From 83dd41f475d6b7f678d4d9baf21902a41c6aad31 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 18 Jun 2024 12:43:43 -0400
Subject: [PATCH 1/9] WIP: use pizzarr and anndataR

---
 R/data_to_zarr.R | 53 +++---------------------------------------------
 1 file changed, 3 insertions(+), 50 deletions(-)

diff --git a/R/data_to_zarr.R b/R/data_to_zarr.R
index 8fa9a3c..dff87ac 100644
--- a/R/data_to_zarr.R
+++ b/R/data_to_zarr.R
@@ -11,56 +11,9 @@
 #' obj <- get_seurat_obj()
 #' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr", assay = "RNA")
 seurat_to_anndata_zarr <- function(seurat_obj, out_path, assay) {
-  if(!requireNamespace("SeuratDisk", quietly = TRUE)) {
-    stop("Install 'SeuratDisk' to enable conversion of Seurat objects to AnnData objects.")
-  }
-
-  h5seurat_path <- paste0(out_path, ".h5Seurat")
-  h5ad_path <- paste0(out_path, ".h5ad")
-
-  # Convert factor columns to string/numeric.
-  seurat_obj@meta.data <- varhandle::unfactor(seurat_obj@meta.data)
-
-  SeuratDisk::SaveH5Seurat(seurat_obj, filename = h5seurat_path, overwrite = TRUE)
-  SeuratDisk::Convert(h5seurat_path, dest = "h5ad", overwrite = TRUE, assay = assay)
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(h5ad_path, out_path) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    adata <- anndata$read_h5ad(h5ad_path)
-
-    cleanup_colnames <- function(df) {
-      # Reference: https://github.com/theislab/scvelo/issues/255#issuecomment-739995301
-      new_colnames <- colnames(df)
-      new_colnames[new_colnames == "_index"] <- "features"
-      return(new_colnames)
-    }
-
-    noop <- function(cond) { }
-
-    tryCatch({
-      colnames(adata$var) <- cleanup_colnames(adata$var)
-    }, error = noop)
-
-    # Reconstruct, omitting raw and uns.
-    adata <- anndata$AnnData(
-      X = adata$X,
-      obs = as.data.frame(adata$obs),
-      var = as.data.frame(adata$var),
-      obsm = adata$obsm,
-      varm = adata$varm
-    )
-
-    adata$write_zarr(out_path)
-
-    return(TRUE)
-  }, h5ad_path = h5ad_path, out_path = out_path)
-  return(success)
+  sce <- Seurat::as.SingleCellExperiment(seurat_obj)
+  store <- pizzarr::DirectoryStore$new(out_path)
+  anndataR::from_SingleCellExperiment(sce, "ZarrAnnData", store = store)
 }
 
 #' Save a SingleCellExperiment to an AnnData-Zarr store.

From a341cf8edb2ff5d037dd5422031f3e9e597187c2 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 10:56:39 -0400
Subject: [PATCH 2/9] WIP: working

---
 R/data_to_zarr.R | 17 +++++++++++++++--
 R/mock_objects.R |  7 +++++++
 2 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/R/data_to_zarr.R b/R/data_to_zarr.R
index dff87ac..ace0ac4 100644
--- a/R/data_to_zarr.R
+++ b/R/data_to_zarr.R
@@ -9,13 +9,26 @@
 #' @export
 #' @examples
 #' obj <- get_seurat_obj()
-#' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr", assay = "RNA")
-seurat_to_anndata_zarr <- function(seurat_obj, out_path, assay) {
+#' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr")
+seurat_to_anndata_zarr <- function(seurat_obj, out_path) {
   sce <- Seurat::as.SingleCellExperiment(seurat_obj)
   store <- pizzarr::DirectoryStore$new(out_path)
   anndataR::from_SingleCellExperiment(sce, "ZarrAnnData", store = store)
 }
 
