AERO·CORTEX ACx · bat brain atlas
Enter the Atlas

A 1-millimeter mission into the flying mammal's mind

The bat brain, mapped.
Synapse by synapse.

AEROCORTEX (ACx) is an open research initiative using electron microscopy and AI to reconstruct the complete wiring diagram of the echolocating bat brain — to learn how a 50-gram animal builds a sonar-guided mind in the dark.

Enter the Atlas Read the Wiki ↓
0bat species on Earth
0mm³ of cortex imaged
0neurons reconstructed
0synapses annotated
0nm per pixel resolution

01 — Why bats

The most extraordinary brain
in the mammal class

Bats are the only mammals that fly — and to fly in total darkness, they evolved a biological sonar with microsecond timing, a three-dimensional cognitive map, and one of the longest-lived small brains on Earth. If we want to understand how neurons build intelligence, the bat is the natural experiment nature already ran.

Living sonar

Echolocating bats scream at up to 200 kHz and reconstruct the world from echoes alone. They resolve pulse-echo pairs 0.5 milliseconds apart — timing precision no engineered sonar matches at their size.

20–200 kHz · 0.5 ms

3D navigation

Flying in three dimensions, bats evolved hippocampal place cells that map volumetric space — with place fields as small as one centimeter, the finest spatial resolution measured in any mammal.

1 cm place fields

Extreme longevity

A Brandt's bat the size of a thumb was recaptured alive after 41 years in the wild. Bats live up to eight times longer than same-sized mammals — their brains are a live model of healthy aging.

8× expected lifespan

Viral tolerance

Bats host coronaviruses, Ebola and Nipah without falling ill. Their immune systems damp inflammation instead of overreacting — a trick researchers are mining for human medicine.

coronavirus reservoirs, symptom-free

Ecosystem engineers

Bats pollinate agave, durian and wild banana, disperse the seeds that regrow rainforests, and save U.S. agriculture an estimated $3.7 billion a year in pest control.

$3.7B / year

One in five mammals

More than 1,400 species — from the 2-gram bumblebee bat to flying foxes with 1.7-meter wingspans. Nearly a fifth of all mammal species is a bat, on every continent except Antarctica.

1,400+ species

02 — How it works

From a living bat
to a machine-readable mind

The same pipeline that produced the largest mammalian connectome to date — the 1 mm³ MICrONS atlas of the mouse visual cortex — applied for the first time to a flying, echolocating brain.

01

Preserve

Within minutes of sacrifice, the brain is perfusion-fixed and stained with heavy metals so every membrane reflects electrons. The bat's last thought is frozen in resin at nanometer fidelity.

02

Image

Serial-section electron microscopy slices the tissue 40 nanometers thin. ~25,000 slices per cubic millimeter, imaged at 4×4 nm per pixel — 1.2 petabytes of raw imagery of primary auditory cortex.

03

Reconstruct AI

Flood-filling networks — the same convolutional architecture as the MICrONS project — segment 95,000+ neurons across the volume, tracing every dendrite and axon automatically. Machine Intelligence, from Cortical Networks.

04

Map

Synapse detectors find every connection — 121 million so far — while a worldwide community of proofreaders edits the result in CAVE. Every "who talks to whom" is versioned like code.

05

Model

Structure meets function: the wiring diagram is joined to recordings of neurons firing during real echolocation flights. The result — circuit models of sonar perception and 3D memory, and blueprints for better AI.

03 — The Atlas

Fig. 1 — Neurons of the
auditory cortex, A1v

A reconstruction of layer 2/3 in the ventral primary auditory cortex of the Egyptian fruit bat (Rousettus aegyptiacus). Click any neuron to inspect its identity, type and synaptic partners. Scroll to zoom, drag to pan.

A1v · L2/3 · v0.3 "Song of the Hunter"
20 µm
x — · y — µm

04 — Circuits

How a brain hears distance

A bat's call bounces off a moth and returns as an echo. The delay between call and echo is distance: one millisecond of delay ≈ 17 centimeters of range. Bat auditory circuits measure that delay with sub-millisecond precision — the founding problem of neuroethology.

