Accessing Public EM Datasets
Practical guide for finding, downloading, and working with public EM datasets.
Connectomics Datasets
Learn with real scientific data from groundbreaking research.
These pages collect datasets from landmark connectomics studies — H01, MICrONS, FlyWire, the hemibrain, and others — with links to the data portals, the papers behind them, and the site material that uses each one.
Guides to working with the data
These are how-to pages, not datasets. Start here if you have chosen a volume and now need credentials, a client, or a pipeline.
Getting Started with Data
A four-level ladder from browser exploration to imagery cutouts, with the auth walkthroughs, calibration checks, and failure fixes that the tool documentation leaves out.
MouseConnects Connectomics Workflow
Seven pipeline steps from fixation to circuit analysis, with the HI-MC project's numbers and a depth link into the unit that teaches each step.
MouseConnects Dataset – Complete Hippocampal Connectome
Overview of the MouseConnects HI-MC dataset, technology stack, collaborators, and scientific goals.
Featured datasets
The volumes this site teaches from. Every number below is rendered from the dataset record itself, so the card, the timeline and the dataset page cannot disagree.
MICrONS — mouse visual cortex
A cubic millimetre of mouse visual cortex where the same neurons were both recorded in a living animal and reconstructed in EM. It is the only large volume that lets you ask what a measured cell is wired to.
- Region: Visual cortex (VISp, VISrl, VISal, VISlm)
- Cells: ~200,000 anatomical; ~75,000 functionally imaged
- Synapses: 523 million
- Size: 1.6 PB
FlyWire — complete adult fly brain
The first complete connectome of an adult animal brain: every neuron, every synapse, hierarchically annotated, and proofread by a distributed community over several years.
- Region: Whole brain, including optic lobes
- Cells: 139,255 neurons; 8,453 cell types
- Synapses: ~54.5 million
- Size: ~50 TB
MouseConnects (HI-MC) — mouse hippocampus
The NIH BRAIN CONNECTS effort to reconstruct 10 mm³ of mouse hippocampal formation — an order of magnitude beyond any volume yet completed.
- Region: Hippocampal formation
- Size: >10 PB projected
H01 — human cortical fragment
A cubic millimetre of human temporal cortex, imaged by serial-section EM and reconstructed automatically. It is the largest published volume of human brain at synaptic resolution, and the only one most learners will ever meet.
- Region: Temporal lobe cerebral cortex
- Cells: ~57,000
- Synapses: ~150 million
- Size: 1.4 PB
Hemibrain — Drosophila central brain
A densely reconstructed half of the Drosophila central brain, imaged by FIB-SEM at isotropic resolution and the dataset on which most fly circuit analysis before FlyWire was built.
- Region: Central brain (~50%)
- Cells: ~25,000 neurons
- Synapses: ~20 million
- Size: ~100 TB
Connectomics timeline
Every dataset in the catalogue, oldest first. Forty years separate the first complete nervous system from the first complete adult brain.
1986
C. elegans complete connectome (White et al.)
The first complete nervous system ever mapped: 302 neurons and about 7,000 synapses, traced by hand over more than a decade. The dataset that founded the field.
- Species: Caenorhabditis elegans
- Region: Whole nervous system
- Cells: 302 neurons
- Synapses: ~7,000
- Method: Serial-section TEM, hand traced
- Size: <1 GB
2011
Bock et al. — mouse visual cortex with physiology
The first volume to link measured physiology to EM wiring: orientation tuning recorded in a living mouse, then the same cells reconstructed.
- Species: Mouse
- Region: Primary visual cortex
- Cells: ~1,500 cell bodies imaged
- Method: ssTEM after in vivo two-photon calcium imaging
- Size: ~12 TB
2011
Briggman et al. — mouse retinal direction selectivity
Serial block-face EM of mouse retina combined with functional imaging, showing that starburst amacrine cells wire asymmetrically onto direction-selective ganglion cells.
- Species: Mouse
- Region: Retina
- Method: SBEM with two-photon calcium imaging
2013
Helmstaedter et al. — mouse retinal connectome
A dense reconstruction of the inner plexiform layer, and the first demonstration that distributed human annotation could scale EM reconstruction.
- Species: Mouse
- Region: Retina (inner plexiform layer)
- Method: SBEM with crowd-sourced annotation
2015
Kasthuri et al. — saturated cortical reconstruction
A saturated reconstruction: every object in a small cortical volume traced, including glia and blood vessels, not just the neurons of interest.
- Species: Mouse
- Region: Visual cortex (neocortex)
- Method: Automated serial-section TEM
- Size: ~1 TB
2016
Lee et al. — mouse visual cortex functional network
Anatomy and function in mouse visual cortex, showing that pyramidal cells with similar tuning are preferentially connected.
- Species: Mouse
- Region: Visual cortex
- Method: ssTEM with in vivo calcium imaging
2017
Larval zebrafish whole brain
The complete brain of a larval zebrafish by serial-section EM — the first vertebrate whole brain at EM resolution, and the dataset that made whole-brain structure-and-function comparison possible in a vertebrate.
- Species: Danio rerio (larva, 5.5 days post-fertilization)
- Region: Complete brain
- Method: Serial-section EM at multiple scales, co-registered with in vivo two-photon imaging
2020
Hemibrain — Drosophila central brain
A densely reconstructed half of the Drosophila central brain, imaged by FIB-SEM at isotropic resolution and the dataset on which most fly circuit analysis before FlyWire was built.
