imageAnnotationToSegmentation: Convert image annotation to segmentation

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Convert image annotation to segmentation

Description

Converts one or more image annotations to a binary segmentation variable in the feature data.frame.

Usage

imageAnnotationToSegmentation(
  object,
  ids,
  segmentation_name,
  inside = "inside",
  outside = "outside",
  overwrite = FALSE
)

Arguments

object	An object of class spata2.
ids	Character vector. Specifies the image annotation(s) of interest. Barcode-spots that fall into the area of these annotations are labeled with the input for argument inside.
segmentation_name	Character value. The name of the new segmentation variable.
inside	Character value. The group name for the barcode-spots that are located inside the area of the image annotation(s).
outside	Character value. The group name for the barcode-spots that are located outside the area of the image annotation(s).
overwrite	Logical. Set to TRUE to overwrite existing variables with the same name.

Value

The input spata2 object containing the added or computed results.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.