Alexander Shakeel Bates
@asbates.bsky.social
Fly Neuroscientist and other good things.
A small and interesting neural controller for object pursuit on the fly:
Delighted to share an updated pre-print on how adaptive control in visual pursuit is implemented at the circuit level. New behavior and neuronal data in females (!) shows how two AOTU pathways are key elements in both sexes.
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
Specialized parallel pathways for adaptive control of visual object pursuit
To pursue a moving visual object, the brain must generate motor commands that continuously steer the object to the center of the visual field via feedback. The gain of this control loop is flexible, y...
doi.org
November 3, 2025 at 11:30 PM
A small and interesting neural controller for object pursuit on the fly:
Reposted by Alexander Shakeel Bates
Delighted to share an updated pre-print on how adaptive control in visual pursuit is implemented at the circuit level. New behavior and neuronal data in females (!) shows how two AOTU pathways are key elements in both sexes.
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
Specialized parallel pathways for adaptive control of visual object pursuit
To pursue a moving visual object, the brain must generate motor commands that continuously steer the object to the center of the visual field via feedback. The gain of this control loop is flexible, y...
doi.org
November 3, 2025 at 4:58 PM
Delighted to share an updated pre-print on how adaptive control in visual pursuit is implemented at the circuit level. New behavior and neuronal data in females (!) shows how two AOTU pathways are key elements in both sexes.
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
Check it out on @biorxiv-neursci.bsky.social :
doi.org/10.1101/2025...
We have been answering redditors questions today on the #BANC fly connectome in a public AMA if anyone wants to take a look: www.reddit.com/r/askscience...
From the askscience community on Reddit
Explore this post and more from the askscience community
www.reddit.com
August 28, 2025 at 6:32 PM
We have been answering redditors questions today on the #BANC fly connectome in a public AMA if anyone wants to take a look: www.reddit.com/r/askscience...
Reposted by Alexander Shakeel Bates
We integrated our atlas with the connectome using shared features, such as lineage, segment, molecular info (i.e. neurotransmitter, Notch) and neurogenesis timing. We mapped 122 transcriptional pools, each one containing an average of 26 anatomically defined neuron types. 4/8
August 21, 2025 at 4:07 PM
We integrated our atlas with the connectome using shared features, such as lineage, segment, molecular info (i.e. neurotransmitter, Notch) and neurogenesis timing. We mapped 122 transcriptional pools, each one containing an average of 26 anatomically defined neuron types. 4/8
Reposted by Alexander Shakeel Bates
With this atlas in place, we mapped sex differences in the atlas and adult connectomes, identifying female-specific apoptosis and transcriptional divergence as drivers of sexually dimorphic development. 7/8
August 21, 2025 at 4:09 PM
With this atlas in place, we mapped sex differences in the atlas and adult connectomes, identifying female-specific apoptosis and transcriptional divergence as drivers of sexually dimorphic development. 7/8
Reposted by Alexander Shakeel Bates
Thanks to all authors and support from #MRC_LMB, @neurohub-cnr.bsky.social , @camzoology.bsky.social , #flyconnectome, @wellcometrust.bsky.social , @erc.europa.eu, @astra-zeneca.bsky.social and @cruk-ci.bsky.social. FIN
August 21, 2025 at 4:10 PM
Thanks to all authors and support from #MRC_LMB, @neurohub-cnr.bsky.social , @camzoology.bsky.social , #flyconnectome, @wellcometrust.bsky.social , @erc.europa.eu, @astra-zeneca.bsky.social and @cruk-ci.bsky.social. FIN
Reposted by Alexander Shakeel Bates
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
August 21, 2025 at 4:04 PM
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
Reposted by Alexander Shakeel Bates
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 #BANC connectome sample was the best dissection of ~150 by @mindyisminsu.bsky.social! Behaviourally characterised by @debivort.bsky.social lab, microCT used to assess integrity before continuing. Then Minsu and @jasper-tms.bsky.social imaged over ~7 months
Details: github.com/jasper-tms/t...