Emitted call FM sweep · 85 → 45 kHz · 2 ms Prey echo 1 ms delay ≈ 17 cm Cochlea frequency map Inferior colliculus sub-ms timing Auditory cortex A1 delay-tuned neurons
Signal chain: call → echo → cochlea → inferior colliculus → auditory cortex. Each stage sharpens time.

Delay-tuned neurons

In the mustached bat's cortex, "FM-FM" combination-sensitive neurons fire only when the echo arrives at a specific delay after the call. Different neurons prefer different delays — together they tile a neural map of target distance, first described by Suga & O'Neill (1979).

preferred delay 5 ms → 85 cm echo delay (ms)
Suga & O'Neill, Science 1979

Doppler-shift compensation

Horseshoe bats listen through an "acoustic fovea" — a razor-thin frequency band where their hearing is sharpest. While flying, they continually lower their call frequency so the echo always returns inside that band, compensating within a few hertz.

fovea ±2 Hz frequency
Schnitzler, Nature 1968
0max call frequency
0ms pulse-echo resolution
0ms from detect to capture
0echoes processed per second

From the literature · PNAS 2024

The resting bat cortex is wired like ours

High-field resting-state fMRI of echolocating bats reveals auditory cortical regions functionally coupled to a default mode-like network — the same large-scale architecture seen in the human brain. Evidence that mammalian brains self-organize along deep, shared lines.

  • 9.4 T small-animal fMRI · University of Antwerp
  • Auditory cortex ↔ default mode-like network coupling
  • Echolocation circuits embedded in distributed cortical loops
Read in PNAS ↗
Figure 4 — resting-state functional connectivity of the auditory cortex in echolocating bats, Washington et al., PNAS 2024
Fig. 4 PNAS · 2024 Read the paper ↗
Auditory cortical regions show resting-state functional connectivity with the default mode-like network in echolocating bats. Washington SD, Shattuck K, Steckel J, Peremans H, Jonckers E, Hinz R, et al. — PNAS 121(27): e2306029121 (2024)

06 — Dataset

Open data,
released like software

Following the MICrONS model: every segmentation, synapse and annotation is versioned, documented and public. Anyone can fly the atlas.

Release v0.3 — "Song of the Hunter"
SpeciesEgyptian fruit bat · Rousettus aegyptiacus
RegionPrimary auditory cortex (A1v) + dorsal hippocampus (Phase II)
Volume imaged1.0 mm³
Voxel size4 × 4 × 40 nm
Neurons segmented95,482
Synapses annotated121.4 M
Functional imaging47 free-flight sessions · 12,208 calcium-imaged neurons
Raw data1.2 PB (stored) · 25.3 TB public
FormatsNeuroglancer precomputed · CAVE · cloudvolume
LicenseCC-BY 4.0
  • v0.1
    "First Echo"Nov 2025 — 0.1 mm³, 9,102 neurons, community preview
    shipped
  • v0.2
    "Night Flight"Feb 2026 — functional imaging matched to EM, first flight sessions
    shipped
  • v0.3
    "Song of the Hunter"May 2026 — delay-tuned neuron annotations, full 1 mm³ volume
    current
  • v1.0
    "The Atlas"Q4 2026 — hippocampus volume + proofread connectome
    roadmap
$ access the connectome 
pip install caveclient cloudvolume

from caveclient import CAVEclient
client = CAVEclient("acx_v03")

# fetch the wiring diagram of delay-tuned cell R-aeg-A1-003847
syn = client.materialize.synapse_query(
    post_ids=[3847], limit=100
)
print(f"{len(syn)} incoming synapses")

Project publications

  • [preprint] The AEROCORTEX Consortium — "A cubic millimeter of echolocating cortex: structure, function, and the neural map of echo delay" (2026)
  • [preprint] "Flood-filling networks generalize to lissencephalic auditory cortex: segmentation of 95k neurons across 1 mm³ of bat brain" (2026)
  • [data descriptor] "Release v0.3 Song of the Hunter — annotation and access guide" (2026)

07 — Conservation

You can't map what's gone

Research and conservation are the same project. Bats face the fastest collapse of any mammal group in recent memory — and their ecological services are worth billions. Every neuron we map belongs to an animal whose wild cousins are vanishing.

