Overview

This repository contains the code to generate the documentation website (https://leburnett.github.io/reiser-documentation). This documentation describes how to run electrophysiological experiments on the G4 ephys setup at HHMI's Janelia Research Campus.

Hardware:

Generation 4 Modular LED Display designed by Reiser lab members. Detailed documentation can be found at https://reiserlab.github.io/Modular-LED-Display/G4/.

Software:

Presenting stimuli to the G4 arena requires a local copy of the G4_Display_Tools repository (https://github.com/leburnett/G4_Display_Tools).

Experimental protocols:

Code for running different experimental protocols can be found in different Github repositories. The code found in these repositories contain a mixture of code that works using the G4 software tools (see link above) that run within a GUI, and custom scripts that work through the command line in MATLAB.

• 1: Direction selectivity probe protocol
• 2: Nested receptive field protocol

Freely-Walking Optomotor

Documentation for the freely-walking optomotor experiments is generated from the freely-walking-optomotor repository and published under the Freely-walking/ section of the site.

Dashboard

An interactive Dash dashboard for visualising processed freely-walking data:

# From anywhere in the terminal (requires the dash-freely alias):
dash-freely              # start the dashboard (opens http://localhost:8050)
dash-freely preprocess   # preprocess .mat files → Parquet first

See the freely-walking-optomotor README for setup instructions.

Pipeline Status Page

The automation pipeline generates a standalone HTML status page on the network drive showing the processing stage of every experiment:

# View on macOS (requires the network drive to be mounted):
open /Volumes/reiserlab/oaky-cokey/pipeline_status.html

This page is auto-regenerated by the processing machine whenever an experiment's pipeline status changes.