imgPipe {biopixR} | R Documentation |
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 |
color1 |
name of color in img1 |
img2 |
image (import by |
color2 |
name of color in img2 |
img3 |
image (import by |
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:
summary of all the microbeads in the image
detailed information about every single bead
(optional) result for every individual color
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
)
)