Pseudogymnoascus destructans

White-nose syndrome

A fungus from Eurasia is killing hibernating bats across North America. Since 2006 it has wiped out millions of bats, driving the northern long-eared bat past 90% population decline — the steepest mammalian decline on record.

Bracken Cave, Texas

20 million bats, one cave

The world's largest bat colony emerges nightly to eat an estimated 100 tons of insects. Protecting roosts like Bracken — and the 1,400+ species they represent — keeps both ecosystems and research subjects alive.

Our field protocol: all atlas specimens are captive-bred R. aegyptiacus under IACUC review. No wild bats are collected — we collaborate with Bat Conservation International, and 5% of every fund allocation goes to WNS research and roost protection.

Visit Bat Conservation International ↗
0decline in hardest-hit species
0billion U.S. ag value / year
0bats in one Texas cave
0in 5 mammal species is a bat

08 — Fund

Fund a cubic millimeter

Imaging time, GPU cycles and open-data hosting cost real money. Name a synapse. Name a neuron. Put your name on the map of a flying mind.

Atlas Fund — 2026 cohort $3.1M raised of $10M
$25 Echo Supporter

Name a synapse in the public map. Certificate + your name in the release notes.

Claim it
$250 Sonar Patron

Name a reconstructed neuron. Its ID page carries your name forever.

Claim it
$2,500 Flight Sponsor

Name a place field — a real region of 3D space in the navigation dataset.

Claim it
$25,000 Colony Partner

Fund a full EM section (25,000 slices). Brand on the Atlas launch page.

Claim it

Illustrative campaign for the concept site — the map is open, the mission is real. 100% of a real fund would go to imaging time and open-data hosting.

09 — FAQ

Frequently asked questions

Mice are the standard, but they never fly and never echolocate. The bat brain solves two problems no mouse brain does: sonar scene analysis with microsecond timing, and true 3D navigation. The connectome is the answer key to questions you can only ask in flight.

Two ways. First, AI does the heavy lifting: convolutional networks (flood-filling networks) segment 95,000+ neurons from petabytes of electron microscopy — human tracing would take millennia. Second, the point of the atlas is to reverse-engineer cortical computation — the "Machine Intelligence from Cortical Networks" idea behind the original MICrONS project — and a sonar brain is the perfect teacher for next-generation perception AI.

The bat emits ultrasonic calls (up to 200 kHz, above human hearing) and listens for echoes. Echo delay encodes distance (~1 ms ≈ 17 cm), echo spectrum encodes texture, and Doppler shift encodes relative speed. Specialized neurons in the auditory cortex fire only for specific delay-and-frequency combinations, building a neural map of the surrounding space.

A connectome is the complete wiring diagram of a nervous system: every neuron and every synapse. The bat connectome documents, at nanometer resolution, exactly which of the 95,482 reconstructed neurons talks to which — the hardware that runs the software of the bat's mind.

Yes. All released data is CC-BY 4.0: Neuroglancer precomputed volumes, CAVE databases, segmentations and annotations. 25.3 TB is already public, with the rest following after proofreading. Anyone can fly the atlas.

Serial-section electron microscopy: the tissue is stained with heavy metals, embedded in resin, and sliced 40 nm thin. Each slice is scanned by an electron microscope at 4×4 nm per pixel. Stack the slices back together and you have a 3D volume where individual synaptic vesicles are visible.

All atlas specimens are captive-bred Egyptian fruit bats under institutional animal-care review (IACUC), following the same ethical standards as mouse connectomics. No wild bats are collected; the project directly funds white-nose syndrome research and roost protection with Bat Conservation International.

Release v0.3 covers the full cubic millimeter of auditory cortex and is public now. The hippocampus volume — the 3D navigation map — ships with v1.0 "The Atlas" in Q4 2026, together with the fully proofread connectome.

The dark is full of answers.

Join the effort to map the most extraordinary brain in the mammal class — one cubic millimeter, one synapse, one flight at a time.

Enter the Atlas Fund a Neuron