Summary analysis of Locomotion experiments on the Multi-worm Tracker

The aim of this project is to create software that can be used after running a 600s basal locomotion experiment using the Multi-worm tracker (Swierczek et al., 2011) to generate summary figures and statistics for that experiment.

Figures it generates

• Speed versus time over experiment duration
• Radial and boxplot pathlength figures from 530-590s
• Spontaneous reversals/minute box plot (averaged over 470-590s)
• Body size box plots (area, length and width)

Statistics reported

• Mean initial speed (averaged over 30-45s) for each strain, and ANCOVA comparing to wild-type
• Mean final speed (averaged over 575-590s) for each strain, and ANCOVA comparing to wild-type
• Mean pathlength measured over 530-590s for each strain, and ANCOVA comparing to wild-type
• Mean number of spontaneous reversals/minute (averaged over 470-590s) for each strain, and ANCOVA comparing to wild-type
• Mean area, length and width for each strain, and ANCOVA comparing to wild-type

How to use it

Installation Dependencies

Java, Python and the Multi-worm Tracker Analysis software (Chore.jar) as a shell script in the executable path named Chore.

To "easily" do this on a Mac or Linux OS, please follow the following installation instructions:

For Mac OSX

1. Install Homebrew by typing the following into the command line:

   ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
   

2. Install the Multi-worm Tracker Analysis software via Homebrew to install Chore.jar and have it accesible as a shell script in the executable path named "Chore":

   brew install homebrew/science/multi-worm-tracker
   

For Linux

1. Install Linuxbrew by typing the following into the command line:

   ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)"
   

2. Put brew in your executable path by adding the commands below to either .bashrc or .zshrc:

   export PATH="$HOME/.linuxbrew/bin:$PATH"
   export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"
   export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"
   

3. Install the Multi-worm Tracker Analysis software via Homebrew to install Chore.jar and have it accesible as a shell script in the executable path named "Chore":

   brew install homebrew/science/multi-worm-tracker

Running the analysis

• Set working directory to project's root directory

• Call locomotion_driver.sh from the Bash Shell

• locomotion_driver.sh requires the following arguments from the user: 1) the gigabytes of memory to be used to run Choreography, 2) the path to the directory containing the data, and 3) the path to the directory where the results should be saved. Note - this script must be called from the parent directory of the bin directory containing the locomotion_driver.sh and locomotion.py scripts

Example:

bash bin/locomotion_driver.sh 16 data results