SWDB 2026 - Connectomics Workshop

Produced for: https://github.com/AllenInstitute/swdb_2026_student/wiki

The function of the nervous system arises out of a combination of the properties of individual neurons and of how they are connected into a larger network. The central goal of connectomics is to produce complete maps of the connectivity of the nervous system with synaptic resolution and analyze them to better understand the organization, development, and function of the nervous system.

Electron Microscopy (EM) data enables morphological reconstruction of neurons and resolution of their synaptic connectivity. The V1DD dataset is one of the largest volume EM datasets currently available, and spans all layers of mouse visual cortex. We will be using this dataset to query the connectivity between neurons in the visual cortex.

Module 1 - code\workshops\Module_1.ipynb will:

• introduce the basics of how synaptic connectivity is measured in EM connectomics
• examine reconstructions of individual neurons and their connectivity
• discuss how morphological features and connectivity suggest cell types
• explore how connectivity changes as function of target and distance

Module 2 - code\workshops\Module_2.ipynb will:

• introduce concepts of network connectivity
• investigate the role of cell type in the structure of networks
• consider connection probability as a function of distance
• incorporate ophys recordings and map the correlation of structure to function

CodeOcean Capsule: https://codeocean.allenneuraldynamics.org/capsule/0103497/tree

Github Repository: https://github.com/AllenSWDB/SWDB_2026_Connectomics

Local development instructions

For locally copying the data asset:

uvx --from awscli aws s3 cp --recursive --no-sign-request \
  "s3://aind-open-data/v1dd-analysis-1196-1_2025-08-14_16-38-00/" \
  "data/v1dd_1196"

For setting the data dir for local runs:

export SWDB_DATA_ROOT="{correct path for your machine}/SWDB_2026_Connectomics/data"

Or put into a .env file

SWDB_DATA_ROOT={correct path for your machine}/SWDB_2026_Connectomics/data

You may need to add a .vscode/settings.json with the following to have that picked up automatically

{
    "python.terminal.useEnvFile": true
}