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Wei-Chung Allen Lee

@darbly.bsky.social
1.4K followers 888 following 70 posts

circuit motifs of action selection, execution, & refinement | functional connectomics | assoc prof | lee.hms.harvard.edu

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Reposted by Wei-Chung Allen Lee
Sven Dorkenwald @sdorkenw.bsky.social · 17/09/2026
Applications are now open for the San Juan Winter School 2027 on Connectomics and Brain Simulation! Join us to learn how to analyze and simulate connectomes. sjcabs.com
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Wei-Chung Allen Lee @darbly.bsky.social · 19/09/2026
Great primer from Chih-Ying Su: journals.plos.org/Plosbiology/... on a first connectomic foray into mosquitoes: journals.plos.org/plosbiology/... Go diptera #neuroskyence!
journals.plos.org
How the mosquito’s carbon dioxide sense gets an internal boost
Mosquitoes use carbon dioxide as a critical cue to sense if humans are nearby. This Primer explores a new study in PLOS Biology that reveals that carbon dioxide-sensing neurons in mosquitoes can ampli...
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Wei-Chung Allen Lee @darbly.bsky.social · 19/09/2026
Very.
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Reposted by Wei-Chung Allen Lee
Dr. Or M. Bialik |📚|🔬|🌊|⚒️ @obialik.bsky.social · 03/09/2026
Fish with electrical senses have unique brain cells specifically to process that information. The real trick they pull is separating the electricity they emit from the ones they sense. 🧪 Link: www.nature.com/articles/s41586-026-…
a, Schematic of the interference problem facing the passive electrosensory system of weakly electric fish. Responses of EAFs to prey are masked by responses to the EOD of the fish, which vary depending on factors such as water conductivity. b, Schematic of prediction and cancellation of responses to the EOD. Predictions are based on electric organ corollary discharge signals conveyed by GCs (granule cell basis) and require specific patterns of synaptic connectivity. c, Summary diagram of the synaptic connectivity patterns revealed in the present study. Only connections comprising >10% of the total synapses to a given cell type are shown in the diagram. d, Two example Output cells (blue and red) are shown along with EAF (pink) and GC (magenta) inputs overlaid on a cutout of the EM volume (424 × 427 × 45 µm; all EM connectomic data are from a single biological specimen). The dorsal–ventral and anterior–posterior dimensions of the skin surface are mapped onto the x- and z-dimensions of the volume, respectively. The top inset shows example excitatory GC synapses (magenta fill and star) onto apical dendritic spines of the ON cell (red fill). The magenta fill marks the example GC axon visualized in the volume; the magenta star marks another GC axon. The white star marks an inhibitory molecular layer interneuron synapse onto the dendritic shaft of the same ON cell. The bottom inset shows an example excitatory EAF synapse (pink fill) onto the ON cell basal dendrite (red fill). mol, molecular layer; ggl, ganglion layer; plex, plexiform layer; gran, granular layer. e–h, Example reconstructions of major ELL cell types. Axons are shown in black. ON/OFF, Output (h); MG+/MG−, medium ganglion (f); SG+/SG−, small ganglion (g); Gr+, granular; SP−, small plexiform (h). The inset in f shows an example inhibitory synapse between an MG+ cell (orange) and an OFF cell soma (blue).
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Wei-Chung Allen Lee @darbly.bsky.social · 06/09/2026
Just missed the Bright Angel flash flood. We were ~100 miles down river when it happened, having passed Phantom Ranch the day before. Had to move uphill last night of camp, but luckily we were unaffected.
Plot of provisional USGS flow gauge readings from Phantom August 23-30. Note, Bright Angel Canyon flash flood occurred August 29 ~2:30p.Plot of provisional USGS water gauge height readings from Phantom August 24-30. Note, Bright Angel Canyon flash flood occurred August 29 ~2:30p.
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Wei-Chung Allen Lee @darbly.bsky.social · 06/09/2026
Included: stunning privy views, thoughts to paper, waterfalls, creeks, and moonlight.
Photo of portable toilet and supplies against a backdrop of canyon rocks and cliffs. Person journaling by red headlamp light.Cascading Havasu Creek with people along trail.Two people seated, waking up to morning moonlight above cliffs.
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Wei-Chung Allen Lee @darbly.bsky.social · 06/09/2026
Hermit (I believe)
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Wei-Chung Allen Lee @darbly.bsky.social · 06/09/2026
Badger Creek Rapid (I believe).
