diff --git a/.Rbuildignore b/.Rbuildignore
index 6e80a81..d461626 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -3,3 +3,4 @@
 docs
 ^.*\.md$
 ^data-raw$
+TODO.md
diff --git a/.gitignore b/.gitignore
index 5e22ad7..9bc2f42 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ vignettes/data
 .DS_Store
 ^.*\.md$
 ^data-raw$
+TODO.md
+data-raw
diff --git a/R/readMethods.R b/R/readMethods.R
index eafa1fc..522601f 100644
--- a/R/readMethods.R
+++ b/R/readMethods.R
@@ -19,6 +19,14 @@
 #' @importFrom SummarizedExperiment rowData
 #'
 #' @return A SpatialExperiment object
+#' @examples
+#'
+#' tenX_output_dir <- system.file("extdata/10x_output_subset", package = "CellSPA")
+#' tenX_output_tif <- system.file("extdata/10x_output_subset/10x_from_csv_subset.tif",
+#'                                 package = "CellSPA")
+#' spe_10x <- readXenium(tenX_output_dir,
+#'                       tiff_path = tenX_output_tif)
+#'
 #' @export
 
 
@@ -87,6 +95,14 @@ readXenium <- function(data_dir,
 #' @importFrom methods as
 #' @importFrom Matrix t
 #' @return A SpatialExperiment object
+#' @examples
+#'
+#' data_dir <- system.file("extdata/BIDCell_csv_output", package = "CellSPA")
+#' tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+#' spe <- readBIDCell(data_dir,
+#'                    tiff_path = tiff_path,
+#'                    method_name = "BIDCell")
+#'
 #' @export
 
 
@@ -177,6 +193,9 @@ readBIDCell <- function(data_dir,
 #' @importFrom tiff readTIFF
 #' @importFrom reshape2 melt
 #' @return A SpatialExperiment object
+#'
+#' tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+#' tiff_res <- readTiffOutput(tiff_path = tiff_path)
 #' @export
 
 readTiffOutput <- function(tiff_path) {
diff --git a/docs/articles/CellSPA.html b/docs/articles/CellSPA.html
index 13a907e..8adf0b2 100644
--- a/docs/articles/CellSPA.html
+++ b/docs/articles/CellSPA.html
@@ -85,7 +85,7 @@ <h2 id="read-bidcell-output">Read BIDCell output<a class="anchor" aria-label="an
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_dir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/BIDCell_csv_output"</span>, package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span>
 <span><span class="va">data_dir</span></span>
-<span><span class="co">#&gt; [1] "/private/var/folders/80/p95h23h55rs4lv59jms7k0fc0000gn/T/RtmprKO5fO/temp_libpath912a6ecf4153/CellSPA/extdata/BIDCell_csv_output"</span></span>
+<span><span class="co">#&gt; [1] "/private/var/folders/80/p95h23h55rs4lv59jms7k0fc0000gn/T/Rtmp5FCHvo/temp_libpathd7804409ffcd/CellSPA/extdata/BIDCell_csv_output"</span></span>
 <span><span class="va">tiff_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/BIDCell_output_subset.tif"</span>, package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span>
 <span><span class="va">spe</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/readBIDCell.html">readBIDCell</a></span><span class="op">(</span><span class="va">data_dir</span>,</span>
 <span>                   tiff_path <span class="op">=</span> <span class="va">tiff_path</span>,</span>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 839947f..b4dc54c 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.6
 pkgdown_sha: ~
 articles:
   CellSPA: CellSPA.html
-last_built: 2023-07-13T18:23Z
+last_built: 2023-07-13T20:28Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
new file mode 100644
index 0000000..17a3580
Binary files /dev/null and b/docs/reference/Rplot001.png differ
diff --git a/docs/reference/readBIDCell.html b/docs/reference/readBIDCell.html
index f87f50a..752612f 100644
--- a/docs/reference/readBIDCell.html
+++ b/docs/reference/readBIDCell.html
@@ -77,6 +77,17 @@ <h2>Value</h2>
 <p>A SpatialExperiment object</p>
     </div>
 