Details: github.com/jasper-tms/t...
August 17, 2025 at 7:52 PM
The #BANC connectome sample was the best dissection of ~150 by @mindyisminsu.bsky.social! Behaviourally characterised by @debivort.bsky.social lab, microCT used to assess integrity before continuing. Then Minsu and @jasper-tms.bsky.social imaged over ~7 months
Details: github.com/jasper-tms/t...
Details: github.com/jasper-tms/t...
Reposted by Alexander Shakeel Bates
It’s surreal to think that every neuron and synapse in the fly brain + cord that was dissected almost five years ago (the photo’s still on the lab slack!) is now just a click away on Codex codex.flywire.ai?dataset=banc. This wouldn’t have been possible without the incredible team behind it!
August 5, 2025 at 6:38 PM
It’s surreal to think that every neuron and synapse in the fly brain + cord that was dissected almost five years ago (the photo’s still on the lab slack!) is now just a click away on Codex codex.flywire.ai?dataset=banc. This wouldn’t have been possible without the incredible team behind it!
The fly #BANC connectome benefits from specialists’ annotations.
@ellenlesser.bsky.social helped us annotate wing sensory neurons and @tony-azevedo.bsky.social wing + other motor neurons, see them here!: ng.banc.community/2025a/wing-n...
In Codex: codex.flywire.ai/app/search?f...
@ellenlesser.bsky.social helped us annotate wing sensory neurons and @tony-azevedo.bsky.social wing + other motor neurons, see them here!: ng.banc.community/2025a/wing-n...
In Codex: codex.flywire.ai/app/search?f...
August 8, 2025 at 10:54 PM
The fly #BANC connectome benefits from specialists’ annotations.
@ellenlesser.bsky.social helped us annotate wing sensory neurons and @tony-azevedo.bsky.social wing + other motor neurons, see them here!: ng.banc.community/2025a/wing-n...
In Codex: codex.flywire.ai/app/search?f...
@ellenlesser.bsky.social helped us annotate wing sensory neurons and @tony-azevedo.bsky.social wing + other motor neurons, see them here!: ng.banc.community/2025a/wing-n...
In Codex: codex.flywire.ai/app/search?f...
Explore neurons that enter/exit the fly central nervous system by body part with this clickable fly!: codex.flywire.ai/app/body_par...
(graphics: @mottcallie.bsky.social, tool: Arie Matisliah)
Vector graphics! github.com/wilson-lab/s...
Effector cells in 3D! ng.banc.community/2025a/effere...
(graphics: @mottcallie.bsky.social, tool: Arie Matisliah)
Vector graphics! github.com/wilson-lab/s...
Effector cells in 3D! ng.banc.community/2025a/effere...
August 7, 2025 at 10:33 PM
Explore neurons that enter/exit the fly central nervous system by body part with this clickable fly!: codex.flywire.ai/app/body_par...
(graphics: @mottcallie.bsky.social, tool: Arie Matisliah)
Vector graphics! github.com/wilson-lab/s...
Effector cells in 3D! ng.banc.community/2025a/effere...
(graphics: @mottcallie.bsky.social, tool: Arie Matisliah)
Vector graphics! github.com/wilson-lab/s...
Effector cells in 3D! ng.banc.community/2025a/effere...
For the BANC, @jasper-tms.bsky.social and I have added layers for neurons in other datasets to our neuroglancer environment. Search by name and see your favourite neurons in the same space! See an example here: ng.banc.community/2025a/DNa01-...
August 6, 2025 at 4:49 PM
For the BANC, @jasper-tms.bsky.social and I have added layers for neurons in other datasets to our neuroglancer environment. Search by name and see your favourite neurons in the same space! See an example here: ng.banc.community/2025a/DNa01-...
