toSpatRasterImage: Convert images to SpatRasterImage

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

Convert images to SpatRasterImage

Description

The resolution specified from the OME-TIFF file will be read into memory and written to disk as a GeoTIFF file that has the extent. The output file will have the same file name as the input file except without the ome in the extension.

Usage

## S4 method for signature 'ExtImage'
toSpatRasterImage(
  x,
  save_geotiff = TRUE,
  file_out = "img.tiff",
  overwrite = FALSE
)

## S4 method for signature 'BioFormatsImage'
toSpatRasterImage(
  x,
  save_geotiff = TRUE,
  resolution = 4L,
  channel = NULL,
  overwrite = FALSE
)

Arguments

x	Either a BioFormatsImage or EBIImage object.
save_geotiff	Logical, whether to save the image to GeoTIFF file.
file_out	File to save the non-OME TIFF file for SpatRaster.
overwrite	Logical, whether to overwrite existing file of the same name.
resolution	Integer, which resolution in the BioFormatsImage to read and convert. Defaults to 4, which is a lower resolution. Ignored if only 1 resolution is present.
channel	Integer vector to indicate channel(s) to read. If NULL, then all channels will be read.

Value

A SpatRasterImage object

See Also

toExtImage

pachterlab/SpatialFeatureExperiment documentation built on Aug. 5, 2024, 8:36 a.m.