Spike Video

Overview

Create different animated plots from electrophysiology data to be synchronsed and added to a video.

Main Features

• Generate Animated Spike Plot
  • Sliding Window -- A clipping window of fixed width slides over the duration
  • Rolling Window -- The spikes apeear with time over the entire duration
• Generate Animated Raster Plot
• Generate Animated Histogram
• Generate Audio to go with the plots
• Merge all animation with video into one video

Additional Features

• Primitive Caching
• Dockerised Applet

Dependencies

• FFmpeg
• ImageMagick
• Python3 requirements

Setup

This package can be used using Docker to avoid tedious installations, especially on Windows.

The included Dockerfile builds an image with all requirements installed. From the associated container, a Jupyter notebook via Jupyter Lab at http://localhost:8887/lab/tree/application.ipynb is served which can give a sandboxed access to the package.

1. Install Docker {Linux, Windows}.

2. Build Docker image.

   docker build . --tag spike_video

3. Create and run Docker container.

   1. Linux

      docker run -d -p 127.0.0.1:8887:8888 --name spike_video -v $(pwd)/data:/app/data -v $(pwd)/output:/app/.temp -v $(pwd)/notebooks:/app/notebooks spike_video

   2. Windows (PowerShell)

      docker run -d -p 127.0.0.1:8887:8888 --name spike_video -v ${pwd}/data:/app/data -v ${pwd}/output:/app/.temp -v ${pwd}/notebooks:/app/notebooks spike_video

   Note: The names of folders used for output are different in the host and the Docker container/application.

   Host	Container
   output	.temp

4. Go to http://localhost:8887/lab/tree/application.ipynb.

The script setup.ps1/setup.sh provides commands 2, 3, and 4 above. Run it with PowerShell/'sh' respectively.

Running/Stopping

Start

docker start spike_video

Stop

docker stop spike_video