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
How do neural circuits generate the walking rhythm?
Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.
w @bingbrunton.bsky.social
www.biorxiv.org/content/10.1...
Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.
w @bingbrunton.bsky.social
www.biorxiv.org/content/10.1...
December 9, 2025 at 5:50 PM
How do neural circuits generate the walking rhythm?
Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.
w @bingbrunton.bsky.social
www.biorxiv.org/content/10.1...
Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.
w @bingbrunton.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Davi Bock
The cryo cyclical multiplexing expansion microscopy (Cy-ExM) preprint from
@seweryn-galecki.bsky.social , @kevin-dean.bsky.social et al is online.
20 targets across an entire cell. Mr. Snouty also joined the fun.
www.biorxiv.org/content/10.6...
@seweryn-galecki.bsky.social , @kevin-dean.bsky.social et al is online.
20 targets across an entire cell. Mr. Snouty also joined the fun.
www.biorxiv.org/content/10.6...
January 2, 2026 at 7:39 PM
The cryo cyclical multiplexing expansion microscopy (Cy-ExM) preprint from
@seweryn-galecki.bsky.social , @kevin-dean.bsky.social et al is online.
20 targets across an entire cell. Mr. Snouty also joined the fun.
www.biorxiv.org/content/10.6...
@seweryn-galecki.bsky.social , @kevin-dean.bsky.social et al is online.
20 targets across an entire cell. Mr. Snouty also joined the fun.
www.biorxiv.org/content/10.6...
Reposted by Davi Bock
my modest collection of flies with WIDE heads 🙇
a hammer-headed Richardia (Ecuador),
a stalk-eyed Chaetodiopsis (Mozambique),
a pointy-eyed Ophthalmoptera (Colombia),
and an antlered Richardia (Colombia)
why though? male-male competition? sexual selection? chime-in if you know!
a hammer-headed Richardia (Ecuador),
a stalk-eyed Chaetodiopsis (Mozambique),
a pointy-eyed Ophthalmoptera (Colombia),
and an antlered Richardia (Colombia)
why though? male-male competition? sexual selection? chime-in if you know!
December 22, 2025 at 6:53 PM
my modest collection of flies with WIDE heads 🙇
a hammer-headed Richardia (Ecuador),
a stalk-eyed Chaetodiopsis (Mozambique),
a pointy-eyed Ophthalmoptera (Colombia),
and an antlered Richardia (Colombia)
why though? male-male competition? sexual selection? chime-in if you know!
a hammer-headed Richardia (Ecuador),
a stalk-eyed Chaetodiopsis (Mozambique),
a pointy-eyed Ophthalmoptera (Colombia),
and an antlered Richardia (Colombia)
why though? male-male competition? sexual selection? chime-in if you know!
Reposted by Davi Bock
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Reposted by Davi Bock
*First preprint from our lab* !!!!!
How does the brain learn to anchor its internal sense of direction to the outside world? 🧭
led by Mark Plitt @markplitt.bsky.social & Dan Turner-Evans, w/ Vivek Jayaraman:
“Octopamine instructs head direction plasticity” www.biorxiv.org/content/10.6...
Thread ⬇️
How does the brain learn to anchor its internal sense of direction to the outside world? 🧭
led by Mark Plitt @markplitt.bsky.social & Dan Turner-Evans, w/ Vivek Jayaraman:
“Octopamine instructs head direction plasticity” www.biorxiv.org/content/10.6...
Thread ⬇️
December 15, 2025 at 6:26 PM
*First preprint from our lab* !!!!!
How does the brain learn to anchor its internal sense of direction to the outside world? 🧭
led by Mark Plitt @markplitt.bsky.social & Dan Turner-Evans, w/ Vivek Jayaraman:
“Octopamine instructs head direction plasticity” www.biorxiv.org/content/10.6...
Thread ⬇️
How does the brain learn to anchor its internal sense of direction to the outside world? 🧭
led by Mark Plitt @markplitt.bsky.social & Dan Turner-Evans, w/ Vivek Jayaraman:
“Octopamine instructs head direction plasticity” www.biorxiv.org/content/10.6...
Thread ⬇️
Reposted by Davi Bock
Our dispatch:
https://www.sciencedirect.com/science/article/pii/S0960982225014691
on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:
#connectomics, without synapses
https://www.sciencedirect.com/science/article/pii/S0960982225013090
#neuroscience
https://www.sciencedirect.com/science/article/pii/S0960982225014691
on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:
#connectomics, without synapses
https://www.sciencedirect.com/science/article/pii/S0960982225013090
#neuroscience
December 16, 2025 at 7:27 AM
Our dispatch:
https://www.sciencedirect.com/science/article/pii/S0960982225014691
on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:
#connectomics, without synapses
https://www.sciencedirect.com/science/article/pii/S0960982225013090
#neuroscience
https://www.sciencedirect.com/science/article/pii/S0960982225014691
on the recent Hydra volume EM paper by Zhang, Rafa Yuste and colleagues:
#connectomics, without synapses
https://www.sciencedirect.com/science/article/pii/S0960982225013090
#neuroscience
Reposted by Davi Bock
🧠🪰 The adult Drosophila brain connectome now gives us a complete wiring diagram of ~140k neurons. But a wiring diagram alone isn’t understanding.
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
New lab paper - will say more about this in a little while
December 15, 2025 at 3:11 PM
🧠🪰 The adult Drosophila brain connectome now gives us a complete wiring diagram of ~140k neurons. But a wiring diagram alone isn’t understanding.