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Wei-Chung Allen Lee @darbly.bsky.social · 06/09/2026
Science break. Six days on the Colorado through Grand Canyon held unfathomable vastness, profound beauty, and renewed connectedness. Sleeping under the stars, lunar eclipse, herons, big horn, bats, 188 miles, and 60+ rapids. Meaty hits at Sockdolager, Granite, Hermit, and Lava. Highly recommended.
Photo of three unfurled blue sleeping bags atop cots and a yellow duffle and dry bag along sandy bank of Colorado River with cliff in the background. Mile 30, Fence/Sand Pile camp, evening 1.Sun setting on the eastern cliffs of the canyon. Blue J-rig raft along the western river bank with people preparing dinner.Eastern cliffs along the Colorado River with raft, cots, packs, chairs, and people sprinkled across the sandy western river bank. Mile 60, Ledges camp, evening 2.Sun setting on the eastern cliffs of the canyon. Raft along the western river bank. People in chairs enjoying their surroundings and around a table discussing the next day’s plans.
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Reposted by Wei-Chung Allen Lee
Janelia FlyEM @janelia-flyem.bsky.social · 04/09/2026
We're thrilled with the publication of the Male CNS Connectome! www.cell.com/cell/fulltex... Also check out this (growing) collection of companion papers: www.cell.com/consortium/m...
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 03/09/2026
The complete #connectome of the adult Drosophila male CNS has allowed researchers, inc @jefferis.bsky.social’s group, to compare male & female brains at synaptic-resolution for the first time. Read more here: mrclmb.ac.uk/news-events/... #LMBResearch 1/2
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Laura Driscoll @lndriscoll.bsky.social · 08/08/2026
Confused about all this talk of compositionality in neuroscience? Read our new perspective www.nature.com/articles/s41... with authors Reidar Riveland and Alex Pouget.
nature.com
The compositionality continuum as a principle for studying the neural basis of intelligence - Nature Neuroscience
Compositionality exists on a continuum of increasing complexity rather than as a binary trait. Studying its implementation in simpler biological and artificial systems is the most tractable path towar...
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Reposted by Wei-Chung Allen Lee
Zhihao Zheng @zhihaozheng.bsky.social · 07/08/2026
Happy to share the CA3 dataset is published. First large-scale dense connectomics from hippocampus. First connectomic dataset imaged in @princetonneuro.bsky.social. A harbinger of many larger datasets to come (for both). doi.org/10.1038/s415... #hippocampus But my personal favorite is (1/2)
doi.org
Hippocampal CA3 connectomics reveals a gradient of mossy fiber inputs and selective feedforward inhibition onto pyramidal cells - Nature Neuroscience
The authors present a dense connectomic reconstruction of a 0.1 mm3 hippocampal CA3 volume and reveal spatial gradients, high convergence and cell-type-selective feedforward inhibition of inputs to py...
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Reposted by Wei-Chung Allen Lee
Yichen Luo 骆奕辰 @camellyc.bsky.social · 03/08/2026
1/8 Breathing seems automatic. But it's a finely tuned motor behavior that has to be controlled. In this preprint, I map the circuits that match a fly's respiration to the metabolic demands of flight and mitigate the risk of dehydration. 🧵🪰 www.biorxiv.org/content/10.6...
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Stanley Heinze @stanley-heinze.bsky.social · 30/07/2026
New preprint! www.biorxiv.org/content/10.6... Nearly a decade after starting the project, the first major results from our comparative connectomics work is online! Comparing the head direction circuits of the central complex in bees, ants and flies, recapitulating >300million years of evolution.
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Wei-Chung Allen Lee @darbly.bsky.social · 12/06/2026
A great privilege of science is working with remarkable people. A nice piece highlighting @mindyisminsu.bsky.social. Her grit, esp through the pandemic, was foundational to the #BANC project. hms.harvard.edu/news/making-...
hms.harvard.edu
Making Connections, in the Brain and in Science
PhD student Minsu Kim gained confidence, experience in the lab of neurobiologist Wei-Chung Allen Lee
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Wei-Chung Allen Lee @darbly.bsky.social · 11/06/2026
Move on from disembodied brains hms.harvard.edu/news/researc...
hms.harvard.edu
Researchers Publish First Complete Connectome of Fruit Fly Brain and ‘Spinal Cord’
Open-source resource poised to propel research on how nervous systems work
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Reposted by Wei-Chung Allen Lee
Jan Drugowitsch @jdrugowitsch.bsky.social · 09/06/2026
The Drugowitsch lab, in particular @zakiajabi.bsky.social, contributed an efficiently computable “influence score”—a scalable way to quantify effective distance and signal propagation in large neural networks. Code at doi.org/10.5281/zeno....
doi.org
Connectome Influence Calculator
Code version used to compute influence scores for the Brain and Nerve Cord (BANC) connectome reported in the updated Bates et al. pre-print. Compared to v0.3, this version contains some updates to the...
