Davi Bock
@dddavi.bsky.social
Rural neuroscientist. Connectomics. Protists.
caveat emptor: https://bsky.app/profile/dddavi.bsky.social/post/3k5bnogiq5r2j
caveat emptor: https://bsky.app/profile/dddavi.bsky.social/post/3k5bnogiq5r2j
Pinned
Davi Bock
@dddavi.bsky.social
· Oct 2
The FlyWire connectome: neuronal wiring diagram of a complete fly brain
Artificial intelligence and human expertise meet to generate a map of all the connections in the fly brain. The resource is already being used by experimentalists and theoreticians to further our unde...
www.nature.com
Hard to overstate how pleased I am that the FlyWire consortium converted our FAFB ("Full Adult Fly Brain") EM volume into a connectome, and that the resulting science has been (and will be) so impactful. Thanks to everyone involved. #neuroscience www.nature.com/immersive/d4...
Reposted by Davi Bock
Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods
Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...
www.nature.com
November 13, 2025 at 1:08 PM
Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Reposted by Davi Bock
For example, you can cut a huge gash and pull out most of the cytoplasm in Stentor and it will flow back in
pubmed.ncbi.nlm.nih.gov/24378633/
pubmed.ncbi.nlm.nih.gov/24378633/
November 10, 2025 at 5:47 PM
For example, you can cut a huge gash and pull out most of the cytoplasm in Stentor and it will flow back in
pubmed.ncbi.nlm.nih.gov/24378633/
pubmed.ncbi.nlm.nih.gov/24378633/
Simultaneously a really nice portrait, time capsule, and economic manifesto. Mr. Grimes' accent is similar to ones I grew up around as a young boy in Jericho Vermont in the late 1970s. (Probably 5 dairy farms on our dirt road alone, back then; all gone now.)
www.youtube.com/watch?v=rVja...
www.youtube.com/watch?v=rVja...
Vermont People: Chester Grimes | A 1971 story of a 70-year-old logger in northern Vermont
YouTube video by Made Here - from Vermont Public
www.youtube.com
November 10, 2025 at 8:24 PM
Simultaneously a really nice portrait, time capsule, and economic manifesto. Mr. Grimes' accent is similar to ones I grew up around as a young boy in Jericho Vermont in the late 1970s. (Probably 5 dairy farms on our dirt road alone, back then; all gone now.)
www.youtube.com/watch?v=rVja...
www.youtube.com/watch?v=rVja...
Reposted by Davi Bock
On the event of James Watson's death, I highly recommend this 2023 commentary from @matthewcobb.bsky.social and Nathaniel Comfort with crucial new insights into the discovery of the double helix. (And also check out Cobb's brand new biography of Francis Crick) www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 7, 2025 at 9:25 PM
On the event of James Watson's death, I highly recommend this 2023 commentary from @matthewcobb.bsky.social and Nathaniel Comfort with crucial new insights into the discovery of the double helix. (And also check out Cobb's brand new biography of Francis Crick) www.nature.com/articles/d41...
Reposted by Davi Bock
That image is from 1961 and an idealization. Here is an actual trajectory of fixational eye movements. The dots are 2 ms apart. If a midget ganglion cell, with single-cone receptive field, fires at 100 Hz, then every spike reports about a different cone. How can we ever read anything?
November 7, 2025 at 6:23 PM
That image is from 1961 and an idealization. Here is an actual trajectory of fixational eye movements. The dots are 2 ms apart. If a midget ganglion cell, with single-cone receptive field, fires at 100 Hz, then every spike reports about a different cone. How can we ever read anything?
Reposted by Davi Bock
In the spirit 👻 of Freaky Friday 🎃, here is a beautiful yet eery video of zebrafish retina development showing horizontal cells (🔵) finding their way out of the crowded amacrine (🟠) layer to settle beneath the photoreceptors. Happy #Halloween!
🎥: PhD student Rae Wong from the @nordenlab.bsky.social
🎥: PhD student Rae Wong from the @nordenlab.bsky.social
October 31, 2025 at 2:29 PM
In the spirit 👻 of Freaky Friday 🎃, here is a beautiful yet eery video of zebrafish retina development showing horizontal cells (🔵) finding their way out of the crowded amacrine (🟠) layer to settle beneath the photoreceptors. Happy #Halloween!
🎥: PhD student Rae Wong from the @nordenlab.bsky.social
🎥: PhD student Rae Wong from the @nordenlab.bsky.social
Reposted by Davi Bock
Our paper is out! Take a look if you’re curious to see how we use expansion microscopy on diatoms ☺️ Very excited to keep using this!!
And it’s a double feature, as shown by @gautamdey.bsky.social ial & @floravincent.bsky.social for the sturdy #Diatoms! Also out today in @currentbiology.bsky.social 🌊
www.cell.com/current-biol...
www.cell.com/current-biol...
