External Sources

SynDB supports importing connectomics data from 20+ major connectome datasets. This page covers the supported imports grouped by organism. See the CLI Reference for the complete command reference.

Note

Dataset UUID

The <syndb-dataset-id> is the UUID of the SynDB dataset that will be associated with the imported data. You can copy and paste it from the dataset management page in the web UI.

What SynDB Needs From External Groups

When we say that we need the “full dataset” for SynDB ingestion, we do not mean the raw imaging volume. We mean the complete analysis-ready release needed to populate the SynDB tables for a dataset version.

For most connectomics imports, that means:

the complete neuron or object table for the release
the complete synapse table for the same release, or an aggregated connection table if that is the available downstream artifact
stable source identifiers such as root_id, pre_pt_root_id, and post_pt_root_id
coordinates and annotations needed to map the source schema into SynDB
optional morphology assets such as swc/ or meshes if they are part of the release

What this usually does not mean:

raw microscopy image stacks or volume tiles
Neuroglancer or CAVE precomputed segmentation volumes by themselves
ongoing operational access to the source group’s infrastructure after a static export has been produced

Preferred handoff

The preferred handoff is a static snapshot in an S3 or MinIO-compatible bucket, or an equivalent directory export with the same files. If the source data lives in CAVE, export the materialized tables first and hand off the files; SynDB imports the exported tables, not CAVE itself.

In practical terms, the source group’s involvement is usually limited to:

granting permission for SynDB to ingest and redistribute the agreed downstream artifacts
providing the exported snapshot in an agreed format
answering schema questions if a column needs clarification

For a typical neuron and synapse release, the handoff looks like:

dataset-name/
  neurons.csv.gz
  synapses.csv.gz
  connections.csv.gz   # optional aggregated fallback
  swc/                 # optional morphology assets
  meshes/              # optional geometry assets

Note

Organelle coverage is separate

Public SynDB support for a dataset’s neuron and synapse import path does not imply that vesicle or mitochondria tables are also available. For the current Hemibrain, MANC/Male CNS, MICrONS, and H01 production paths, SynDB imports neurons and synapses only. Any organelle-backed workflow such as manuscript CF08 needs a separate upstream snapshot or manual export path plus matching ETL wiring before production can populate those tables.

Drosophila melanogaster

FlyWire

Whole-brain Drosophila connectome reconstructed from a full adult female brain (FAFB). Data is exported from CAVE in CSV format.

Source: FlyWire Codex | Publication: Dorkenwald et al., 2024. Nature

Validate your FlyWire data directory:

syndb etl flywire validate --data-dir external_datasets/FlyWire

Import into your dataset:

syndb etl flywire import \
  --data-dir external_datasets/FlyWire \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

FlyWire also supports a synapses-detailed table for individual synapse positions (large, batched import).

Hemibrain

Half-brain connectome of an adult Drosophila from the Janelia FlyEM project (v1.2.1). Contains ~25,000 neurons with traced morphology and synaptic connections.

Source: Janelia FlyEM Hemibrain | Publication: Scheffer et al., 2020. eLife

Download the dataset:

syndb etl hemibrain download --output-dir external_datasets/Hemibrain --extract

Validate and import:

syndb etl hemibrain validate --data-dir external_datasets/Hemibrain

syndb etl hemibrain import \
  --data-dir external_datasets/Hemibrain \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

MANC (Male Adult Nerve Cord)

Connectome of the male Drosophila ventral nerve cord (VNC). Data is distributed as Apache Arrow Feather files.

Source: Janelia FlyEM MANC | Publication: Takemura et al., 2024. Nature

Download the dataset:

syndb etl manc download --output-dir external_datasets/MANC

Validate and import:

syndb etl manc validate --data-dir external_datasets/MANC

syndb etl manc import \
  --data-dir external_datasets/MANC \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Warning

Download size

The MANC dataset includes the connectome-weights Feather file (~1.1 GB). Ensure sufficient disk space before downloading.

