diff --git a/DESCRIPTION b/DESCRIPTION
index a1f603d..07c15b6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,7 +14,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0),
-    Matrix
+    Matrix,
+    SeuratObject (>= 5.0.0)
 Config/testthat/edition: 3
 Imports:
     methods,
diff --git a/NAMESPACE b/NAMESPACE
index 12bc2ec..f91a3b1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(counts_matrix_from_assay)
 export(create_bugreport)
 export(create_bugreport_from_seurat)
 export(create_loupe)
diff --git a/R/err.R b/R/err.R
index dd9b50f..5735b55 100644
--- a/R/err.R
+++ b/R/err.R
@@ -60,9 +60,10 @@ create_bugreport_from_seurat <- function(obj) {
   assay <- namedAssay[[1]]
   clusters <- select_clusters(obj)
   projections <- select_projections(obj)
+  counts <- counts_matrix_from_assay(assay)
 
   create_bugreport(
-    assay@counts,
+    counts,
     clusters,
     projections,
     assay_name = assay_name,
diff --git a/R/lib.R b/R/lib.R
index 6c92fcf..d7645a1 100644
--- a/R/lib.R
+++ b/R/lib.R
@@ -44,6 +44,7 @@ create_loupe_from_seurat <- function(
 
   assay_name <- names(namedAssay)
   assay <- namedAssay[[1]]
+  counts <- counts_matrix_from_assay(assay)
 
   clusters <- select_clusters(obj, dedup=dedup_clusters)
   projections <- select_projections(obj)
@@ -58,7 +59,7 @@ create_loupe_from_seurat <- function(
   }
 
   success <- create_loupe(
-    assay@counts,
+    counts,
     clusters=clusters,
     projections=projections,
     output_dir=output_dir,
diff --git a/R/util.R b/R/util.R
index 343c93d..26c223d 100644
--- a/R/util.R
+++ b/R/util.R
@@ -56,8 +56,9 @@ select_assay <- function(obj) {
   for (i in seq_along(assay_priority)) {
     name <- names(assay_priority[i])
     assay <- Seurat::GetAssay(obj, assay=name)
+    counts <- counts_matrix_from_assay(assay)
 
-    if (length(assay@counts) > 0) {
+    if (length(counts) > 0) {
       result = list()
       result[[name]] = assay
       return(result)
@@ -67,6 +68,25 @@ select_assay <- function(obj) {
   NULL
 }
 
+#' Extract the counts matrix from the Assay
+#'
+#' @param assay A SeuratObject::Assay or SeuratObject::Assay5
+#'
+#' @return A sparse counts matrix
+#'
+#' @export
+counts_matrix_from_assay <- function(assay) {
+  if (packageVersion("Seurat") >= 5) {
+    return(assay$counts)
+  } else {
+    if (is(assay, 'Assay5')) {
+      stop("Cannot get count matrix: Please upgrade to Seurat > 5 to support dataset")
+    }
+
+    return(assay@counts)
+  }
+}
+
 #' Select clusters from the assay
 #'
 #' @param obj A Seurat Object
diff --git a/README.md b/README.md
index c99fefa..d901987 100644
--- a/README.md
+++ b/README.md
@@ -37,9 +37,12 @@ library("loupeR")
 # Gene Expression RNA assay
 assay <- seurat_obj[["RNA"]]
 
+# get counts matrix from either the old or newer formats of assay
+counts <- counts_matrix_from_assay(assay)
+
 # convert the count matrix, clusters, and projections into a Loupe file
 create_loupe(
-    assay@counts,
+    counts,
     clusters = select_clusters(seurat_obj),
     projections = select_projections(seurat_obj)
 )
diff --git a/man/counts_matrix_from_assay.Rd b/man/counts_matrix_from_assay.Rd
new file mode 100644
index 0000000..09d4c76
--- /dev/null
+++ b/man/counts_matrix_from_assay.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/util.R
+\name{counts_matrix_from_assay}
+\alias{counts_matrix_from_assay}
+\title{Extract the counts matrix from the Assay}
+\usage{
+counts_matrix_from_assay(assay)
+}
+\arguments{
+\item{assay}{A SeuratObject::Assay or SeuratObject::Assay5}
+}
+\value{
+A sparse counts matrix
+}
+\description{
+Extract the counts matrix from the Assay
+}
diff --git a/tests/testthat/test-util.R b/tests/testthat/test-util.R
index 7d72acd..0ba587f 100644
--- a/tests/testthat/test-util.R
+++ b/tests/testthat/test-util.R
@@ -4,15 +4,29 @@ test_that("select_assay selects active assay", {
   rna3 <- create_count_mat(5, 5)
 
   obj <- Seurat::CreateSeuratObject(rna1, assay="rna1")
-  obj[["rna2_"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
-  obj[["rna3_"]] = Seurat::CreateAssayObject(rna3, key="rna3_")
+  obj[["rna2"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
+  obj[["rna3"]] = Seurat::CreateAssayObject(rna3, key="rna3_")
 
   expect_equal(Seurat::DefaultAssay(object = obj), "rna1")
-  Seurat::DefaultAssay(object = obj) <- "rna2_"
-  expect_equal(Seurat::DefaultAssay(object = obj), "rna2_")
+  Seurat::DefaultAssay(object = obj) <- "rna2"
+  expect_equal(Seurat::DefaultAssay(object = obj), "rna2")
 
   assay <- select_assay(obj)
-  expect_equal(names(assay), "rna2_")
+  expect_equal(names(assay), "rna2")
+})
+
+test_that("counts_matrix_from_assay works on different assay version", {
+  rna1 <- create_count_mat(5, 5)
+  rna2 <- create_count_mat(5, 5)
+  rna3 <- create_count_mat(5, 5)
+
+  obj <- Seurat::CreateSeuratObject(rna1, assay="rna1")
+  obj[["rna2"]] = Seurat::CreateAssayObject(rna2, key="rna2_")
+  obj[["rna3"]] = SeuratObject::CreateAssay5Object(rna3, key="rna3_")
+
+  expect_equal(counts_matrix_from_assay(obj[["rna1"]]), rna1)
+  expect_equal(counts_matrix_from_assay(obj[["rna2"]]), rna2)
+  expect_equal(counts_matrix_from_assay(obj[["rna3"]]), rna3)
 })
 
 test_that("select_clusters selects Idents", {