Reposted by Alexander Shakeel Bates
How is the nervous system organized to coordinate behavior? To approach this massive question, a team led by @asbates.bsky.social, @jasper-tms.bsky.social, @mindyisminsu.bsky.social, & Helen Yang present the BANC: a Brain and Nerve Cord connectome.
Preprint: doi.org/10.1101/2025...
🧪#Neuroskyence
Preprint: doi.org/10.1101/2025...
🧪#Neuroskyence
August 3, 2025 at 3:16 PM
How is the nervous system organized to coordinate behavior? To approach this massive question, a team led by @asbates.bsky.social, @jasper-tms.bsky.social, @mindyisminsu.bsky.social, & Helen Yang present the BANC: a Brain and Nerve Cord connectome.
Preprint: doi.org/10.1101/2025...
🧪#Neuroskyence
Preprint: doi.org/10.1101/2025...
🧪#Neuroskyence
Reposted by Alexander Shakeel Bates
So happy to share this project detailing fly wing sensory neurons! I started this project just by asking what the axons of the wing chordotonal organ looked like, and I found many other cool structures along the way.
new preprint, led by @ellenlesser.bsky.social, on proprioceptive sensing of the Drosophila wing. tldr, there are a lot of proprioceptors out in the wing and they are wildly diverse and complex (eg, compared to the fly leg). just one example in this image...(1/4)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 3, 2025 at 3:50 PM
So happy to share this project detailing fly wing sensory neurons! I started this project just by asking what the axons of the wing chordotonal organ looked like, and I found many other cool structures along the way.
Reposted by Alexander Shakeel Bates
What a joy to work on such an incredibly collaborative project!! Congrats to all who poured time energy and effort into this new resource.
(So excited about this that I had to make a bluesky account!)
(So excited about this that I had to make a bluesky account!)
Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
August 4, 2025 at 1:50 PM
What a joy to work on such an incredibly collaborative project!! Congrats to all who poured time energy and effort into this new resource.
(So excited about this that I had to make a bluesky account!)
(So excited about this that I had to make a bluesky account!)
Reposted by Alexander Shakeel Bates
The dataset includes ~160,000 cells, segmented nuclei and mitochondria, synapses and neurotransmitter predictions, and annotations linking the CNS to peripheral sensory, motor, and visceral systems.
Info: banc.community
Data: codex.flywire.ai?dataset=banc
Viewer: ng.banc.community/view
Info: banc.community
Data: codex.flywire.ai?dataset=banc
Viewer: ng.banc.community/view
August 3, 2025 at 3:16 PM
The dataset includes ~160,000 cells, segmented nuclei and mitochondria, synapses and neurotransmitter predictions, and annotations linking the CNS to peripheral sensory, motor, and visceral systems.
Info: banc.community
Data: codex.flywire.ai?dataset=banc
Viewer: ng.banc.community/view
Info: banc.community
Data: codex.flywire.ai?dataset=banc
Viewer: ng.banc.community/view
Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
August 2, 2025 at 2:30 PM
Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Different from prior connectomes - it is brain + cord (think spinal cord)
We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...
Reposted by Alexander Shakeel Bates
Happy Friday! The female adult fly brain-and-nerve-cord (BANC) connectome is now LIVE!
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
a man with a mustache in a blue suit says tiny celebration in front of a group of people
ALT: a man with a mustache in a blue suit says tiny celebration in front of a group of people
media.tenor.com
August 1, 2025 at 10:22 PM
Happy Friday! The female adult fly brain-and-nerve-cord (BANC) connectome is now LIVE!
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
Reposted by Alexander Shakeel Bates
The first full central nervous system connectome dataset of an adult fly, with the most comprehensive annotation of sensory and motor neurons to date.
A heroic effort with contributions from many groups, a product of the collaborative spirit of the Drosophila neuroscience community.
A heroic effort with contributions from many groups, a product of the collaborative spirit of the Drosophila neuroscience community.
