% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/import.R

\name{generateXeniumImage}

\alias{generateXeniumImage}

\title{generateXeniumImage}

\usage{

generateXeniumImage(

  dir.path,

  increase.contrast = TRUE,

  resolution_level = 7,

  overwrite_resolution = FALSE,

  output.path = NULL,

  file.name = "morphology_lowres.tif",

  verbose = TRUE,

  ...

)

}

\arguments{

\item{dir.path}{Xenium output folder}

\item{increase.contrast}{increase the contrast of the image before writing}

\item{resolution_level}{the level of resolution within Xenium OME-TIFF image. Default: 7 (553x402)}

\item{overwrite_resolution}{if TRUE, the image "file.name" will be generated again although it exists at "dir.path"}

\item{output.path}{The path to the new morphology image created if the image should be saved to a location other than Xenium output folder.}

\item{file.name}{the name of the lowred morphology image. Default: morphology_lowres.tif}

\item{verbose}{verbose}

\item{...}{additional parameters passed to the \link{writeImage} function}

}

\description{

Generate a low resolution DAPI image of the Xenium experiment

}

\details{

The Xenium morphology_mip.ome.tif file that is found under the outs folder comes is an hyperstack of different resolutions of the DAPI image.

\link{generateXeniumImage} allows extracting only one of these layers by specifying the \code{resolution} parameter (Default: 7 for 553x402) among 1 to 8.

Lower incides of resolutions have higher higher resolutions, e.g. 1 for 35416x25778. Note that you may need to allocate larger memory of Java to import

higher resolution images.

}