brain and muscles. #HHMIJanelia, Google, and the University of Cambridge released this work in 2023.
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The #HHMIJanelia FlyEM team's project page for the hemibrain:
www.janelia.org/project-team...
The neuVid system, used for creating the video:
github.com/connectome-n...
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On this day 5 years ago #HHMIJanelia and Google released the "hemibrain", a map of neural connections in much of the #Drosophila fly brain. At the time it was the largest such #connectome ever created. Here's a video from the release (polished a bit), showing the interesting shapes of the neurons.
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...then proofreaders from #HHMIJanelia made fixes. Here's a tool proofreaders used, to cleave false merges by designating seeds on different neurons, which Stuart Berg's graph algorithm then separated. The video's from 5 years ago so it looks a bit old fashioned, but the tool still works!
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Long fibers from neurons at the center of a fruit fly's brain.
A use of #MicroscopyMonday data is making segmentations. Here's one, of #Drosophila protocerebral bridge and nodulus neurons, from the 2020 Hemibrain by #HHMIJanelia and Google. Michał Januszewski and @stardazed0.bsky.social 's team made an initial segmentation with #AI flood-fill algorithms...
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On this day 5 years ago, I released version 1.0 of neuVid. It takes high-level descriptions of #Neuroscience or #CellBiology videos and renders them with #Blender or VVD Viewer. Here's a montage of how I've used it. Thanks to #HHMIJanelia for support, especially Steve Plaza and Stuart Berg of FlyEM.
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Erhardt et al. 2023 paper on these neurons:
doi.org/10.1101/2023...
The #HHMIJanelia FlyLight project's Split-GAL4 driver collection:
splitgal4.janelia.org/cgi-bin/spli...
Using neuVid with VVD Viewer:
github.com/connectome-n...
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This #FluorescenceFriday video shows 89 volumes from the #HHMIJanelia FlyLight Split-GAL4 collection: premotor and related neurons from the #Drosophila fruit fly's equivalent of a spinal cord. I gave a high-level description of the video to neuVid, which drove rendering by VVD Viewer.
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This video was fun. I matched the #Neuroscience segmentations shown first (from the #HHMIJanelia FlyEM team) to the #CellBiology segmentations shown later (from Alyson Petruncio, @herrsaalfeld.bsky.social and the CellMap team). I described the animation with neuVid and rendered it with #Blender.
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The #HHMIJanelia FlyLight project's Split-GAL4 driver collection:
splitgal4.janelia.org/cgi-bin/spli...
Using neuVid with VVD Viewer:
github.com/connectome-n...
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I used VVD Viewer for this #FluorescenceFriday video: 141 volumes from the #HHMIJanelia FlyLight Split-GAL4 #Drosophila driver collection. The animation comes from a high-level description processed by neuVid. Such a rapid tour of the data has questionable scientific value, but it's fun to watch!
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My favorite volume renderer for fluorescence #microscopy is VVD Viewer, by Takashi Kawase and Hideo Otsuna at #HHMIJanelia. Takashi wrote fast GPU code. Hideo wrote a transfer function with 3D sampling and a final 2D power function, which together show just enough low data values for visual context.
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Fenestrae are unusual holes in hepatic endothelia cells. Here they are in a data set from OpenOrganelle, reconstructed by Aubrey Weigel and the CellMap team at #HHMIJanelia. This video was rendered in #Blender driven by neuVid (which has been helpful for #CellBiology as well as #Neuroscience).
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Another OpenOrganelle data set from Aubrey Weigel and the #HHMIJanelia CellMap team is this HeLa cell, rendered with #Blender driven by neuVid. The HeLa cell line, a critical resource for biomedical research, originated with cells taken without consent from Henrietta Lacks in 1951.
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OpenOrganelle is a repo of #CellBiology data, segmented from electron #microscopy at #HHMIJanelia by Aubrey Weigel and the CellMap team, the Saalfeld lab ( @herrsaalffeld.sky.social) and the Hess lab. Here's a macrophage cell, rendered with #Blender driven by neuVid (helpful for more than neurons).
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The #HHMIJanelia MouseLight project page:
www.janelia.org/project-team...
Using SWC files in neuVid:
github.com/connectome-n...
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Neurons reconstructed from #microscopy data can be expressed as polygonal meshes, or as skeletons in SWC format. Here's an example of SWC: 1227 neurons from a mouse, reconstructed by the #HHMIJanelia MouseLight project. I made the video with neuVid driving #Blender, with advice from Tiago Ferreira.
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The #HHMIJanelia FlyEM team's optic lobe page:
www.janelia.org/project-team...
Documentation for neuVid:
github.com/connectome-n...
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The #HHMIJanelia FlyEM team's MANC page:
www.janelia.org/project-team...
Documentation for neuVid:
github.com/connectome-n...
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#AIScientist|s are independent principal scientists who will develop, lead, or participate in collaborative projects with other scientists and engineers, including the labs and project teams at #HHMIJanelia and @hhmi.bsky.social .
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You may know that #HHMIJanelia was built to experiment with new ways to do science, and so we are trying something slightly different than our established small labs and project teams this time.
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AI@HHMI teaser saying "AI@HHMI | Accelerating Innovation in Biology". The backdrop is an artistic rendering of the compute graph of a network architecture for semantic image segmentation that I think looks really cute.
We are looking for exceptional #AIScientist|s to join our #AI@HHMI initiative at #HHMIJanelia. We want to uncover fundamental principles underlying complex biological systems that are inaccessible without new innovations that combine #AI with experimental design.
ai.hhmi.org#join-our-team
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Janelia Theory Fellows Magdalena and Tosif discussing something in front of a computer.
Come and join us as a Theory Fellow at #HHMIJanelia! www.janelia.org/our-research...
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