Happy Friday! The female adult fly brain-and-nerve-cord (BANC) connectome is now LIVE!
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
Explore the data here: codex.flywire.ai?dataset=banc
Check out the preprint here: doi.org/10.1101/2025...
a man with a mustache in a blue suit says tiny celebration in front of a group of people
ALT: a man with a mustache in a blue suit says tiny celebration in front of a group of people
media.tenor.com
August 1, 2025 at 11:14 PM
The first full central nervous system connectome dataset of an adult fly, with the most comprehensive annotation of sensory and motor neurons to date.
A heroic effort with contributions from many groups, a product of the collaborative spirit of the Drosophila neuroscience community.
A heroic effort with contributions from many groups, a product of the collaborative spirit of the Drosophila neuroscience community.
Reposted by Alexander Shakeel Bates
If you want a narrative version of this project, check out our blog post on the newly re-minted Funke Lab website!
funkelab.github.io/blog/2024/qu...
Thanks to @bobqubit.bsky.social, @asbates.bsky.social, and @jefferis.bsky.social, & @janfunkey.bsky.social for this 🦆ing awesome collaboration!
6/6
funkelab.github.io/blog/2024/qu...
Thanks to @bobqubit.bsky.social, @asbates.bsky.social, and @jefferis.bsky.social, & @janfunkey.bsky.social for this 🦆ing awesome collaboration!
6/6
What's in a QuAC? | Funke Lab
The Funke lab at HHMI Janelia.
funkelab.github.io
January 15, 2025 at 8:31 PM
If you want a narrative version of this project, check out our blog post on the newly re-minted Funke Lab website!
funkelab.github.io/blog/2024/qu...
Thanks to @bobqubit.bsky.social, @asbates.bsky.social, and @jefferis.bsky.social, & @janfunkey.bsky.social for this 🦆ing awesome collaboration!
6/6
funkelab.github.io/blog/2024/qu...
Thanks to @bobqubit.bsky.social, @asbates.bsky.social, and @jefferis.bsky.social, & @janfunkey.bsky.social for this 🦆ing awesome collaboration!
6/6
With so many new in blue, I thought I would repost this thread about our neurotransmitter prediction across the entire fly brain connectome! Should prove a very useful hypothesis generator for the insect neuroscience community.
Our fly brain connectome papers are now live (www.nature.com/immersive/d4...), and is getting traction (www.bbc.co.uk/news/article...). With ~139k neurons, >8k cell types, synapses annotated, transmitters predicted, ~134 evo-devo units denoted, so much is now possible in the fly.
November 21, 2024 at 4:22 PM
With so many new in blue, I thought I would repost this thread about our neurotransmitter prediction across the entire fly brain connectome! Should prove a very useful hypothesis generator for the insect neuroscience community.
Reposted by Alexander Shakeel Bates
In a fly's brain, there are some 140,000 neurons that connect via 54.5 million synapses. Researchers have now mapped *all of them*. That story and more of the best in Science and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪 🧠
October 3, 2024 at 9:16 PM
In a fly's brain, there are some 140,000 neurons that connect via 54.5 million synapses. Researchers have now mapped *all of them*. That story and more of the best in Science and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪 🧠
Reposted by Alexander Shakeel Bates
And our contribution to FlyWire, cell typing the connectome with @jefferis.bsky.social and colleagues, is here: www.nature.com/articles/s41...
Whole-brain annotation and multi-connectome cell typing of Drosophila
Nature - A consensus cell type atlas for the fly brain provides both an intellectual framework and open-source toolchains for brain-scale comparative connectomics.
www.nature.com
October 2, 2024 at 7:10 PM
And our contribution to FlyWire, cell typing the connectome with @jefferis.bsky.social and colleagues, is here: www.nature.com/articles/s41...
Reposted by Alexander Shakeel Bates
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...
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
October 2, 2024 at 7:08 PM
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...