pixSum: Sum pixel intensity above threshold

In jtheorell/pixSum: Summation of pixel intensities above threshold in png images and tiff movies

Description

In this function, we use the input from the quantCutoff function to sum the pixel intensity in the fraction above the threshold for individual images.

Usage

pixSum(imageList, quantCutThreshold)

Arguments

imageList	Either a named list of images, as with the example file, or a vector of RGB png file names, e.g. generated with list.files(). The second option is preferred, as this is a more reasonable method from a memory perspective.
quantCutThreshold	A result from the quantCutoff function on a relevant control dataset. NB! The same controls can be included in the imageList too.

Value

A named vector with the sum of pixel intensities above the quantCutThreshold normalized to the total number of pixels in the frame.

Examples

#Load example data.
data(testImages)

#Run the function with the output in the current directory
pixSum(testImages, quantCutoff(testImages[1], 0.99))
#Expected result:
#       A33        P79
#0.00140716 0.02007561

jtheorell/pixSum documentation built on April 2, 2020, 5:03 a.m.