+test_conversion <- function(num_workers = 8) {
+  options(
+    pizzarr.parallel_read_enabled = TRUE,
+    pizzarr.parallel_write_enabled = TRUE
+  )
+  doParallel::registerDoParallel(num_workers)
+  
+  obj <- get_seurat_obj()
+  seurat_to_anndata_zarr(obj, "test.zarr")
+  
+  doParallel::stopImplicitCluster()
+}
+
 #' Save a SingleCellExperiment to an AnnData-Zarr store.
 #'
 #' @param sce_obj The object to save.
diff --git a/R/mock_objects.R b/R/mock_objects.R
index 866435c..3c98185 100644
--- a/R/mock_objects.R
+++ b/R/mock_objects.R
@@ -1,3 +1,6 @@
+library(Seurat)
+library(SeuratObject)
+
 #' Create a mock Seurat object for tests and examples.
 #' @return The object.
 #' @keywords internal
@@ -9,6 +12,10 @@ get_seurat_obj <- function() {
   if(!requireNamespace("Seurat", quietly = TRUE)) {
     stop("Install 'Seurat' to enable creation of Seurat objects.")
   }
+  
+  SeuratData::InstallData("pbmcsca")
+  obj <- SeuratData::LoadData("pbmcsca")
+  return(obj)
 
   ncells <- 100
   u <- matrix(rpois(20000, 5), ncol=ncells)

From 722e7db71195cfafaca7f81e29ba352cd2e199f0 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:26:04 -0400
Subject: [PATCH 3/9] Refactoring

---
 DESCRIPTION                          |   2 +-
 NAMESPACE                            |   3 +
 R/{data_to_zarr.R => bioc_to_zarr.R} | 116 +--------------------------
 R/giotto_to_bioc.R                   |   3 +
 R/mock_objects.R                     |  19 +++--
 R/seurat_to_bioc.R                   |  62 ++++++++++++++
 6 files changed, 86 insertions(+), 119 deletions(-)
 rename R/{data_to_zarr.R => bioc_to_zarr.R} (52%)
 create mode 100644 R/giotto_to_bioc.R
 create mode 100644 R/seurat_to_bioc.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 279374c..53eb6d6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -24,7 +24,7 @@ LazyData: false
 Language: en-US
 StagedInstall: no
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Imports:
     Matrix,
diff --git a/NAMESPACE b/NAMESPACE
index 6d02c14..2a43186 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,6 +3,7 @@
 export(get_giotto_obj)
 export(get_sce_obj)
 export(get_seurat_obj)
+export(get_seurat_v5_obj)
 export(get_spe_obj)
 export(giotto_to_anndata_zarr)
 export(obj_list)
@@ -10,6 +11,8 @@ export(sce_to_anndata_zarr)
 export(seurat_to_anndata_zarr)
 export(spe_to_anndata_zarr)
 export(spe_to_ome_zarr)
+import(Seurat)
+import(SeuratObject)
 importFrom(SingleCellExperiment,"reducedDims<-")
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,reducedDims)
diff --git a/R/data_to_zarr.R b/R/bioc_to_zarr.R
similarity index 52%
rename from R/data_to_zarr.R
rename to R/bioc_to_zarr.R
index ace0ac4..157dd2e 100644
--- a/R/data_to_zarr.R
+++ b/R/bioc_to_zarr.R
@@ -1,34 +1,3 @@
-
-#' Save a Seurat object to an AnnData-Zarr store.
-#'
-#' @param seurat_obj The object to save.
-#' @param out_path A path to the output Zarr store.
-#' @param assay The name of the assay to save.
-#' @return TRUE if the conversion succeeds.
-#'
-#' @export
-#' @examples
-#' obj <- get_seurat_obj()
-#' seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr")
-seurat_to_anndata_zarr <- function(seurat_obj, out_path) {
-  sce <- Seurat::as.SingleCellExperiment(seurat_obj)
-  store <- pizzarr::DirectoryStore$new(out_path)
-  anndataR::from_SingleCellExperiment(sce, "ZarrAnnData", store = store)
-}
-
-test_conversion <- function(num_workers = 8) {
-  options(
-    pizzarr.parallel_read_enabled = TRUE,
-    pizzarr.parallel_write_enabled = TRUE
-  )
-  doParallel::registerDoParallel(num_workers)
-  
-  obj <- get_seurat_obj()
-  seurat_to_anndata_zarr(obj, "test.zarr")
-  
-  doParallel::stopImplicitCluster()
-}
-
 #' Save a SingleCellExperiment to an AnnData-Zarr store.
 #'
 #' @param sce_obj The object to save.
@@ -48,20 +17,10 @@ sce_to_anndata_zarr <- function(sce_obj, out_path) {
     # Reference: https://github.com/theislab/zellkonverter/blob/e1e95b1/R/SCE2AnnData.R#L159
     colnames(reducedDims(sce_obj)[[obsm_key]]) <- NULL
   }
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(sce_obj, out_path) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    adata <- zellkonverter::SCE2AnnData(sce_obj)
-    adata$write_zarr(out_path)
-    return(TRUE)
-  }, sce_obj = sce_obj, out_path = out_path)
-  return(success)
+  
+  store <- pizzarr::DirectoryStore$new(out_path)
+  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store)
+  return(TRUE)
 }
 
