A MATLAB function for analysing worm movement / growth from movies. The variance through time for each pixel in the plate is calculated, and the distribution of these variances examined. Pixels whose variance is greater than a threshold of the mean plus one standard deviation are determined to be “motile”.
Calls invappParagon for series of image files in a directory, then assembles a large table containing movement index and thrashing rate with the filename as experiment descriptor, and produces a movement image as a diagnostic.
invappParagonBatch(folder)
where folder is the path to a folder containing the image files
output will be written there in an analysis folder
invappParagonBatch(folder, optionalArguments)
where optional arguments is a cell array list of first the name of an optional argument, and then the value to use
for example: invappParagonBatch(folder,{'plateRows',4})
Arguments:
'plateColumns' Default: 12
'plateRows' Default: 8
'movementIndexThreshold' Default: 1 Threshold for movement index moving/not moving pixels.
'wellCircularMark' Default: 0
An array of circular masks can be applied to the movie to ignore apparent movement outside circular wells (typically due to changes in illumination or vibration during movie capture). If 0 there is no masking of areas of a plate outside the well. Otherwise values from 0-1 = circular mask radius as a proportion of the width/height of the rectangle containing the well