Core Concepts & Methods
Build scientific and technical fluency in nanoscale connectomics from motivation through analysis methods.
Fadel: Knowledge, Skills
Pathways: technical foundation, methods depth, analytical reasoning
Connectomics Datasets
Learn with real scientific data from groundbreaking research.
Explore carefully curated datasets from landmark connectomics studies. Each dataset represents years of cutting-edge research and offers unique insights into neural circuit organization.
How Datasets Fit the Tracks
Datasets power all three tracks: concept-building, hands-on research practice, and professional growth through authentic scientific context.
Research in Action
Apply concepts in practical workflows, quality control, tools, and reproducible research operations.
Fadel: Skills, Meta-learning
Pathways: research workflow, reproducibility, project execution
Career & Community
Navigate hidden curriculum, mentorship, professional growth, and inclusive research identity development.
Fadel: Character, Meta-learning
Pathways: mentoring, professional growth, hidden curriculum
Dataset Pages (Generated Cards)
Accessing Public EM Datasets
Electron microscopy
Practical guide for finding, downloading, and working with public EM datasets.
MouseConnects Connectomics Workflow
Electron microscopy pipeline
Step-by-step MouseConnects pipeline from sample preparation to connectome analysis.
MouseConnects Dataset – Complete Hippocampal Connectome
Serial electron microscopy with multi-modal integration
Overview of the MouseConnects HI-MC dataset, technology stack, collaborators, and scientific goals.
MouseConnects: HI-MC Spotlight
A flagship $40M NIH BRAIN CONNECTS effort to reconstruct 10 mm³ of mouse hippocampal formation at nanometer resolution—the most ambitious connectomics project ever undertaken.
- Species: Mouse (C57BL/6)
- Target Volume: 10 mm³
- Estimated Size: >10 PB
- Resolution: 8 nm isotropic
🌟 Featured Datasets
A 1.4 petabyte rendering of a small sample of human brain tissue, imaged at 4nm-resolution by serial section electron microscopy, reconstructed and annotated by automated computational techniques. The dataset comprises roughly one cubic millimeter of brain tissue, including tens of thousands of reconstructed neurons, millions of neuron fragments, 130 million annotated synapses, 104 proofread cells, and many additional subcellular annotations.
- Species: Human
- Region: Temporal lobe cerebral cortex
- Volume: ~1 mm³
- Neurons: ~50,000 cells
- Synapses: 130 million
- Size: 1.4 PB
Dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher visual areas (VISrl, VISal and VISlm) in an awake mouse viewing natural and synthetic stimuli. The functional data were co-registered with a volumetric electron microscopy reconstruction containing more than 200,000 cells and 0.5 billion synapses.
- Species: Mouse
- Region: Visual cortex (VISp, VISrl, VISal, VISlm)
- Volume: 1.4mm × 0.87mm × 0.84mm
- Functional Neurons: ~75,000
- Anatomical Cells: ~200,000
- Synapses: 523 million
- Size: 1.6 PB
AI-segmented, expert-proofread neurons of a whole-brain connectome of an adult female Drosophila with 139,255 neurons and 50 million synaptic connections. The first complete connectome of an adult animal brain, including systematic hierarchical annotation of neuronal classes, cell types and developmental units.
- Species: Drosophila melanogaster (female)
- Region: Complete brain and optic lobes
- Volume: Whole brain
- Neurons: 139,255
- Synapses: 50+ million
- Cell Types: 8,453
- Size: ~50 TB
Dense reconstruction of a portion of the central brain of Drosophila melanogaster, revealing circuits for learning, navigation, and circadian rhythms.
- Species: Drosophila melanogaster (female)
- Region: Central brain (~50%)
- Volume: 250×250×250 μm
- Neurons: ~25,000
- Synapses: ~20 million
- Size: ~100 TB
📅 Connectomics Timeline
1986
C. elegans Complete Connectome (White et al.)
The structure of the nervous system of the nematode Caenorhabditis elegans - the first complete nervous system ever mapped, establishing the field of connectomics.
- Species: C. elegans
- Neurons: 302
- Synapses: ~7,000
- Size: <1 GB
2011
Bock et al. - Mouse Retinal Circuits
Network anatomy and in vivo physiology of visual cortical neurons mapping mouse retinal circuits for visual motion detection using serial block-face scanning electron microscopy.
- Species: Mouse
- Region: Retina
- Volume: ~250 μm³
- Size: ~12 TB
2013
Helmstaedter et al. - Mouse Retinal Connectome
Connectomic reconstruction of the inner plexiform layer in the mouse retina providing dense circuit reconstruction and analysis of retinal circuitry.
- Species: Mouse
- Region: Retina (inner plexiform layer)
- Volume: TBD
- Size: TBD
2015
Kasthuri et al. - Mouse Visual Cortex
Saturated reconstruction of a volume of neocortex - first high-resolution connectome of mammalian cortex using automated methods to reconstruct neural circuits.
- Species: Mouse
- Region: Visual cortex
- Volume: ~1,700 μm³
- Size: ~1 TB
2016
Lee et al. - Mouse Visual Cortex Network
Anatomy and function of an excitatory network in the visual cortex examining local circuit organization in mouse primary visual cortex.
