External sources

SynDB supports importing connectomics data from 20+ major connectome datasets. This page covers the most common imports. See the CLI Reference for the full list of supported datasets.

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 on the GUI.

FlyWire

FlyWire connectomics data can be imported from CAVE CSV exports.

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

The Hemibrain v1.2.1 dataset from Janelia FlyEM can be downloaded directly from Google Cloud Storage.

Download the dataset:

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

Validate the data directory:

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

Import into your dataset:

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

MANC (Male Adult Nerve Cord)

The MANC / MaleCNS v0.9 dataset from Janelia FlyEM uses Apache Arrow Feather files.

Download the dataset:

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

Validate the data directory:

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

Import into your dataset:

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.