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

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

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.