 #' Save a SpatialExperiment to an AnnData-Zarr store.
@@ -166,70 +125,3 @@ spe_to_ome_zarr <- function(spe_obj, sample_id, image_id, out_path) {
   }, img_arr = img_arr, sample_id = sample_id, image_id = image_id, out_path = out_path)
   return(success)
 }
-
-#' Save a Giotto object to an AnnData-Zarr store
-#'
-#' @param giotto_obj The object to save.
-#' @param out_path A path to the output Zarr store.
-#' @param X_slot The name of the slot in the Giotto object to use for adata.X
-#' @return TRUE if the conversion succeeds.
-#'
-#' @export
-#' @examples
-#' obj <- get_giotto_obj()
-#' giotto_to_anndata_zarr(obj, "data/giotto.zarr")
-#' @importFrom methods slot
-giotto_to_anndata_zarr <- function(giotto_obj, out_path, X_slot = "raw_exprs") {
-
-  # Use basilisk
-  proc <- basilisk::basiliskStart(py_env)
-  on.exit(basilisk::basiliskStop(proc))
-
-  success <- basilisk::basiliskRun(proc, function(giotto_obj, out_path, X_slot) {
-    anndata <- reticulate::import("anndata")
-    zarr <- reticulate::import("zarr")
-
-    # Reference: https://github.com/theislab/zellkonverter/blob/master/R/SCE2AnnData.R#L237
-    make_numpy_friendly <- function(x, transpose = TRUE) {
-      if (transpose) {
-        x <- Matrix::t(x)
-      }
-      if (DelayedArray::is_sparse(x)) {
-        methods::as(x, "dgCMatrix")
-      } else {
-        as.matrix(x)
-      }
-    }
-
-    X <- make_numpy_friendly(slot(giotto_obj, X_slot))
-    obs <- slot(giotto_obj, "cell_metadata")
-    var <- slot(giotto_obj, "gene_metadata")
-
-    adata <- anndata$AnnData(X = X, obs = obs, var = var)
-
-    obsm <- list()
-
-    if(!is.null(slot(giotto_obj, "spatial_locs"))) {
-      spatial_locs <- slot(giotto_obj, "spatial_locs")
-      obsm[['spatial']] <- t(as.matrix(spatial_locs[, c("sdimx", "sdimy")]))
-    }
-
-    if(!is.null(slot(giotto_obj, "dimension_reduction"))) {
-      dim_reducs <- slot(giotto_obj, "dimension_reduction")$cells
-      for(dim_reduc_name in names(dim_reducs)) {
-        dim_reduc_coords <- dim_reducs[[dim_reduc_name]][[dim_reduc_name]]$coordinates
-        obsm[[dim_reduc_name]] <- t(as.matrix(dim_reduc_coords))
-      }
-    }
-
-    if(length(obsm) > 0) {
-      # TODO make_numpy_friendly is outside scope
-      obsm <- lapply(obsm, make_numpy_friendly)
-      adata$obsm <- obsm
-    }
-
-    adata$write_zarr(out_path)
-    return(TRUE)
-  }, giotto_obj = giotto_obj, out_path = out_path, X_slot = X_slot)
-  return(success)
-}
diff --git a/R/giotto_to_bioc.R b/R/giotto_to_bioc.R
new file mode 100644
index 0000000..6a3dc69
--- /dev/null
+++ b/R/giotto_to_bioc.R
@@ -0,0 +1,3 @@
+giotto_to_spe <- function(gio) {
+  return(GiottoClass::giottoToSpatialExperiment(gio))
+}
\ No newline at end of file
diff --git a/R/mock_objects.R b/R/mock_objects.R
index 3c98185..7d33b7a 100644
--- a/R/mock_objects.R
+++ b/R/mock_objects.R
@@ -1,5 +1,16 @@
-library(Seurat)
-library(SeuratObject)
+#' Get a Seurat v5 object for tests and examples.
+#' @return The object.
+#' @keywords internal
+#' @export
+#' @examples
+#' obj <- get_seurat_v5_obj()
+#' @import Seurat
+#' @import SeuratObject
+get_seurat_v5_obj <- function() {
+  SeuratData::InstallData("pbmcsca")
+  obj <- SeuratData::LoadData("pbmcsca")
+  return(obj)
+}
 