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">data_dir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/BIDCell_csv_output"</span>, package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">tiff_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/BIDCell_output_subset.tif"</span>, package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">spe</span> <span class="op">&lt;-</span> <span class="fu">readBIDCell</span><span class="op">(</span><span class="va">data_dir</span>,</span></span>
+<span class="r-in"><span>                   tiff_path <span class="op">=</span> <span class="va">tiff_path</span>,</span></span>
+<span class="r-in"><span>                   method_name <span class="op">=</span> <span class="st">"BIDCell"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
diff --git a/docs/reference/readTiffOutput.html b/docs/reference/readTiffOutput.html
index 38fb5a1..6113d57 100644
--- a/docs/reference/readTiffOutput.html
+++ b/docs/reference/readTiffOutput.html
@@ -61,6 +61,10 @@ <h2>Value</h2>
     
 
 <p>A SpatialExperiment object</p>
+
+
+<p>tiff_path &lt;- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+tiff_res &lt;- readTiffOutput(tiff_path = tiff_path)</p>
     </div>
 
   </div>
diff --git a/docs/reference/readXenium.html b/docs/reference/readXenium.html
index 15fe646..72efbe4 100644
--- a/docs/reference/readXenium.html
+++ b/docs/reference/readXenium.html
@@ -88,6 +88,18 @@ <h2>Value</h2>
 <p>A SpatialExperiment object</p>
     </div>
 
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">tenX_output_dir</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/10x_output_subset"</span>, package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">tenX_output_tif</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/10x_output_subset/10x_from_csv_subset.tif"</span>,</span></span>
+<span class="r-in"><span>                                package <span class="op">=</span> <span class="st">"CellSPA"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">spe_10x</span> <span class="op">&lt;-</span> <span class="fu">readXenium</span><span class="op">(</span><span class="va">tenX_output_dir</span>,</span></span>
+<span class="r-in"><span>                      tiff_path <span class="op">=</span> <span class="va">tenX_output_tif</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> as(&lt;dgTMatrix&gt;, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead</span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
diff --git a/man/readBIDCell.Rd b/man/readBIDCell.Rd
index 95b96a9..c6aed61 100644
--- a/man/readBIDCell.Rd
+++ b/man/readBIDCell.Rd
@@ -23,3 +23,12 @@ A SpatialExperiment object
 \description{
 Read BIDCell output
 }
+\examples{
+
+data_dir <- system.file("extdata/BIDCell_csv_output", package = "CellSPA")
+tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+spe <- readBIDCell(data_dir,
+                   tiff_path = tiff_path,
+                   method_name = "BIDCell")
+
+}
diff --git a/man/readTiffOutput.Rd b/man/readTiffOutput.Rd
index dddd057..aa1a0d2 100644
--- a/man/readTiffOutput.Rd
+++ b/man/readTiffOutput.Rd
@@ -11,6 +11,9 @@ readTiffOutput(tiff_path)
 }
 \value{
 A SpatialExperiment object
+
+tiff_path <- system.file("extdata/BIDCell_output_subset.tif", package = "CellSPA")
+tiff_res <- readTiffOutput(tiff_path = tiff_path)
 }
 \description{
 Read Tiff output from BIDCell
diff --git a/man/readXenium.Rd b/man/readXenium.Rd
index a1bb5fc..66a226d 100644
--- a/man/readXenium.Rd
+++ b/man/readXenium.Rd
@@ -32,3 +32,12 @@ A SpatialExperiment object
 \description{
 Read Xenium output
 }
+\examples{
+
+tenX_output_dir <- system.file("extdata/10x_output_subset", package = "CellSPA")
+tenX_output_tif <- system.file("extdata/10x_output_subset/10x_from_csv_subset.tif",
+                                package = "CellSPA")
+spe_10x <- readXenium(tenX_output_dir,
+                      tiff_path = tenX_output_tif)
+
+}