biopixR (version 1.1.0)

sizeFilter: Size-based exclusion

Description

Takes the size of the objects in an image and discards objects based on a lower and an upper size limit. (Input can be obtained by objectDetection function)

Usage

sizeFilter(centers, coordinates, lowerlimit = "auto", upperlimit = "auto")

Value

list of 2 objects:

• Remaining centers after discarding according to size.

• Remaining coordinates after discarding according to size.

Arguments

centers

center coordinates of objects (value|mx|my|size data frame)

coordinates

all coordinates of the objects (x|y|value data frame)

lowerlimit

smallest accepted object size (numeric / 'auto' / 'interactive')

upperlimit

highest accepted object size (numeric / 'auto' / 'interactive')

Details

The sizeFilter function is designed to filter detected objects based on their size, either through automated detection or user-defined limits. The automated detection of size limits uses the 1.5*IQR method to identify and remove outliers. This approach is most effective when dealing with a large number of objects, (typically more than 50), and when the sizes of the objects are relatively uniform. For smaller samples or when the sizes of the objects vary significantly, the automated detection may not be as accurate, and manual limit setting is recommended.

Examples

res_objectDetection <- objectDetection(
  beads,
  method = 'edge',
  alpha = 1,
  sigma = 0
  )
res_sizeFilter <- sizeFilter(
  centers = res_objectDetection$centers,
  coordinates = res_objectDetection$coordinates,
  lowerlimit = 50, upperlimit = 150
  )
changePixelColor(
  beads,
  res_sizeFilter$coordinates,
  color = "darkgreen",
  visualize = TRUE
  )