 #' Create a mock Seurat object for tests and examples.
 #' @return The object.
@@ -12,10 +23,6 @@ get_seurat_obj <- function() {
   if(!requireNamespace("Seurat", quietly = TRUE)) {
     stop("Install 'Seurat' to enable creation of Seurat objects.")
   }
-  
-  SeuratData::InstallData("pbmcsca")
-  obj <- SeuratData::LoadData("pbmcsca")
-  return(obj)
 
   ncells <- 100
   u <- matrix(rpois(20000, 5), ncol=ncells)
diff --git a/R/seurat_to_bioc.R b/R/seurat_to_bioc.R
new file mode 100644
index 0000000..b87cdff
--- /dev/null
+++ b/R/seurat_to_bioc.R
@@ -0,0 +1,62 @@
+seurat_to_sce <- function(seu) {
+  sce <- Seurat::as.SingleCellExperiment(seu)
+  return(sce)
+}
+
+seurat_to_spe <- function(seu, sample_id = NA, img_id = NA) {
+  # Reference: https://github.com/drighelli/SpatialExperiment/issues/115
+  sce <- seurat_to_sce(seu)
+  
+  if(is.na(sample_id)) {
+    sample_id <- "sample0"
+  }
+  
+  if(length(object@images) >= 1) {
+  
+    if(is.na(img_id)) {
+      img_id <- names(object@images)[1]
+    }
+    
+    ## Extract spatial coordinates
+    if("VisiumV2" %in% class(seu@images[[img_id]])) {
+      spatialCoords <- as.matrix(
+        seu@images[[img_id]]@boundaries$centroids@coords
+      )
+    } else {
+      spatialCoords <- as.matrix(
+        seu@images[[img_id]]@coordinates[, c("imagecol", "imagerow")]
+      )
+    }
+    
+    
+    ## Extract and process image data
+    img <- SpatialExperiment::SpatialImage(
+      x = as.raster(seu@images[[img_id]]@image)
+    )
+    
+    imgData <- S4Vectors::DataFrame(
+      sample_id = sample_id,
+      image_id = img_id,
+      data = I(list(img)),
+      scaleFactor = seu@images[[img_id]]@scale.factors$lowres
+    )
+  }
+  
+  # Convert to SpatialExperiment
+  spe <- SpatialExperiment::SpatialExperiment(
+    assays = SummarizedExperiment::assays(sce),
+    rowData = SingleCellExperiment::rowData(sce),
+    colData = SingleCellExperiment::colData(sce),
+    metadata = S4Vectors::metadata(sce),
+    reducedDims = SingleCellExperiment::reducedDims(sce),
+    altExps = SingleCellExperiment::altExps(sce),
+    sample_id = sample_id,
+    spatialCoords = spatialCoords,
+    imgData = imgData
+  )
+  # indicate all spots are on the tissue
+  spe$in_tissue <- 1
+  spe$sample_id <- sample_id
+  # Return Spatial Experiment object
+  return(spe)
+}
\ No newline at end of file

