imgPipe: 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, for example the analysis of dual-color micro particles. 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",
  method = "edge",
  alpha = 1,
  sigma = 2,
  sizeFilter = FALSE,
  upperlimit = "auto",
  lowerlimit = "auto",
  proximityFilter = FALSE,
  radius = "auto"
)

Value

list of 2 to 3 objects:

Summary of all the objects in the image.
Detailed information about every single object.
(optional) Result for every individual color.

Arguments

img1: image (import by importImage)
color1: name of color in img1
img2: image (import by importImage)
color2: name of color in img2
img3: image (import by importImage)
color3: name of color in img3
method: choose method for object detection ('edge' / 'threshold') (from objectDetection)
alpha: threshold adjustment factor (numeric / 'static' / 'interactive' / 'gaussian') (from objectDetection)
sigma: smoothing (numeric / 'static' / 'interactive' / 'gaussian') (from objectDetection)
sizeFilter: applying sizeFilter function (default - FALSE)
upperlimit: highest accepted object size (numeric / 'auto') (only needed if sizeFilter = TRUE)
lowerlimit: smallest accepted object size (numeric / 'auto') (only needed if sizeFilter = TRUE)
proximityFilter: applying proximityFilter function (default - FALSE)
radius: distance from one object in which no other centers are allowed (in pixels) (only needed if proximityFilter = TRUE)

Examples

Run this code

result <- imgPipe(
  beads,
  alpha = 1,
  sigma = 2,
  sizeFilter = TRUE,
  upperlimit = 150,
  lowerlimit = 50
  )

# Highlight remaining microparticles
plot(beads)
with(
  result$detailed,
  points(
    result$detailed$x,
    result$detailed$y,
    col = "darkgreen",
    pch = 19
    )
  )

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