Interacting with the Fish1.5 Dataset

This page covers scripts for programmatic access to the Fish1.5 dataset using CAVE (Connectome Annotation and Versioning Engine).

Setup CAVE

  • To install CAVEclient use pip:
pip install caveclient
  • Once you have installed the CAVEclient, you need to set up your user token using the following notebook:

CAVE_setup.ipynb

Download Cellular Morphologies and Connectivity

  • This notebook explains how to retrieve morphology and input/output synapses for segmented objects:

download_mesh_and_synapses.ipynb

Retrieve Neuronal Activity

  • This part does not require CAVE setup.
  • The Fish1.5 calcium imaging dataset is available on Zenodo: Zenodo DOI
  • Use the following notebook to explore functional responses to random dots and sine gratings:

functional_responses.ipynb

Environment Setup

To ensure reproducibility and access to all dependencies, clone the GitHub repo and set up the environment using Conda:

git clone https://github.com/jboulanger91/fish1.5-notebooks.git
cd fish1.5-notebooks
conda env create -f environment.yml
conda activate fish-env

All necessary dependencies are included in the environment.yml file.

GitHub repository: https://github.com/jboulanger91/fish1.5-notebooks