hctsa_phenotypingFly

Running hctsa analysis on movement speed data of fruit flies, Drosophila melanogaster, restricted to a one-dimensional tube and tracked continuously for between 3 and 6 days using video tracking. Data were measured and kindly provided by Quentin Geissmann (@qgeissmann) and Giorgio Gilestro (@giorgiogilestro). Movement speed was estimated as the maximum speed in each non-overlapping 10 s time window, from position measurements measured at approximately 2 Hz, where displacements were measured as the euclidean distance between successive coordinates of the fly.

A summary of key analysis results are in our Cell Systems publication.

Data are labeled with keywords M (male), F (female), day, and night, as well as region numbers, and day numbers (for multi-day experiments).

This repository requires hctsa to be installed and paths to this package added (through the startup.m script in hctsa). Also requires the data file, HCTSA.mat, containing the time-series data and the results of hctsa feature extraction. This file can be downloaded by running downloadComputedData (can also be found on figshare)

A summary of the functions included are below:

• dayNightAnalysis contains the main steps for determining movement differences between day and night
• maleFemaleAnalysis contains the main steps for distinguishing male from female movement
• fourWayClass contains the main steps for four-class classification across: (1) male-day, (2) male-night, (3) female-day, (4) female-night
• flyClassificationResults contains the steps for reproducing the classification accuracies of the different classification tasks.
• reproduceFigures reproduces the results in the figure of the implementation paper.