From 299b754562458563ef5887924adfc6d61f37c4f3 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:36:15 -0400
Subject: [PATCH 4/9] Update

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index a8d0986..5e4b6ef 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,9 @@ Installation requires R 4.0.0 or greater.
 
 ```r
 install.packages("devtools")
+devtools::install_github("keller-mark/pizzarr")
+devtools::install_github("keller-mark/anndataR", ref="keller-mark/zarr-and-rarr")
+
 devtools::install_github("vitessce/vitessceAnalysisR")
 ```
 

From 7c7ac878f69e3e39df22b2d7566bf2715db256f5 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:48:49 -0400
Subject: [PATCH 5/9] Update exports

---
 NAMESPACE                     |  3 ---
 man/get_seurat_v5_obj.Rd      | 18 ++++++++++++++++++
 man/giotto_to_anndata_zarr.Rd | 25 -------------------------
 man/sce_to_anndata_zarr.Rd    |  2 +-
 man/seurat_to_anndata_zarr.Rd | 25 -------------------------
 man/spe_to_anndata_zarr.Rd    |  2 +-
 man/spe_to_ome_zarr.Rd        |  2 +-
 7 files changed, 21 insertions(+), 56 deletions(-)
 create mode 100644 man/get_seurat_v5_obj.Rd
 delete mode 100644 man/giotto_to_anndata_zarr.Rd
 delete mode 100644 man/seurat_to_anndata_zarr.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 2a43186..72cd43e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,10 +5,8 @@ export(get_sce_obj)
 export(get_seurat_obj)
 export(get_seurat_v5_obj)
 export(get_spe_obj)
-export(giotto_to_anndata_zarr)
 export(obj_list)
 export(sce_to_anndata_zarr)
-export(seurat_to_anndata_zarr)
 export(spe_to_anndata_zarr)
 export(spe_to_ome_zarr)
 import(Seurat)
@@ -22,7 +20,6 @@ importFrom(SummarizedExperiment,colData)
 importFrom(grDevices,as.raster)
 importFrom(grDevices,col2rgb)
 importFrom(methods,new)
-importFrom(methods,slot)
 importFrom(stats,rnorm)
 importFrom(stats,rpois)
 importFrom(stats,runif)
diff --git a/man/get_seurat_v5_obj.Rd b/man/get_seurat_v5_obj.Rd
new file mode 100644
index 0000000..9b1e337
--- /dev/null
+++ b/man/get_seurat_v5_obj.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mock_objects.R
+\name{get_seurat_v5_obj}
+\alias{get_seurat_v5_obj}
+\title{Get a Seurat v5 object for tests and examples.}
+\usage{
+get_seurat_v5_obj()
+}
+\value{
+The object.
+}
+\description{
+Get a Seurat v5 object for tests and examples.
+}
+\examples{
+obj <- get_seurat_v5_obj()
+}
+\keyword{internal}
diff --git a/man/giotto_to_anndata_zarr.Rd b/man/giotto_to_anndata_zarr.Rd
deleted file mode 100644
index 9f4a786..0000000
--- a/man/giotto_to_anndata_zarr.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_to_zarr.R
-\name{giotto_to_anndata_zarr}
