locate_and_measure_particles: Function to extract morphological measurements and X- and...

In pennekampster/bemovi: BEMOVI, software for extracting BEhaviour and MOrphology from VIdeos

Description

Function calls ImageJ software and its ParticleAnalyzer function to extract for each frame of the video several morphological descriptors and the X- and Y-coordinates of all moving particles. All videos in the raw.video.folder are analyses, separately.

Usage

locate_and_measure_particles(to.data, raw.video.folder, particle.data.folder,
  difference.lag, min_size = 0, max_size = 10000, thresholds = c(10, 255),
  IJ.path, memory = 512)

Arguments

to.data	path to the working directory
raw.video.folder	directory with the raw video files
particle.data.folder	directory to which the data is saved as a text file
difference.lag	numeric value specifying the offset between two video frames to compute the difference image. If 0, then no differencing applied.
min_size	minimum size for detection of particles
max_size	maximum size for detection of particles
thresholds	vector containing the min and max threshold values (defaults to c(10,255))
IJ.path	path to ImageJ folder, containing the 'ij.jar' executable
memory	numeric value specifying the amount of memory available to ImageJ (defaults to 512)

Value

saves the output of the ParticleAnalyzer function of ImageJ as a text file in the output directory and then assembles the data into a single database called 'particle.RData'. This data.frame contains information about the following properties: the area (transversal cut), the mean, minimum and maximum of the grey value, the perimeter, width, length and angle with the dominant-axis of a fitted ellipse, and finally shape parameters such as circularity, aspect ratio, roundness and solidity. For details of the morphological output, please refer to http://rsbweb.nih.gov/ij/docs/guide/146-30.html

pennekampster/bemovi documentation built on May 25, 2019, 12:46 a.m.