--- a
+++ b/man/as.AnnData.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/conversion.R
+\name{as.AnnData}
+\alias{as.AnnData}
+\title{as.AnnData}
+\usage{
+as.AnnData(
+  object,
+  file,
+  assay = NULL,
+  flip_coordinates = FALSE,
+  method = "anndata",
+  create.ometiff = FALSE,
+  python.path = NULL,
+  ...
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{file}{the name of the h5ad file.}
+
+\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+if NULL, the default assay will be used, see \link{vrMainAssay}.}
+
+\item{flip_coordinates}{if TRUE, the spatial coordinates (including segments) will be flipped.}
+
+\item{method}{the package to use for conversion: "anndataR" or "anndata".}
+
+\item{create.ometiff}{should an ometiff file be generated of default image of the object}
+
+\item{python.path}{the path to the python binary, otherwise either \code{basilisk} package is used or \code{getOption("voltron.python.path")} should be not NULL.}
+
+\item{...}{additional parameters passed to \link{vrImages}.}
+}
+\description{
+Converting a VoltRon object into a AnnData (.h5ad) object
+}
+\details{
+This function converts a VoltRon object into an AnnData object (.h5ad file). It extracts assay data,
+spatial coordinates, and optionally flips coordinates. Images associated with the assay can be included in the 
+resulting AnnData file, with additional customization parameters like channel, scale.perc.
+}