-\alias{giotto_to_anndata_zarr}
-\title{Save a Giotto object to an AnnData-Zarr store}
-\usage{
-giotto_to_anndata_zarr(giotto_obj, out_path, X_slot = "raw_exprs")
-}
-\arguments{
-\item{giotto_obj}{The object to save.}
-
-\item{out_path}{A path to the output Zarr store.}
-
-\item{X_slot}{The name of the slot in the Giotto object to use for adata.X}
-}
-\value{
-TRUE if the conversion succeeds.
-}
-\description{
-Save a Giotto object to an AnnData-Zarr store
-}
-\examples{
-obj <- get_giotto_obj()
-giotto_to_anndata_zarr(obj, "data/giotto.zarr")
-}
diff --git a/man/sce_to_anndata_zarr.Rd b/man/sce_to_anndata_zarr.Rd
index 372681b..efe07b1 100644
--- a/man/sce_to_anndata_zarr.Rd
+++ b/man/sce_to_anndata_zarr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_to_zarr.R
+% Please edit documentation in R/bioc_to_zarr.R
 \name{sce_to_anndata_zarr}
 \alias{sce_to_anndata_zarr}
 \title{Save a SingleCellExperiment to an AnnData-Zarr store.}
diff --git a/man/seurat_to_anndata_zarr.Rd b/man/seurat_to_anndata_zarr.Rd
deleted file mode 100644
index 76633ff..0000000
--- a/man/seurat_to_anndata_zarr.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_to_zarr.R
-\name{seurat_to_anndata_zarr}
-\alias{seurat_to_anndata_zarr}
-\title{Save a Seurat object to an AnnData-Zarr store.}
-\usage{
-seurat_to_anndata_zarr(seurat_obj, out_path, assay)
-}
-\arguments{
-\item{seurat_obj}{The object to save.}
-
-\item{out_path}{A path to the output Zarr store.}
-
-\item{assay}{The name of the assay to save.}
-}
-\value{
-TRUE if the conversion succeeds.
-}
-\description{
-Save a Seurat object to an AnnData-Zarr store.
-}
-\examples{
-obj <- get_seurat_obj()
-seurat_to_anndata_zarr(obj, out_path = "data/seurat.zarr", assay = "RNA")
-}
diff --git a/man/spe_to_anndata_zarr.Rd b/man/spe_to_anndata_zarr.Rd
index 59596d8..0d340ef 100644
--- a/man/spe_to_anndata_zarr.Rd
+++ b/man/spe_to_anndata_zarr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_to_zarr.R
+% Please edit documentation in R/bioc_to_zarr.R
 \name{spe_to_anndata_zarr}
 \alias{spe_to_anndata_zarr}
 \title{Save a SpatialExperiment to an AnnData-Zarr store.}
diff --git a/man/spe_to_ome_zarr.Rd b/man/spe_to_ome_zarr.Rd
index bdbe5cb..d8cde20 100644
--- a/man/spe_to_ome_zarr.Rd
+++ b/man/spe_to_ome_zarr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_to_zarr.R
+% Please edit documentation in R/bioc_to_zarr.R
 \name{spe_to_ome_zarr}
 \alias{spe_to_ome_zarr}
 \title{Save an image in a SpatialExperiment to an OME-Zarr store}

From 9a1521e6b7c8e970c99a2f398e26f9c41d111b13 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:56:05 -0400
Subject: [PATCH 6/9] Update