- Species: Drosophila melanogaster (female)
- Region: Central brain (~50%)
- Cells: ~25,000 neurons
- Synapses: ~20 million
- Method: FIB-SEM
- Size: ~100 TB
2020
Witvliet et al. — C. elegans connectomes across development
Eight complete worm brains at different developmental stages — the only dataset that shows how a connectome changes as an animal grows, and how much varies between individuals.
- Species: Caenorhabditis elegans
- Region: Whole brain, 8 isogenic individuals
- Method: Serial-section EM
2021
H01 — human cortical fragment
A cubic millimetre of human temporal cortex, imaged by serial-section EM and reconstructed automatically. It is the largest published volume of human brain at synaptic resolution, and the only one most learners will ever meet.
- Species: Human
- Region: Temporal lobe cerebral cortex
- Cells: ~57,000
- Synapses: ~150 million
- Method: Serial-section EM (ssEM)
- Size: 1.4 PB
2021
Phelps, Hildebrand & Graham — Drosophila ventral nerve cord
Motor control circuits in the adult fly ventral nerve cord, and the dataset that introduced GridTape automated section collection.
- Species: Drosophila melanogaster (female)
- Region: Ventral nerve cord
- Cells: 507 limb motor neurons reconstructed
- Method: GridTape automated TEM
2023
MANC — male adult nerve cord
A dense connectome of the male fly ventral nerve cord, and the counterpart to FANC — the pair is the field's best evidence on how much of a connectome is sex-specific rather than species-typical.
- Species: Drosophila melanogaster (male)
- Region: Ventral nerve cord
- Method: FIB-SEM, dense reconstruction
2023
MouseConnects (HI-MC) — mouse hippocampus
The NIH BRAIN CONNECTS effort to reconstruct 10 mm³ of mouse hippocampal formation — an order of magnitude beyond any volume yet completed.
- Species: Mouse (C57BL/6)
- Region: Hippocampal formation
- Method: High-throughput EM
- Size: >10 PB projected
2023
Wildenberg et al. — cortical synapse development across species
Synaptic development compared across mouse and primate cortex — one of the few EM datasets built for a cross-species question.
- Species: Mouse and primate
- Region: Cortical synapses
- Method: EM reconstruction, developmental comparison
2024
FANC — female adult nerve cord
The reconstructed female fly ventral nerve cord: 14,600 cell bodies and about 45 million synapses, with leg and wing motor neurons mapped to the muscles they drive.
- Species: Drosophila melanogaster (female)
- Region: Ventral nerve cord
- Cells: 14,600 neuronal cell bodies
- Synapses: ~45 million
- Method: Serial-section TEM (GridTape), automated segmentation
2024
FlyWire — complete adult fly brain
The first complete connectome of an adult animal brain: every neuron, every synapse, hierarchically annotated, and proofread by a distributed community over several years.
- Species: Drosophila melanogaster (female)
- Region: Whole brain, including optic lobes
- Cells: 139,255 neurons; 8,453 cell types
- Synapses: ~54.5 million
- Method: Serial-section TEM, community proofread
- Size: ~50 TB
2025
MICrONS — mouse visual cortex
A cubic millimetre of mouse visual cortex where the same neurons were both recorded in a living animal and reconstructed in EM. It is the only large volume that lets you ask what a measured cell is wired to.
- Species: Mouse
- Region: Visual cortex (VISp, VISrl, VISal, VISlm)
- Cells: ~200,000 anatomical; ~75,000 functionally imaged
- Synapses: 523 million
- Method: Serial-section EM co-registered with two-photon calcium imaging
- Size: 1.6 PB
2026
BANC — brain and nerve cord connectome
The first connectome to join a fly's brain and ventral nerve cord in one reconstruction, closing the gap that made descending and ascending neurons untraceable.
- Species: Drosophila melanogaster
- Region: Brain and ventral nerve cord, united
- Method: Serial-section EM, dense reconstruction
BossDB hosts many datasets beyond these. Browse bossdb.org/projects for the rest.
Dataset Categories
Connectomics datasets vary in scope, species, and methodology. Understanding these categories helps you choose the right data for your learning goals.
By Species
- C. elegans: Simple, complete nervous system (302 neurons)
- Drosophila: Complex invertebrate brain (~140,000 neurons)
- Mouse: Mammalian cortical circuits (thousands to millions of neurons)
- Human: Cortical samples (tens of thousands of neurons)
By Resolution
- Synaptic: Individual synapses and connections
- Cellular: Complete neuronal morphologies
- Circuit: Functional neural networks
- Regional: Large-scale brain organization
By Data Type
- Structural: Electron microscopy-based anatomy
- Functional: Calcium imaging or electrophysiology
- Multimodal: Combined structural and functional data
- Comparative: Multiple species or conditions
Accessing These Datasets
Most datasets are freely available through dedicated platforms. Each dataset entry above includes direct links to data portals, original publications, and popular press coverage where available.
The gap between "the data is public" and "I have a DataFrame" is where most new teams stall. This guide closes it: a four-level ladder from browser to imagery cutouts, the CAVE token walkthrough start to finish, version pinning, byte math, and a failure-signature table for when it breaks.
Curated example notebooks for downloading connectomics data from Google, the Allen Institute, Janelia, and bossDB — the notebook collection behind the getting-started ladder.