scatter_HE: Function used to generate a 2D set of points from an HE image

scatter_HER Documentation

Function used to generate a 2D set of points from an HE image

Description

The defualt segmentation uses the HE image as input and defines any pixel with an intensity value below a threshold to be a point. The number of points can be downsampeld to limit the maximum number.

Usage

scatter_HE(
  object,
  type = "masked.masks",
  sample.index = NULL,
  limit = 0.5,
  maxnum = 50000,
  edges = FALSE,
  custom.edge.detector = NULL
)

Arguments

object

Staffli object

type

Sets the image type to run segmentation on

sample.index

Integer value specifying the index of the sample to be analyzed

limit

Sets the intensity threshold in the interval [0, 1]

maxnum

Integer value specifying the maximum number of points

edges

Extracts the coordinates of the edges instead

custom.edge.detector

Custom function used to detect edges


jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.