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
Reposted by Davi Bock
A paper from my PhD lab is on Science! This is a really cool new way to utilize EM connectome datasets. Congrats to the team!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Spatial and morphological organization of mitochondria in neurons across a connectome
Neuronal function depends on mitochondria, but little is known about their organization across neurons. Using an electron microscopy Drosophila connectome, we uncovered quantitative rules governing th...
www.science.org
December 14, 2025 at 9:46 AM
A paper from my PhD lab is on Science! This is a really cool new way to utilize EM connectome datasets. Congrats to the team!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Davi Bock
Love the caption of Fig. 3 in this impressive preprint:
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
December 12, 2025 at 8:38 AM
Love the caption of Fig. 3 in this impressive preprint:
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
Reposted by Davi Bock
In addition to the Comments linked to below, this news article ("Technology Feature") ties together perspectives from many additional workers in the field, including yours truly: www.nature.com/articles/s41...
December 9, 2025 at 5:13 PM
In addition to the Comments linked to below, this news article ("Technology Feature") ties together perspectives from many additional workers in the field, including yours truly: www.nature.com/articles/s41...
Reposted by Davi Bock
I had heard this was coming, but it’s still an amazing indication of how far we’ve come in the last decade or so!
Our Method of the Year 2025 is...drumroll please...EM-based connectomics!!
Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬
www.nature.com/articles/s41...
Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬
www.nature.com/articles/s41...
Method of the Year 2025: electron microscopy-based connectomics - Nature Methods
A large network of interconnected neurons serves as the basis of brain function and of behavior. Methodological advances have enabled the reconstruction of large-scale and even whole-brain connectomes...
www.nature.com
December 8, 2025 at 5:47 PM
I had heard this was coming, but it’s still an amazing indication of how far we’ve come in the last decade or so!
Reposted by Davi Bock
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too!
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
December 6, 2025 at 2:01 PM
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too!
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
Reposted by Davi Bock
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Reposted by Davi Bock
Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
November 27, 2025 at 4:40 AM
Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
Reposted by Davi Bock
I will be co-teaching a summer course at Allen Institute on connectomics education please apply. Travel support, new connectomics data sets and learning directly from the scientists who built these datasets. Details here: alleninstitute.org/events/incor...
Incorporating open connectomics data into teaching neuroscience
Learn to analyze open neuroscience data and introduce dry lab modules into your existing classes at the Incorporating Open Connectomics data into...
alleninstitute.org
November 24, 2025 at 1:53 AM
I will be co-teaching a summer course at Allen Institute on connectomics education please apply. Travel support, new connectomics data sets and learning directly from the scientists who built these datasets. Details here: alleninstitute.org/events/incor...
Reposted by Davi Bock
SO HAPPY to share our new paper in @currentbiology.bsky.social! Using volumetric EM, we found daily shifts in synapses, vesicles, and mitochondria that accompany neuronal remodeling, linking structural plasticity to changes in how s-LNv neurons influence their targets
www.cell.com/current-biol...
www.cell.com/current-biol...
Daily ultrastructural remodeling of clock neurons
A cluster of Drosophila clock neurons remodel their axonal arbors daily. Using volumetric
electron microscopy at different times of day, Ispizua, Rodriguez-Caron, and colleagues
reveal ultrastructural...
www.cell.com
November 19, 2025 at 5:03 PM
SO HAPPY to share our new paper in @currentbiology.bsky.social! Using volumetric EM, we found daily shifts in synapses, vesicles, and mitochondria that accompany neuronal remodeling, linking structural plasticity to changes in how s-LNv neurons influence their targets
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by Davi Bock
This bring me back to one of my favorite anecdotes.
In the early 1980s, a chemical physicist submitted a proposal to NIH that was assigned to NIGMS.
It received a fairly poor score (~60th percentile).
7/13
In the early 1980s, a chemical physicist submitted a proposal to NIH that was assigned to NIGMS.
It received a fairly poor score (~60th percentile).
7/13
November 14, 2025 at 3:31 PM
This bring me back to one of my favorite anecdotes.
In the early 1980s, a chemical physicist submitted a proposal to NIH that was assigned to NIGMS.
It received a fairly poor score (~60th percentile).
7/13
In the early 1980s, a chemical physicist submitted a proposal to NIH that was assigned to NIGMS.
It received a fairly poor score (~60th percentile).
7/13
Reposted by Davi Bock
How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
November 18, 2025 at 4:15 PM
How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
Reposted by Davi Bock
Stop by Wangchu's poster Tuesday (11/18) afternoon to learn about circuit motifs supporting touch processing in the spinal cord.
November 18, 2025 at 6:07 AM
Stop by Wangchu's poster Tuesday (11/18) afternoon to learn about circuit motifs supporting touch processing in the spinal cord.
Reposted by Davi Bock
Check these positions at @crick.ac.uk! It’s an outstanding opportunity to shape the way we can map neuronal circuits - and more broadly biological tissues.
Enthusiastic about connectomics and X-rays?
Several positions in our group at Crick for postdocs and senior scientists (permanent!).
DM me if interested – and let’s talk if you are at Sfn next days or at the NIH BRAIN CONNECTS meeting today!
Please share!
Several positions in our group at Crick for postdocs and senior scientists (permanent!).
DM me if interested – and let’s talk if you are at Sfn next days or at the NIH BRAIN CONNECTS meeting today!
Please share!
November 15, 2025 at 8:24 PM
Check these positions at @crick.ac.uk! It’s an outstanding opportunity to shape the way we can map neuronal circuits - and more broadly biological tissues.
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...