Accessing Public EM Datasets

Resources and notebooks for downloading and exploring connectomics data.

# Example Notebooks for EM Connectomics Datasets A collection of example notebooks for accessing major public Electron Microscopy (EM) connectomics datasets.

New to the data entirely? Start with Getting Started with Data — the four-level ladder that tells you which of these ecosystems your question lives in, walks through token setup, and lists the failure signatures. The notebooks below are the per-platform examples behind it.

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Fly & Human

Google Research (FAFB & H01)

Access FlyWire and the H01 human cortex dataset using caveclient.

pip install caveclient
CAVEclient Basics
Advanced Queries

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Mouse Cortex

Allen Institute MICrONS

Download the MICrONS dataset via the allensdk Python library.

pip install allensdk
MICrONS Data Access
Visualizing Meshes

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Fly Brain

Janelia Hemibrain

Work with the hemibrain connectome using neuprint-python.

pip install neuprint-python
neuPrint Starter Guide
Common Recipes

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Multiple Datasets

bossDB Resources

Explore a variety of EM volumes hosted on bossDB using the intern client.

pip install intern
bossDB Cutout Example

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Visualization

General Tools

Visualize data in-browser with Neuroglancer or analyze it locally with Napari.