Zebrafish

The implementation of the paper : An Automatic Method to Calculate Heart Rate from Zebrafish Larval Cardiac Videos

Setup

1. mkdir input output
2. Install dependencies or use our docker image:

Install dependencies

1. install libav
2. install cairo
3. install node.js
4. npm i

Use docker image

For building a local image: docker build -t zebrafish:standalone .

For using a existing image: docker pull st9007a/zebrafish:standalone

Run docker: docker run -it st9007a/zebrafish:standalone /bin/bash

Usage

For running in local:

1. Put you video into input folder
2. Run the software:

Usage: node zebrafish.js [video] [theda]

Arguments:
  video  the relative path of the video (.mov format) to analyze
  theda  the threshold to binarize a grayscale image (`0.96` is suggested)

The result is stored in `output/[VIDEO]/[THEDA]/custom-init-kmeans-centroids/result.json`

For running in the docker container:

1. Put you video into input folder
2. Start the container:

Usage: ./run_docker.sh [input directory] [output directory]

Arguments:
  input directory   the absolute path of your `input` folder
  output directory  the absolute path of your `output` folder

3. Run the software:

Usage: node zebrafish.js [video] [theda]

Arguments:
  video  the relative path of the video (.mov format) to analyze (ex: input/xxx.mov)
  theda  the threshold to binarize a grayscale image (`0.96` is suggested)

The result is stored in `output/[VIDEO]/[THEDA]/custom-init-kmeans-centroids/result.json`