ExtImage: Use the EBImage 'Image' class in SFE objects

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Use the EBImage Image class in SFE objects

Description

This is a thin wrapper around the Image class in the EBImage package so it inherits from VirtualSpatialImage to be compatible with SpatialExperiment from which SFE inherits. An ext field is added to specify the spatial extent of the image in microns to facilitate geometric operations on the SFE object (including the images) and plotting with Voyager.

Usage

## S4 method for signature 'ExtImage'
show(object)

ExtImage(img, ext = NULL)

Arguments

object	An ExtImage object.
img	An Image object or anything that inherits from Image such as AnnotatedImage in RBioFormats.
ext	Numeric vector with names "xmin", "xmax", "ymin", "ymax" in microns indicating the spatial extent covered by the image. If NULL, then the extent will be inferred from the metadata, from physical pixel size and the number of pixels.

Value

An ExtImage object.

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.