Male CNS

Male Drosophila central nervous system connectome from Janelia FlyEM. Covers the brain and ventral nerve cord with neuron-level connectivity.

Source: Google Cloud Storage | Publication: Takemura et al., 2024. Nature

Download and import:

syndb etl male-cns download --output-dir external_datasets/MaleCNS

syndb etl male-cns validate --data-dir external_datasets/MaleCNS

syndb etl male-cns import \
  --data-dir external_datasets/MaleCNS \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

FANC (Female Adult Nerve Cord)

Connectome of the female Drosophila ventral nerve cord, enabling sex-specific comparisons with MANC. SynDB imports a static export of the FANC neuron and synapse tables, not the live CAVE deployment itself.

Publication: Phelps et al., 2021. Cell

Download the maintained public export:

syndb etl fanc download --output-dir external_datasets/FANC

If you are working from a custom local export instead, you can still prepare it separately:

syndb-export fanc --out-dir external_datasets/FANC --no-upload

Then validate and import:

syndb etl fanc validate --data-dir external_datasets/FANC

syndb etl fanc import \
  --data-dir external_datasets/FANC \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Optic Lobe

Drosophila optic lobe connectome from Janelia FlyEM. Maps the visual processing circuitry of the fly brain.

Source: Google Cloud Storage | Publication: Matsliah et al., 2024. Nature

syndb etl optic-lobe download --output-dir external_datasets/OpticLobe

syndb etl optic-lobe validate --data-dir external_datasets/OpticLobe

syndb etl optic-lobe import \
  --data-dir external_datasets/OpticLobe \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

BANC (Brain And Nerve Cord)

Whole-body Drosophila connectome covering the brain and ventral nerve cord in a single female specimen.

Publication: Jasper et al., 2024

syndb etl banc download --output-dir external_datasets/BANC

syndb etl banc validate --data-dir external_datasets/BANC

syndb etl banc import \
  --data-dir external_datasets/BANC \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

L1 Larval

Complete connectome of the first-instar Drosophila larval brain (~3,000 neurons), the first whole-brain connectome of any insect.

Source: GitHub | Publication: Winding et al., 2023. Science

syndb etl larval download --output-dir external_datasets/L1Larval

syndb etl larval validate --data-dir external_datasets/L1Larval

syndb etl larval import \
  --data-dir external_datasets/L1Larval \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Mouse

MICrONS (Minnie65)

Cubic millimeter of mouse visual cortex reconstructed at synaptic resolution by the MICrONS Consortium. Contains ~80,000 neurons and millions of synapses.

Source: MICrONS Explorer | Publication: MICrONS Consortium et al., 2021. bioRxiv

syndb etl microns download --output-dir external_datasets/MICrONS

syndb etl microns validate --data-dir external_datasets/MICrONS

syndb etl microns import \
  --data-dir external_datasets/MICrONS \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Spine Morphometry

Dendritic spine morphological measurements from electron microscopy. Three sub-datasets are supported:

Variant	Key	Source	Publication
Kasthuri	`kasthuri`	Columbia Academic Commons	Kasthuri et al., 2015. Cell
Ofer	`ofer-confocal`	Zenodo	Ofer et al., 2022
MICrONS	`microns`	Zenodo	Derived from MICrONS cortical data

syndb etl spine-morphometry download --source kasthuri --output-dir external_datasets/SpineKasthuri

syndb etl spine-morphometry validate \
  --source kasthuri \
  --data-dir external_datasets/SpineKasthuri

syndb etl spine-morphometry import \
  --data-dir external_datasets/SpineKasthuri \
  --dataset-id <syndb-dataset-id> \
  --source kasthuri

Human

H01

One cubic millimeter of human temporal cortex at nanometer resolution. Contains reconstructed neurons, synapses, and glia from a neurosurgical tissue sample.