---
 NAMESPACE          | 3 +++
 R/giotto_to_bioc.R | 1 +
 R/seurat_to_bioc.R | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 72cd43e..6bb8769 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,8 +5,11 @@ export(get_sce_obj)
 export(get_seurat_obj)
 export(get_seurat_v5_obj)
 export(get_spe_obj)
+export(giotto_to_spe)
 export(obj_list)
 export(sce_to_anndata_zarr)
+export(seurat_to_sce)
+export(seurat_to_spe)
 export(spe_to_anndata_zarr)
 export(spe_to_ome_zarr)
 import(Seurat)
diff --git a/R/giotto_to_bioc.R b/R/giotto_to_bioc.R
index 6a3dc69..9be701a 100644
--- a/R/giotto_to_bioc.R
+++ b/R/giotto_to_bioc.R
@@ -1,3 +1,4 @@
+#' @export
 giotto_to_spe <- function(gio) {
   return(GiottoClass::giottoToSpatialExperiment(gio))
 }
\ No newline at end of file
diff --git a/R/seurat_to_bioc.R b/R/seurat_to_bioc.R
index b87cdff..8e0b7e5 100644
--- a/R/seurat_to_bioc.R
+++ b/R/seurat_to_bioc.R
@@ -1,8 +1,10 @@
+#' @export
 seurat_to_sce <- function(seu) {
   sce <- Seurat::as.SingleCellExperiment(seu)
   return(sce)
 }
 
+#' @export
 seurat_to_spe <- function(seu, sample_id = NA, img_id = NA) {
   # Reference: https://github.com/drighelli/SpatialExperiment/issues/115
   sce <- seurat_to_sce(seu)

From ca6757bc1d0905a128c273b6414a466adf65d7d3 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 12:57:57 -0400
Subject: [PATCH 7/9] Update

---
 R/seurat_to_bioc.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/seurat_to_bioc.R b/R/seurat_to_bioc.R
index 8e0b7e5..27e034c 100644
--- a/R/seurat_to_bioc.R
+++ b/R/seurat_to_bioc.R
@@ -13,10 +13,10 @@ seurat_to_spe <- function(seu, sample_id = NA, img_id = NA) {
     sample_id <- "sample0"
   }
   
-  if(length(object@images) >= 1) {
+  if(length(seu@images) >= 1) {
   
     if(is.na(img_id)) {
-      img_id <- names(object@images)[1]
+      img_id <- names(seu@images)[1]
     }
     
     ## Extract spatial coordinates

From ed889a0bac8e6ffc293db11b8ae76468369ffd40 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:46:42 -0400
Subject: [PATCH 8/9] to_dense

---
 R/bioc_to_zarr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/bioc_to_zarr.R b/R/bioc_to_zarr.R
index 157dd2e..9c08ee9 100644
--- a/R/bioc_to_zarr.R
+++ b/R/bioc_to_zarr.R
@@ -19,7 +19,7 @@ sce_to_anndata_zarr <- function(sce_obj, out_path) {
   }
   
   store <- pizzarr::DirectoryStore$new(out_path)
-  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store)
+  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store, to_dense = TRUE)
   return(TRUE)
 }
 

From 3000b4d42516097a57357f825dbd203dd4d3b7bf Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:46:49 -0400
Subject: [PATCH 9/9] Update param

---
 R/bioc_to_zarr.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/bioc_to_zarr.R b/R/bioc_to_zarr.R
index 9c08ee9..9b271e2 100644
--- a/R/bioc_to_zarr.R
+++ b/R/bioc_to_zarr.R
@@ -9,7 +9,7 @@
 #' obj <- get_sce_obj()
 #' sce_to_anndata_zarr(obj, out_path = "data/sce.zarr")
 #' @importFrom SingleCellExperiment reducedDims reducedDims<-
-sce_to_anndata_zarr <- function(sce_obj, out_path) {
+sce_to_anndata_zarr <- function(sce_obj, out_path, to_dense = TRUE) {
   obsm_keys <- names(as.list(reducedDims(sce_obj)))
   for(obsm_key in obsm_keys) {
     # If there are column names, then the obsm element will be stored as a data.frame,
@@ -19,7 +19,7 @@ sce_to_anndata_zarr <- function(sce_obj, out_path) {
   }
   
   store <- pizzarr::DirectoryStore$new(out_path)
-  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store, to_dense = TRUE)
+  anndataR::from_SingleCellExperiment(sce_obj, "ZarrAnnData", store = store, to_dense = to_dense)
   return(TRUE)
 }