iiinova — where your digital self keeps evolving

Philip Hubbard @philiphubbard.bsky.social · 08/09/2026

We wanted another video to highlight the #Drosophila MCNS connectome, and Alexandra Fragniere suggested showing the spatial distributions of male-specific and dimorphic neurons. @stuartberg.bsky.social suggested adding the synapses. The result turned out well. www.janelia.org/project-team...

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Philip Hubbard @philiphubbard.bsky.social · 04/09/2026

New work by Berg et al. on the male #Drophila central nervous system is out now: www.cell.com/cell/issue?p... An amazing effort by @beckett14.bsky.social, @mmcosta.bsky.social, @preibischs.bsky.social, @jefferis.bsky.social and many others. Making the cover image with neuVid and #Blender was fun.

A colorful image of about 11K fruit fly neurons, each being an example of a cell type.

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Philip Hubbard @philiphubbard.bsky.social · 05/06/2026

Did you miss the "View in 3D" button? It's on the right side of the page showing your chosen match.

Two pages from neuronbridge.janelia.org: a list of matches, then one match with the "View in 3D" button.

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Philip Hubbard @philiphubbard.bsky.social · 05/06/2026

Do you use neuronbridge.janelia.org to match electron and light #microscopy? The "View in 3D" button lets you visually confirm the match right in your browser. And now it does a quick sweep to pick a better initial saturation for the light microscopy. Here are some examples (EM green, LM magenta).

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Reposted by Philip Hubbard

San Francisco Chronicle @sfchronicle.com · 23/04/2026

San Francisco Symphony music director Michael Tilson Thomas battled aggressive brain cancer for years but continued to guest-conduct and teach, leaving a lasting legacy in the classical music world.

bit.ly

Michael Tilson Thomas, transformative music director of S.F. Symphony, dies at 81

The longtime San Francisco Symphony music director battled aggressive brain cancer for years but continued to guest conduct and teach, leaving a lasting legacy in the classical music world.

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Philip Hubbard @philiphubbard.bsky.social · 02/02/2026

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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Philip Hubbard @philiphubbard.bsky.social · 02/02/2026

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).

11.7K neurons, one for each cell type in the male Drosophila CNS connectome.

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Philip Hubbard @philiphubbard.bsky.social · 27/10/2025

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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Philip Hubbard @philiphubbard.bsky.social · 20/10/2025

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

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Philip Hubbard @philiphubbard.bsky.social · 08/10/2025

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.

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Philip Hubbard @philiphubbard.bsky.social · 07/10/2025

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.

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Philip Hubbard @philiphubbard.bsky.social · 06/10/2025

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.

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Philip Hubbard @philiphubbard.bsky.social · 06/10/2025

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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Reposted by Philip Hubbard

Janelia Research Campus @hhmijanelia.bsky.social · 18/09/2025

🌟 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 👉 janelia.link/groupleader

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Philip Hubbard @philiphubbard.bsky.social · 18/09/2025

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...

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Philip Hubbard @philiphubbard.bsky.social · 16/09/2025

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...

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Philip Hubbard @philiphubbard.bsky.social · 16/09/2025

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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Ben de Bivort @debivort.bsky.social · 20/08/2025

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

clip art of Drosophila flies at different life stages

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Philip Hubbard @philiphubbard.bsky.social · 14/08/2025

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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Philip Hubbard @philiphubbard.bsky.social · 23/07/2025

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

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Philip Hubbard @philiphubbard.bsky.social · 23/07/2025

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...

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Philip Hubbard @philiphubbard.bsky.social · 18/07/2025

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

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Reposted by Philip Hubbard

HHMI @hhmi-science.bsky.social · 15/07/2025

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.

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Lost Women of Science @lostwomenofsci.bsky.social · 19/06/2025

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

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Philip Hubbard @philiphubbard.bsky.social · 18/06/2025

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

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

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Philip Hubbard @philiphubbard.bsky.social · 18/06/2025

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.

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Philip Hubbard @philiphubbard.bsky.social · 18/06/2025

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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Philip Hubbard @philiphubbard.bsky.social · 23/05/2025

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.

