Philip Hubbard
@philiphubbard.bsky.social
Pinned
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.
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.
October 27, 2025 at 8:16 AM
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
vimeo.com/142648727
October 20, 2025 at 8:46 AM
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
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.
October 8, 2025 at 9:11 AM
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.
October 7, 2025 at 8:27 AM
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.
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.
🪰 A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system—a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the millions of connections between them.
🔗 https://hhmi.news/4o3EJnk
🔗 https://hhmi.news/4o3EJnk
October 6, 2025 at 2:37 PM
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.
Reposted by Philip Hubbard
🌟 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
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
September 18, 2025 at 3:00 PM
🌟 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
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
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...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
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.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
More openings coming soon. Interesting AI is widespread at Janelia, like this diffusion model from Larissa Heinrich.
September 18, 2025 at 12:43 PM
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...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
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.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
More openings coming soon. Interesting AI is widespread at Janelia, like this diffusion model from Larissa Heinrich.
September 16, 2025 at 4:55 PM
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.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
More openings coming soon. Interesting AI is widespread at Janelia, like this diffusion model from Larissa Heinrich.
Reposted by Philip Hubbard
Fly labs — Now is the time to show some solidarity and chip in support for this vital resource!
August 20, 2025 at 1:53 AM
Fly labs — Now is the time to show some solidarity and chip in support for this vital resource!
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...
www.janelia.org/project-team...
August 14, 2025 at 5:08 PM
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...
www.janelia.org/project-team...
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...
Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
July 23, 2025 at 9:22 AM
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...
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
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
#FediHire
July 18, 2025 at 8:57 PM
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
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
#FediHire
Reposted by Philip Hubbard
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.
July 15, 2025 at 4:15 PM
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.
Reposted by Philip Hubbard
This Juneteenth we're spotlighting the work of the first Black trained TV meteorologist, June Bacon-Bercey.
June 19, 2025 at 8:58 PM
This Juneteenth we're spotlighting the work of the first Black trained TV meteorologist, June Bacon-Bercey.
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.
June 18, 2025 at 10:46 PM
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.
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.
🪰 A team of Janelia researchers & collaborators have created a new set of tools for studying motor control of wing movements in fruit flies, providing an important #openscience resource for future studies of fly flight & courtship 🧠
hhmi.news/3H3ohn8
hhmi.news/3H3ohn8
May 23, 2025 at 7:17 PM
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.
Reposted by Philip Hubbard
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...
www.biorxiv.org/content/10.1...
April 22, 2025 at 1:02 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Philip Hubbard
🎉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
💻Explore the site ➡️ www.hhmi.org/beautifulbio...
📷Igor Siwanowicz
April 24, 2025 at 7:00 PM
🎉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
💻Explore the site ➡️ www.hhmi.org/beautifulbio...
📷Igor Siwanowicz
Reposted by Philip Hubbard
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!
I am in sunny San Francisco for a meeting on AI in bioimaging at CZI headquarters! Looking forward to 🤯🤩 data and great conversations!
May 15, 2025 at 4:39 PM
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!
Reposted by Philip Hubbard
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
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...
bit.ly
April 11, 2025 at 7:27 PM
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
Reposted by Philip Hubbard
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!
March 11, 2025 at 8:47 PM
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!
Reposted by Philip Hubbard
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...
🔗 www.nature.com/articles/s41...
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.
www.nature.com
March 27, 2025 at 10:58 PM
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...
🔗 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
www.hhmi.org/beautifulbiology
March 28, 2025 at 9:02 AM
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
www.hhmi.org/beautifulbiology
Reposted by Philip Hubbard
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!
The first preprint of my postdoc with @dudman.bsky.social is now online! Here we wanted to understand the algorithms mice use when learning to forage in large environments with many potential resources. www.biorxiv.org/content/10.1...
March 24, 2025 at 4:11 PM
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.
March 17, 2025 at 1:08 AM
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.