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Wei-Chung Allen Lee @darbly.bsky.social · 10/06/2026
It is nice in such times to see there is so much 🧪#neuroskyence still to be discovered.
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
more co-authors on Bluesky! (and apologies to any missed): @justinellis-joyce.bsky.social, @mottcallie.bsky.social, @sophia-renauld.bsky.social, @dipacheco.bsky.social, @jefferis.bsky.social, @amysterling.bsky.social, @zandawala.bsky.social, @sandpkr.bsky.social, @hokuba.bsky.social 18/18
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Call-out to other co-authors on Bluesky, excellent collaborators all! @sebastianseung.bsky.social, @debivort.bsky.social, @janfunkey.bsky.social, @adjavon.bsky.social, @sdorkenw.bsky.social, @tuthill.bsky.social, @ellenlesser.bsky.social, @tmckim.bsky.social, @camellyc.bsky.social 17/18
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Lead by @asbates.bsky.social @mindyisminsu.bsky.social, @jasper-tms.bsky.social, @helenhyang.bsky.social, @perlman.bsky.social, and labs of Mala Murthy, @jdrugowitsch.bsky.social, and @rachelirenewilson.bsky.social. #NIH BRAIN Initiative, @hhmi-science.bsky.social, @wellcometrust.bsky.social. 16/18
Slide: preprint and resource links.
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
This was a big effort, led by @harvardmed.bsky.social, @bostonchildrens.bsky.social, with FlyWire based at @princetonneuro.bsky.social. The BANC is the work of over 100 authors, the BANC-FlyWire Consortium of proofreaders and citizen scientists, and the SixEleven and Aelysia teams. 15/18
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Second half of the video! Narration by @asbates.bsky.social Full video: www.youtube.com/watch?v=cTqV... 1.5/18
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Now published - the #BANC! A full central nervous system (CNS) connectome of a limbed animal at single-synapse resolution, enabling us to follow sensory-motor arcs and understand how the CNS controls the body. rdcu.be/fncjS. #neuroscience. Video by @quorumetrix.bsky.social 1/18
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Aaron Kuan @kuanawanda.bsky.social · 27/11/2025
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)
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Adrian Wanner @adrianawanner.bsky.social · 27/11/2025
Happy to share the first paper from my journey at @psich.bsky.social towards X-ray connectomics, now out in @natmethods.nature.com: www.nature.com/articles/s41...
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Wei-Chung Allen Lee @darbly.bsky.social · 18/11/2025
Meet Wangchu and connectomics in the spinal cord this afternoon at LBP077.04 / LBP036 #SFN25
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Wei-Chung Allen Lee @darbly.bsky.social · 18/11/2025
Stop by Wangchu's poster Tuesday (11/18) afternoon to learn about circuit motifs supporting touch processing in the spinal cord.
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Reposted by Wei-Chung Allen Lee
Greg Jefferis @jefferis.bsky.social · 05/10/2025
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....
janelia.org
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 ...
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Davi Bock @dddavi.bsky.social · 14/08/2025
It was a good experience to step back and briefly take stock of the amazing progress in connectomics since I started working on this stuff (20 years ago!) thanks as well to @natrevneuro.nature.com for the constructive editorial interactions.
