Philip Hubbard

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.

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...

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

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...

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.'

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

More about FlyWire:
flywire.ai

More about neuVid:
github.com/connectome-n...

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.

‘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

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!

U.S. early-career researchers struggling amid chaos Uncertain funding, government firings, and distressed universities hit vulnerable groups especially hard

"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...

#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...

YouTube video by IF THEN REAL life superheroes!⁠ If/Then Women in STEM

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...

Nothing in life is to be feared, it is only to be understood. Marie Curie, Physicist and chemist.

Today is International Day of Women & Girls in Science.

Marie Curie, the first woman to win a Nobel Prize. Her contributions have left an indelible mark on the world of science & health & continue to inspire generations of scientists & innovators. 🔬 #WomenInScience #WomenInSTEM

Colormaps in Matplotlib:
matplotlib.org/stable/users...

Analysis of colormap perceptual properties:
mpetroff.net/2019/08/disc...

Colormaps for visualization:
www.kennethmoreland.com/color-advice

Paper on EPG neurons (Hulse et al. 2021):
doi.org/10.7554/eLif...