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Andy Moore @aaandmoore.bsky.social · 22/04/2025

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...

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Janelia Research Campus @hhmijanelia.bsky.social · 24/04/2025

🎉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

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Rita Strack @ritastrack.bsky.social · 15/05/2025

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!

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Reposted by Philip Hubbard

Luke Lavis @rhodamine110.bsky.social · 11/04/2025

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

bit.ly

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...

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Reposted by Philip Hubbard

Melissa Baese-Berk @m2b2.bsky.social · 11/03/2025

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!

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Michael Reiser @michaelreiser.bsky.social · 27/03/2025

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...

nature.com

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.

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Philip Hubbard @philiphubbard.bsky.social · 28/03/2025

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

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Reposted by Philip Hubbard

Laura Grima @lauragrima.bsky.social · 24/03/2025

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!

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Philip Hubbard @philiphubbard.bsky.social · 17/03/2025

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.

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Philip Hubbard @philiphubbard.bsky.social · 10/03/2025

We made the experimental system with a toolkit of software packages built on the #Unity3D game engine. Here's an example of a "meadow" world: on top is the fly's view warped for a panorama of four display screens, below is some simulated fly motion. github.com/JaneliaSciCo...

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Philip Hubbard @philiphubbard.bsky.social · 10/03/2025

It's fascinating to see #Drosophila #Neuroscience experiments run in virtual reality (VR), with a fruit fly walking on a tiny trackball looking at tiny video displays. Here's a schematic of @hannah-haberkern.bsky.social 's rig, from our 2022 preprint: doi.org/10.1101/2022...

A fly on a spherical treadmill surrounded by four display screen and a microscope.

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WHO @who.int · 08/03/2025

Today is #InternationalWomensDay Progress on #GenderEquality in health care is too slow. Women have distinct & changing health needs at different stages of their lives. Health care should be easy to access, fair & tailored to meet each woman’s unique needs & circumstances. 🔗 bit.ly/3DmZQ2o

Against a blue background, graphic representation shows a diverse group of women holding a megaphone and placard. In the background are two yellow and black striped tapes. The text reads 'Women's health needs change from the time they are born to older age. But they often hit roadblocks to receive the right diagnosis and treatment they need.'

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Philip Hubbard @philiphubbard.bsky.social · 23/02/2025

More about FlyWire: flywire.ai More about neuVid: github.com/connectome-n...

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Philip Hubbard @philiphubbard.bsky.social · 23/02/2025

I wanted a distraction from the news so I made this video, of some #Drosophila neurons with interesting morphologies: the mushroom body output neurons (MBONs). I used reconstructions from the FlyWire data set, and rendered with #Blender3D driven by neuVid.

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Denise Wheeler @denisedwheeler.bsky.social · 23/02/2025

2 PhD students recently met at a conference & Trump's slashing of research & science bound them With only 3 other scientists they started a movement that's growing around the country On March 7 in Washington DC, and state capitals, "Stand Up for Science" will take place All details below & bravo!

science.org

‘I really wanted something to happen.’ The students behind the Stand Up for Science protests

New group hopes to turn out researchers for 7 March demonstrations against Trump administration policies

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Katie Langin @klangin.bsky.social · 22/02/2025

"These kinds of shocks are going to lead to a mass exodus … for minorities in particular.” For my latest @science.org story, I spoke with early career researchers who have been affected by the federal upheaval and are concerned about what it means for their future. www.science.org/content/arti...

science.org

U.S. early-career researchers struggling amid chaos

Uncertain funding, government firings, and distressed universities hit vulnerable groups especially hard

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Reposted by Philip Hubbard

Carsen Stringer @computingnature.bsky.social · 12/02/2025

#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...

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Dr. Wendy Bohon @drwendyrocks.bsky.social · 12/02/2025

Wow! When If/Then kicked off almost 6 years we had no idea what a ride it would be! We’ve been featured in museums, textbooks, on TV shows and in the largest exhibit of statues of women in the world! What is If/Then? youtube.com/shorts/hcxDo...

youtube.com

REAL life superheroes!⁠ If/Then Women in STEM

YouTube video by IF THEN

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