Source: Google Cloud Storage | Publication: Shapson-Coe et al., 2024. Science

syndb etl h01 download --output-dir external_datasets/H01

syndb etl h01 validate --data-dir external_datasets/H01

syndb etl h01 import \
  --data-dir external_datasets/H01 \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

C. elegans

C. elegans Hermaphrodite

Complete connectome of the adult hermaphrodite C. elegans (~300 neurons), the first organism with a fully mapped nervous system. Data sourced from the OpenWorm ConnectomeToolbox.

Source: OpenWorm ConnectomeToolbox | Publication: Cook et al., 2019. Nature

syndb etl celegans download --output-dir external_datasets/CElegansHerm

syndb etl celegans validate --data-dir external_datasets/CElegansHerm

syndb etl celegans import \
  --data-dir external_datasets/CElegansHerm \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

C. elegans Male

Complete connectome of the adult male C. elegans, enabling sex-specific neural circuit comparisons.

Source: OpenWorm ConnectomeToolbox | Publication: Cook et al., 2019. Nature

syndb etl celegans-male download --output-dir external_datasets/CElegansMale

syndb etl celegans-male validate --data-dir external_datasets/CElegansMale

syndb etl celegans-male import \
  --data-dir external_datasets/CElegansMale \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

C. elegans Developmental

Connectomes across eight developmental stages of C. elegans, tracking how neural circuits are assembled during growth.

Source: GitHub | Publication: Witvliet et al., 2021. Nature

syndb etl witvliet download --output-dir external_datasets/CElegansDev

syndb etl witvliet validate --data-dir external_datasets/CElegansDev

syndb etl witvliet import \
  --data-dir external_datasets/CElegansDev \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Other Organisms

Platynereis dumerilii

Whole-body connectome of the marine annelid Platynereis dumerilii, a three-day-old larva with ~5,000 neurons.

Source: GitHub | Publication: Verasztó et al., 2024. bioRxiv

syndb etl platynereis download --output-dir external_datasets/Platynereis

syndb etl platynereis validate --data-dir external_datasets/Platynereis

syndb etl platynereis import \
  --data-dir external_datasets/Platynereis \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Fish1 (Larval Zebrafish)

Larval zebrafish (Danio rerio) brain connectome. Data is accessed through CAVE and requires manual export with Google OAuth authentication.

Note

Manual export

Fish1 data requires CAVE API access with Google credentials. Export a static neuron table plus either a full synapse table or an aggregated connections table, then use the validate and import commands.

Show the expected export layout:

syndb etl fish1 cave-instructions

Or export directly to a local directory:

syndb-export fish1 --out-dir external_datasets/Fish1 --no-upload

syndb etl fish1 validate --data-dir external_datasets/Fish1

syndb etl fish1 import \
  --data-dir external_datasets/Fish1 \
  --dataset-id <syndb-dataset-id> \
  --table neurons \
  --table synapses

Multi-species Databases

Allen Cell Types

Reference electrophysiology and morphology data from the Allen Institute for Brain Science. Covers mouse and human cortical neuron types with standardized measurements.

Source: Allen Cell Types Database | API: Allen Brain Map API

syndb etl allen-cell-types download --output-dir external_datasets/AllenCellTypes

syndb etl allen-cell-types validate --data-dir external_datasets/AllenCellTypes

syndb etl allen-cell-types import \
  --data-dir external_datasets/AllenCellTypes \
  --dataset-id <syndb-dataset-id> \
  --table neurons

NeuroMorpho

Curated archive of digitally reconstructed neuron morphologies from NeuroMorpho.org. Contains 200,000+ reconstructions across 100+ species.

Source: NeuroMorpho.org | Publication: Ascoli et al., 2007. Journal of Neuroscience

syndb etl neuromorpho download --output-dir external_datasets/NeuroMorpho

syndb etl neuromorpho validate --data-dir external_datasets/NeuroMorpho

syndb etl neuromorpho import \
  --data-dir external_datasets/NeuroMorpho \
  --dataset-id <syndb-dataset-id> \
  --table neurons

Keyboard shortcuts

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