- Species: Mouse
- Region: Visual cortex
- Volume: TBD
- Size: TBD
2020
Hemibrain - Drosophila Central Brain
Dense reconstruction of a portion of the central brain (hemibrain) of Drosophila melanogaster, containing circuits critical for associative learning in the mushroom body, navigation and sleep in the central complex, and circadian rhythms among clock circuits.
- Species: Drosophila melanogaster (female)
- Region: Central brain (~50%)
- Volume: 250×250×250 μm
- Neurons: ~25,000
- Synapses: ~20 million
- Size: ~100 TB
2021
H01 - Human Cortical Sample
A 1.4 petabyte rendering of a small sample of human brain tissue from the temporal lobe, imaged at nanoscale-resolution and reconstructed by automated computational techniques.
- Species: Human
- Region: Temporal lobe cerebral cortex
- Volume: ~1 mm³
- Cells: ~57,000 total
- Synapses: 130 million
- Size: 1.4 PB
2024
FlyWire - Complete Adult Fly Brain
Whole-brain connectome of an adult female Drosophila with AI-segmented, expert-proofread neurons and comprehensive cell type annotations - the first complete connectome of an adult animal brain.
- Species: Drosophila melanogaster (female)
- Region: Complete brain and optic lobes
- Volume: Whole brain
- Neurons: 139,255
- Synapses: 50+ million
- Size: ~50 TB
2025
MICrONS - Mouse Visual Cortex Functional Connectome
Functional connectomics dataset spanning multiple areas of mouse visual cortex with dense calcium imaging co-registered with electron microscopy reconstruction, linking structural connectomics with functional recordings.
- Species: Mouse
- Region: Visual cortex (VISp, VISrl, VISal, VISlm)
- Volume: ~1 mm³
- Functional Neurons: ~75,000
- Total Cells: ~200,000
- Synapses: 523 million
- Size: 1.6 PB
🗃️ Additional BossDB Hosted Datasets
BossDB is a great resource for many additional connectomics datasets (though not all). Explore bossdb.org/projects for more. Notable examples include:
Wildenberg et al. (2023)
Isochronic development of cortical synapses in primates and mice - investigating synaptic development across species using electron microscopy and connectomic reconstruction approaches.
- Species: Mouse, Primate
- Region: Cortical synapses
- Type: Developmental comparison
- Size: TBD
Phelps, Hildebrand & Graham (2021)
Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. GridTape technology enabled automated serial-section collection with high-throughput TEM to generate a synaptic resolution dataset of the adult female Drosophila ventral nerve cord.
- Species: Drosophila melanogaster (female)
- Region: Ventral nerve cord (VNC)
- Motor Neurons: 507 limb motor neurons
- Method: GridTape automated TEM
- Size: TBD
Witvliet et al. (2020)
Connectomes across development reveal principles of brain maturation in C. elegans. Serial-section electron microscopy reconstruction of the full brain of eight isogenic C. elegans individuals across postnatal stages to investigate developmental changes with age.
- Species: C. elegans
- Individuals: 8 isogenic animals
- Developmental Stages: Birth to adulthood
- Focus: Developmental brain maturation
- Size: TBD
Morgan et al. (2020)
An individual interneuron participates in many kinds of inhibition and innervates much of the mouse visual thalamus. Serial electron microscopy annotation of all input synapses (862) and output synapses (626) associated with one inhibitory interneuron in the visual thalamus.
- Species: Mouse
- Region: Visual thalamus (lateral geniculate nucleus)
- Synapses: 1,488 total (862 input, 626 output)
- Focus: Single interneuron connectivity
- Size: TBD
Wilson et al. (2019)
Developmental Rewiring between Cerebellar Climbing Fibers and Purkinje Cells Begins with Positive Feedback Synapse Addition. Serial electron microscopy datasets reconstructed from mice during the first postnatal week to understand climbing fiber-Purkinje cell synaptic reorganization during cerebellar development.
- Species: Mouse
- Region: Cerebellum (cerebellar cortex)
- Ages: Postnatal days 3 and 7 (P3, P7)
- Focus: Climbing fiber-Purkinje cell connectivity
- Method: Serial-section scanning electron microscopy
- Size: TBD
Wanner et al. (2016)
Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb. Reconstruction of ~98% of all neurons (>1,000) in the olfactory bulb of a zebrafish larva using 3D electron microscopy with high accuracy and annotated synapses.
- Species: Zebrafish (larva)
- Region: Olfactory bulb
- Neurons: >1,000 (~98% coverage)
- Method: 3D electron microscopy
- Size: TBD
Takemura et al. (2013)
A visual motion detection circuit suggested by Drosophila connectomics. Semi-automated electron microscopy pipeline to reconstruct a connectome containing 379 neurons and 8,637 chemical synaptic contacts within the Drosophila optic medulla, identifying cell types constituting a motion detection circuit.
- Species: Drosophila melanogaster
- Region: Optic medulla
- Neurons: 379
- Synapses: 8,637 chemical
- Size: TBD
🔍 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.
Step-by-step guides and example notebooks for downloading connectomics data from Google, the Allen Institute, Janelia, and bossDB.