Diatom ultrastructural diversity across controlled and natural environments
Flori et al. establish high-resolution and generalizable immunofluorescence in cultured
and environmental diatoms, thanks to 4-fold cryo-expansion microscopy. This represents
a step-change for compara...
www.cell.com
October 31, 2025 at 3:22 PM
Our paper is out! Take a look if you’re curious to see how we use expansion microscopy on diatoms ☺️ Very excited to keep using this!!
Reposted by Davi Bock
After 13 years in the US, I’ve made the difficult decision to leave. Having packed up everything and rethought about priorities, rather painstakingly, while I’m sad to leave the life I’ve made here, I’m also relieved that I won’t have to plan my life around immigration policies anymore.
October 31, 2025 at 4:08 AM
After 13 years in the US, I’ve made the difficult decision to leave. Having packed up everything and rethought about priorities, rather painstakingly, while I’m sad to leave the life I’ve made here, I’m also relieved that I won’t have to plan my life around immigration policies anymore.
Reposted by Davi Bock
What a time to be alive
The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1
October 27, 2025 at 5:02 PM
What a time to be alive
Reposted by Davi Bock
Thank you so much @wellcometrust.bsky.social for supporting us to push the the limits of #X-ray #nanoimaging and #connectomics, and to make technology more broadly available to the scientific community! 🙏
ESRF scientist Alexandra Pacureanu is the recipient of the Wellcome Discovery Award, together with a team at the Francis Crick Institute, to develop X-ray nanoimaging technology to study the mechanisms of information processing in the neural circuits of olfaction.
www.esrf.fr/home/news/ge...
www.esrf.fr/home/news/ge...
October 27, 2025 at 5:39 PM
Thank you so much @wellcometrust.bsky.social for supporting us to push the the limits of #X-ray #nanoimaging and #connectomics, and to make technology more broadly available to the scientific community! 🙏
Nice visualization. Maximize for full effect.
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 9:08 AM
Nice visualization. Maximize for full effect.
Reposted by Davi Bock
Edward Kravitz, a Harvard biochemist who proved GABA's inhibitory power, passed away last month. He will "be remembered for his humanity, for his social conscience and his desire to help those less fortunate than he,” says Ronald Harris-Warrick.
By @claudia-lopez.bsky.social
bit.ly/479Ggmo
By @claudia-lopez.bsky.social
bit.ly/479Ggmo
Remembering GABA pioneer Edward Kravitz
The biochemist, who died last month at age 92, was part of the first neurobiology department in the world and showed that gamma-aminobutyric acid is inhibitory.
bit.ly
October 24, 2025 at 1:41 PM
Edward Kravitz, a Harvard biochemist who proved GABA's inhibitory power, passed away last month. He will "be remembered for his humanity, for his social conscience and his desire to help those less fortunate than he,” says Ronald Harris-Warrick.
By @claudia-lopez.bsky.social
bit.ly/479Ggmo
By @claudia-lopez.bsky.social
bit.ly/479Ggmo
Reposted by Davi Bock
“Cellular Olympics” our catalog of freeky ultra fast cellular superhero’s is freely available “Ann Rev of microbiology”
www.annualreviews.org/content/jour...
This is a compilation of world’s fastest single cell organisms - enjoy this buffet of rare delightful protists with mind bending speeds. 🧪
www.annualreviews.org/content/jour...
This is a compilation of world’s fastest single cell organisms - enjoy this buffet of rare delightful protists with mind bending speeds. 🧪
October 24, 2025 at 10:57 AM
“Cellular Olympics” our catalog of freeky ultra fast cellular superhero’s is freely available “Ann Rev of microbiology”
www.annualreviews.org/content/jour...
This is a compilation of world’s fastest single cell organisms - enjoy this buffet of rare delightful protists with mind bending speeds. 🧪
www.annualreviews.org/content/jour...
This is a compilation of world’s fastest single cell organisms - enjoy this buffet of rare delightful protists with mind bending speeds. 🧪
Reposted by Davi Bock
New preprint from the lab: A reference brain for the clonal raider ant.
With this resource, which is based on 40 individual brains, you can register and compare all kinds of samples in a common space. It comes with lots of detailed protocols and a user-friendly GUI.
www.biorxiv.org/content/10.1...
With this resource, which is based on 40 individual brains, you can register and compare all kinds of samples in a common space. It comes with lots of detailed protocols and a user-friendly GUI.
www.biorxiv.org/content/10.1...
October 17, 2025 at 5:35 PM
New preprint from the lab: A reference brain for the clonal raider ant.
With this resource, which is based on 40 individual brains, you can register and compare all kinds of samples in a common space. It comes with lots of detailed protocols and a user-friendly GUI.
www.biorxiv.org/content/10.1...
