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diff --git a/docs/404.html b/docs/404.html
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   <title>Page not found | Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="Page not found | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
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@@ -361,10 +361,11 @@
 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>

diff --git a/docs/contributing-to-giotto.html b/docs/contributing-to-giotto.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>18 Contributing to Giotto | Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="18 Contributing to Giotto | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39 and GitBook 2.6.7" />
 
   <meta property="og:title" content="18 Contributing to Giotto | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
   <meta property="og:type" content="book" />
@@ -55,7 +55,7 @@
 
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@@ -361,10 +361,11 @@
 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>
@@ -577,7 +578,7 @@ <h1>
 <h1><span class="header-section-number">18</span> Contributing to Giotto<a href="contributing-to-giotto.html#contributing-to-giotto" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>Jiaji George Chen</p>
 <p>August 7th 2024</p>
-<div class="sourceCode" id="cb474"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb474-1"><a href="contributing-to-giotto.html#cb474-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/03_session7&quot;</span></span></code></pre></div>
+<div class="sourceCode" id="cb493"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb493-1"><a href="contributing-to-giotto.html#cb493-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/03_session7&quot;</span></span></code></pre></div>
 <div id="contribution-guideline" class="section level2 hasAnchor" number="18.1">
 <h2><span class="header-section-number">18.1</span> Contribution guideline<a href="contributing-to-giotto.html#contribution-guideline" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p><a href="https://drieslab.github.io/Giotto_website/CONTRIBUTING.html" class="uri">https://drieslab.github.io/Giotto_website/CONTRIBUTING.html</a></p>

diff --git a/docs/creating-a-giotto-object.html b/docs/creating-a-giotto-object.html
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   <title>6 Creating a Giotto object | Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="6 Creating a Giotto object | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
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@@ -55,7 +55,7 @@
 
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@@ -361,10 +361,11 @@
 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>

diff --git a/docs/data-formatting-and-pre-processing.html b/docs/data-formatting-and-pre-processing.html
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   <title>5 Data formatting and Pre-processing | Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="5 Data formatting and Pre-processing | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
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 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>

diff --git a/docs/datasets-packages.html b/docs/datasets-packages.html
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   <title>2 Datasets &amp; Packages | Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="2 Datasets &amp; Packages | Workshop: Spatial multi-omics data analysis with Giotto Suite" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
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 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>

diff --git a/docs/index.html b/docs/index.html
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   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Workshop: Spatial multi-omics data analysis with Giotto Suite</title>
   <meta name="description" content="Workshop: Spatial multi-omics data analysis with Giotto Suite" />
-  <meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.39 and GitBook 2.6.7" />
 
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 <li class="chapter" data-level="10.6" data-path="xenium-1.html"><a href="xenium-1.html#spatial-aggregation"><i class="fa fa-check"></i><b>10.6</b> Spatial aggregation</a></li>
 <li class="chapter" data-level="10.7" data-path="xenium-1.html"><a href="xenium-1.html#aggregate-analyses-workflow"><i class="fa fa-check"></i><b>10.7</b> Aggregate analyses workflow</a>
 <ul>
-<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.1</b> Filtering</a></li>
-<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.2</b> Normalization</a></li>
-<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.3</b> Dimension Reduction</a></li>
-<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.4</b> Clustering</a></li>
+<li class="chapter" data-level="10.7.1" data-path="xenium-1.html"><a href="xenium-1.html#transcripts-per-cell"><i class="fa fa-check"></i><b>10.7.1</b> Transcripts per cell</a></li>
+<li class="chapter" data-level="10.7.2" data-path="xenium-1.html"><a href="xenium-1.html#filtering-1"><i class="fa fa-check"></i><b>10.7.2</b> Filtering</a></li>
+<li class="chapter" data-level="10.7.3" data-path="xenium-1.html"><a href="xenium-1.html#normalization-1"><i class="fa fa-check"></i><b>10.7.3</b> Normalization</a></li>
+<li class="chapter" data-level="10.7.4" data-path="xenium-1.html"><a href="xenium-1.html#dimension-reduction-1"><i class="fa fa-check"></i><b>10.7.4</b> Dimension Reduction</a></li>
+<li class="chapter" data-level="10.7.5" data-path="xenium-1.html"><a href="xenium-1.html#clustering-1"><i class="fa fa-check"></i><b>10.7.5</b> Clustering</a></li>
 </ul></li>
 <li class="chapter" data-level="10.8" data-path="xenium-1.html"><a href="xenium-1.html#niche-clustering-1"><i class="fa fa-check"></i><b>10.8</b> Niche clustering</a>
 <ul>