shapeFeatures: Extraction of Shape Features

In biopixR: Extracting Insights from Biological Images

Extraction of Shape Features

Description

This function analyzes the objects detected in an image and calculates distinct shape characteristics for each object, such as circularity, eccentricity, radius, and perimeter. The resulting shape attributes can then be grouped using a Self-Organizing Map (SOM) from the 'Kohonen' package.

Usage

shapeFeatures(
  img,
  alpha = 1,
  sigma = 2,
  xdim = 2,
  ydim = 1,
  SOM = FALSE,
  visualize = FALSE
)

Arguments

img	image (import by load.image)
alpha	threshold adjustment factor (numeric / 'static' / 'interactive' / 'gaussian') (from objectDetection)
sigma	smoothing (numeric / 'static' / 'interactive' / 'gaussian') (from objectDetection)
xdim	x-dimension for the SOM-grid (grid = hexagonal)
ydim	y-dimension for the SOM-grid (xdim * ydim = number of neurons)
SOM	if TRUE runs SOM algorithm on extracted shape features, grouping the detected objects
visualize	visualizes the groups computed by SOM

Value

data.frame containing detailed information about every single object.

See Also

objectDetection(), resultAnalytics(), som

Examples

shapeFeatures(
  beads,
  alpha = 1,
  sigma = 0,
  SOM = TRUE,
  visualize = TRUE
)

biopixR documentation built on April 4, 2025, 1:07 a.m.