imgPipe {biopixR}

Image analysis pipeline

Description

This function serves as a pipeline that integrates tools for complete start-to-finish image analysis. It enables the handling of images from different channels, including the analysis of dual-color microbeads. This approach simplifies the workflow, providing a straightforward method to analyze complex image data.

Usage

imgPipe(
  img1 = img,
  color1 = "color1",
  img2 = NULL,
  color2 = "color2",
  img3 = NULL,
  color3 = "color3",
  alpha = 1,
  sigma = 2,
  sizeFilter = TRUE,
  upperlimit = "auto",
  lowerlimit = "auto",
  proximityFilter = TRUE,
  radius = "auto",
  parallel = FALSE
)

Arguments

img1

image (import by load.image)

color1

name of color in img1

img2

image (import by load.image)

color2

name of color in img2

img3

image (import by load.image)

color3

name of color in img3

alpha

threshold adjustment factor

sigma

smoothing

sizeFilter

applying sizeFilter function (default - TRUE)

upperlimit

highest accepted object size (only needed if sizeFilter = TRUE)

lowerlimit

smallest accepted object size (when 'auto' both limits are calculated by using the mean and the standard deviation)

proximityFilter

applying proximityFilter function (default - TRUE)

radius

distance from one center in which no other centers are allowed (in pixels)

parallel

if TRUE uses multiple cores (75 %) to process results

Value

list of 3 to 4 objects:

1. summary of all the microbeads in the image

2. detailed information about every single bead

3. (optional) result for every individual color

4. unfiltered coordinates of img1

Examples

result <- imgPipe(beads,
  alpha = 1, sigma = 2, upperlimit = 150,
  lowerlimit = 50
  )
plot(beads)
with(
  result$detailed,
  points(
    result$detailed$x,
    result$detailed$y,
    col = "darkgreen",
    pch = 19
    )
  )