rebuild documentation

- fix error message in example notebook - add stitching and parsing example notebooks
MannLabs · Sep 11, 2024 · 3190c2b · 3190c2b
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/nbsphinx/pages/notebooks/example_scPortrait_project.ipynb b/docs/doctrees/nbsphinx/pages/notebooks/example_scPortrait_project.ipynb
diff --git a/docs/doctrees/nbsphinx/pages/tools/parsing/example_parsing_notebook.ipynb b/docs/doctrees/nbsphinx/pages/tools/parsing/example_parsing_notebook.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6fc618c5",
+   "metadata": {},
+   "source": [
+    "# Example Parsing Notebook to rename phenix experiments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_13_0.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_13_0.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_1.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_1.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_10.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_10.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_11.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_11.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_12.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_12.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_13.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_13.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_15.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_15.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_2.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_2.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_3.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_3.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_5.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_5.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_6.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_16_6.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_18_1.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_18_1.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_18_2.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_18_2.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_3.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_3.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_4.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_4.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_5.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_23_5.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_33_0.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_33_0.png
diff --git a/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_41_13.png b/docs/doctrees/nbsphinx/pages_notebooks_example_scPortrait_project_41_13.png
diff --git a/docs/doctrees/pages/notebooks/example_scPortrait_project.doctree b/docs/doctrees/pages/notebooks/example_scPortrait_project.doctree
diff --git a/docs/doctrees/pages/tools/parsing/example_parsing_notebook.doctree b/docs/doctrees/pages/tools/parsing/example_parsing_notebook.doctree
diff --git a/docs/doctrees/pages/tools/parsing/parsing.doctree b/docs/doctrees/pages/tools/parsing/parsing.doctree
diff --git a/docs/doctrees/pages/tools/stitching/stitching.doctree b/docs/doctrees/pages/tools/stitching/stitching.doctree
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_13_0.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_13_0.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_1.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_1.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_10.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_10.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_11.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_11.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_12.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_12.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_13.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_13.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_15.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_15.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_2.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_2.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_3.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_3.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_5.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_5.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_16_6.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_16_6.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_18_1.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_18_1.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_18_2.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_18_2.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_23_3.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_23_3.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_23_4.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_23_4.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_23_5.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_23_5.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_33_0.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_33_0.png
diff --git a/docs/html/_images/pages_notebooks_example_scPortrait_project_41_13.png b/docs/html/_images/pages_notebooks_example_scPortrait_project_41_13.png
diff --git a/docs/html/_sources/pages/notebooks/example_scPortrait_project.ipynb.txt b/docs/html/_sources/pages/notebooks/example_scPortrait_project.ipynb.txt
diff --git a/docs/html/_sources/pages/pipeline/stitching.rst.txt b/docs/html/_sources/pages/pipeline/stitching.rst.txt
@@ -1,2 +1,3 @@
 stitching
-=========
+=========
+
diff --git a/docs/html/_sources/pages/tools/parsing/example_parsing_notebook.ipynb.txt b/docs/html/_sources/pages/tools/parsing/example_parsing_notebook.ipynb.txt
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6fc618c5",
+   "metadata": {},
+   "source": [
+    "# Example Parsing Notebook to rename phenix experiments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

diff --git a/docs/html/_sources/pages/tools/parsing/parsing.rst.txt b/docs/html/_sources/pages/tools/parsing/parsing.rst.txt
@@ -1,2 +1,9 @@
 parsing
-=======
+=======
+
+Example notebook showing the use of the parsing module.
+
+.. toctree::
+   :maxdepth: 2
+
+   example_parsing_notebook.ipynb
diff --git a/docs/html/_sources/pages/tools/stitching/stitching.rst.txt b/docs/html/_sources/pages/tools/stitching/stitching.rst.txt
@@ -1,2 +1,9 @@
 stitching
 =========
+
+Example notebook showing how to use the stitching module.
+
+.. toctree::
+   :maxdepth: 2
+
+   example_stitching_notebook.ipynb
diff --git a/docs/html/genindex.html b/docs/html/genindex.html
@@ -152,8 +152,29 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -156,8 +156,29 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>
@@ -322,8 +343,14 @@ <h1>Documentation<a class="headerlink" href="#documentation" title="Link to this
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a></li>
+</ul>
+</li>
 </ul>
 </div>
 <div class="toctree-wrapper compound">

diff --git a/docs/html/objects.inv b/docs/html/objects.inv
diff --git a/docs/html/pages/example_notebooks.html b/docs/html/pages/example_notebooks.html
@@ -157,8 +157,29 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>

diff --git a/docs/html/pages/module.html b/docs/html/pages/module.html
@@ -25,7 +25,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pipeline" href="module/pipeline.html" />
-    <link rel="prev" title="stitching" href="tools/stitching/stitching.html" /> 
+    <link rel="prev" title="Example Stitching Notebook" href="tools/stitching/example_stitching_notebook.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -155,8 +155,28 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a><ul class="simple">
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul class="current">
@@ -438,7 +458,7 @@ <h1>Module Documentation<a class="headerlink" href="#module-documentation" title
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="tools/stitching/stitching.html" class="btn btn-neutral float-left" title="stitching" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="tools/stitching/example_stitching_notebook.html" class="btn btn-neutral float-left" title="Example Stitching Notebook" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="module/pipeline.html" class="btn btn-neutral float-right" title="pipeline" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/docs/html/pages/module/io.html b/docs/html/pages/module/io.html
@@ -155,8 +155,28 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tools/parsing/parsing.html">parsing</a><ul class="simple">
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul class="current">

diff --git a/docs/html/pages/module/pipeline.html b/docs/html/pages/module/pipeline.html
@@ -155,8 +155,28 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tools/parsing/parsing.html">parsing</a><ul class="simple">
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="../tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul class="current">