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Alexandra Pacureanu @apacureanu.bsky.social · 11/02/2025
X-ray nanotomography can be your new friend for neuronal imaging. In our new #preprint (tinyurl.com/nanoXneuro) we present advances that push the spatial resolution limit for X-ray holographic nanotomography (XNH). We can now resolve synapses. 🧵
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Yuxin Zhang @yuxinzhang.bsky.social · 01/05/2025
My PhD project is out as a preprint! We combined 2P and synchrotron X-ray to understand mouse olfactory bulb circuits, linking physiology to structure in 3 animals! doi.org/10.1101/2025... 🙌 @carlesbosch.bsky.social, @apacureanu.bsky.social, @andreas-t-schaefer.bsky.social, @esrf.fr, @crick.ac.uk
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Wei-Chung Allen Lee @darbly.bsky.social · 10/08/2025
Couldn't agree more. There’s still so much to be uncovered in the dataset. One thing that wasn’t emphasized before is how it enables access to specific circuit motifs down to identified cells. 12 examples are highlighted in the preprint, but again just the tip of the iceberg.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Key annotations from: Tony Azevedo, @tuthill.bsky.social , @zandawala.bsky.social‬, @hokuba.bsky.social‬, Steffi Hampel, @andrew-seeds.bsky.social, Kathi Eichler @jefferis.bsky.social, Michael Pankratz, @fleyes.bsky.social, & Marie Suver. Renderings by @amysterling.bsky.social and Arie Matsliah
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Neurotransmitter predictions from Kevin Delgado, @adjavon.bsky.social, & @janfunkey.bsky.social . Key analysis from Mohammed Osman. @sdorkenw.bsky.social & Forrest Collman for CAVE. (cont'd 2)
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Thanks and congratulations to others on the phenomenal team including: Arie Matsliah for Codex, its development, and integration of the BANC. Key technical work from @perlman.bsky.social‬ & Zetta AI. Aelysia for specialist proofreading. (cont'd)
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
An incredible collaboration with Rachel Wilson & her lab, Zaki Ajabi & @jdrugowitsch.bsky.social @harvardmed.bsky.social‬; Mala Murthy, Sebastian Seung, & the FlyWire team @princetonneuro.bsky.social for their huge proofreading effort; and Ryan Maloney & @debivort.bsky.social for the specimen.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Our data support an architecture of distributed, parallelized, and embodied control, reminiscent of “subsumption architectures” from autonomous robotics, where behavior-centric feedback loops are organized s that they can be combined or subsumed to generate complex or resolve competing behaviors.
Schematic example of subsumption architecture. This example has two local loops (behavior 1 and behavior 2), corresponding e.g.
the control of individual legs. Behavior 3 is positioned to take control of both local loops (subsumption), contingent on some input from
both sensors. Behavior 4 is positioned to subsume all other behaviors, based on some other input from both sensors.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
* Brain regions involved in learning and navigation supervise these circuits.
Strongest links between CNS networks. The size of each arrow represents the number of postsynaptic cells in that link.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
* Long-range pathways are organized to permit coordination within and across modules to fine-tune, prioritize, resolve conflicts, and link related behaviors in sequences. This may offer structural substrates for behavioral compositionality.
Summary of the strongest adjusted influences between behavioral modules as a network graph.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
* Long-range ascending and descending neurons can combine local loops into behavioral modules. bsky.app/profile/mott...
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Using the this influence metric, we find: * Local sensorimotor loops linking matched sensors and effectors are basic building blocks of behavioral control.
(left) Schematic of body parts associated with annotated effector cells in the BANC. (middle) Heatmap of mean adjusted influence of sensory cells (columns) on effector cells. Sensory and effector cells are pooled by body part. Each row is minmax normalized to the same range (0-1). (right) Schematic of an example local loop (top) that is also linked to specific sensors via long-range connections (bottom).
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Moreover, Zaki Ajabi developed a computationally efficient method for quantifying the “influence” any neuron has on any other neuron in the CNS. We applied this method to estimate the pairwise interactions between all cells in the CNS, amounting to more than 20 billion influence scores.
Cartoon of directed network graph and schematic depicting the influence of source cells on target cells is estimated via linear dynamical modeling.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
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
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
The BANC is the first connectome that explicitly links the brain to the nerve cord, & through it, to the body. It offers a new “embodied” perspective for connectomes, one that changes how we think about neural networks for control, behavior, & even artificial intelligence. bsky.app/profile/mott...
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
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
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Thanks to those that supported the work including: @wellcometrust.bsky.social‬, @klingensteinorg.bsky.social, @simonsfoundation.org, ‪@sloanfoundation.bsky.social, Searle Scholars Program, the Smith Family Foundation, and the Pew Charitable Trusts.
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
These results offer a new view of how host cues are processed in the mosquito brain and comparative and evolutionary perspectives on neuronal circuits. Congrats to the authors and collaborators including Jialu Bao and Wesley Alford who lead this effort!
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Wei-Chung Allen Lee @darbly.bsky.social · 03/08/2025
Using a connectome-informed computational model, @briandepasquale.bsky.social showed that recurrent primary sensory connectivity boosts the downstream neurons output under realistic background odor conditions, meaning recurrent synapses make CO₂ detection robust, even in a noisy world.
(left) Model architecture. CO2 is processed by Glomerulus 1, which includes recurrent connections. Co-occurring odorants (‘background’) activate glomeruli which inhibit other glomeruli through inhibitory local neurons (LNs). (right) Plot of OSN to PN response curves for OSNs with and without recurrent connections, for two different background odor strengths.
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