With this resource, which is based on 40 individual brains, you can register and compare all kinds of samples in a common space. It comes with lots of detailed protocols and a user-friendly GUI.
www.biorxiv.org/content/10.1...
Reposted by Davi Bock
Ingenious concept - light sheet on serial sections by photo-etching the expanded hydrogel, layer by layer.
Photo-sectioning is quite slow, and the volumetric images are insanely large and complex, but the data look wonderful.
www.science.org/doi/10.1126/...
Photo-sectioning is quite slow, and the volumetric images are insanely large and complex, but the data look wonderful.
www.science.org/doi/10.1126/...
October 17, 2025 at 7:00 AM
Ingenious concept - light sheet on serial sections by photo-etching the expanded hydrogel, layer by layer.
Photo-sectioning is quite slow, and the volumetric images are insanely large and complex, but the data look wonderful.
www.science.org/doi/10.1126/...
Photo-sectioning is quite slow, and the volumetric images are insanely large and complex, but the data look wonderful.
www.science.org/doi/10.1126/...
Reposted by Davi Bock
Final version of our paper on ciliary metachronal waves out now in Science Advances! doi.org/10.1126/scia...
This is the main thesis work of my PhD student Rebecca Poon, who caught many #platnereis larvae and tirelessly ablated them with a laser. THREAD
This is the main thesis work of my PhD student Rebecca Poon, who caught many #platnereis larvae and tirelessly ablated them with a laser. THREAD
October 15, 2025 at 8:53 PM
Final version of our paper on ciliary metachronal waves out now in Science Advances! doi.org/10.1126/scia...
This is the main thesis work of my PhD student Rebecca Poon, who caught many #platnereis larvae and tirelessly ablated them with a laser. THREAD
This is the main thesis work of my PhD student Rebecca Poon, who caught many #platnereis larvae and tirelessly ablated them with a laser. THREAD
Reposted by Davi Bock
Excited to share our new #biorxivpreprint:
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
October 15, 2025 at 4:17 PM
Excited to share our new #biorxivpreprint:
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
And he's off! Well-deserved. :)
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics.
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
MIT’s McGovern Institute and Department of Brain and Cognitive Sciences welcome new faculty member Sven Dorkenwald - MIT McGovern Institute
The McGovern Institute and the Department of Brain and Cognitive Sciences are pleased to announce the appointment of Sven Dorkenwald as an assistant professor starting in January 2026. A trailblazer i...
mcgovern.mit.edu
October 15, 2025 at 5:12 PM
And he's off! Well-deserved. :)
Reposted by Davi Bock
That's what we're saying people should try to do here: www.sciencedirect.com/science/arti...
Testing methods of neural systems understanding
Neuroscientists apply a range of analysis tools to recorded neural activity in order to glean insights into how neural circuits drive behavior in orga…
www.sciencedirect.com
October 10, 2025 at 8:31 PM
That's what we're saying people should try to do here: www.sciencedirect.com/science/arti...
Interesting answer from Mark to a question I had about his piece on recurrence and active filtering in sensory cortex (at www.annualreviews.org/content/jour...)
October 8, 2025 at 6:15 PM
Interesting answer from Mark to a question I had about his piece on recurrence and active filtering in sensory cortex (at www.annualreviews.org/content/jour...)
Reposted by Davi Bock
Our group at the Allen Institute is recruiting a technician and postdoc to work on light microscopy-based connectomics. Please DM me or share with anyone you think may be interested in this NIH BRAIN CONNECTS funded project.
October 8, 2025 at 12:28 AM
Our group at the Allen Institute is recruiting a technician and postdoc to work on light microscopy-based connectomics. Please DM me or share with anyone you think may be interested in this NIH BRAIN CONNECTS funded project.
I love this piece!
It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions.
And it makes me feel good about having helped to generate the thing. :)
It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions.
And it makes me feel good about having helped to generate the thing. :)
To celebrate the first anniversary of the release of FlyWire, we asked nine neuroscientists to share how they are using connectome data in their research and what they hope is in store for the future of fly connectomics.
By @franciscorr25.bsky.social
#neuroskyence
bit.ly/3Wx5nt3
By @franciscorr25.bsky.social
#neuroskyence
bit.ly/3Wx5nt3
How FlyWire is redefining Drosophila research, one year in
Nine Drosophila researchers share how the connectome transformed the field and what additional new tools they would like to see.
bit.ly
October 7, 2025 at 3:53 PM
I love this piece!
It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions.
And it makes me feel good about having helped to generate the thing. :)
It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions.
And it makes me feel good about having helped to generate the thing. :)
Reposted by Davi Bock
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 Davi Bock
Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....
Male CNS Connectome
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 ...
www.janelia.org
October 5, 2025 at 3:40 PM
Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....
Reposted by Davi Bock
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...