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+++ b/docs/tutorials.html
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+</style>
+
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+
+
+
+
+</head>
+
+<body>
+
+
+<div class="container-fluid main-container">
+
+
+
+
+<div class="navbar navbar-default  navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="navbar-brand" href="index.html">VoltRon</a>
+    </div>
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="tutorials.html">Explore</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Vignette
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Spatial Data Integration</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="registration.html">Spatial Data Alignment</a>
+        </li>
+        <li>
+          <a href="multiomic.html">Multi-omic Integration</a>
+        </li>
+        <li>
+          <a href="nicheclustering.html">Niche Clustering</a>
+        </li>
+      </ul>
+    </li>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Downstream Analysis</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="roianalysis.html">ROI Analysis</a>
+        </li>
+        <li>
+          <a href="spotanalysis.html">Cell/Spot Analysis</a>
+        </li>
+        <li>
+          <a href="moleculeanalysis.html">Molecule Analysis</a>
+        </li>
+        <li>
+          <a href="pixelanalysis.html">Pixels (Image Only) Analysis</a>
+        </li>
+      </ul>
+    </li>
+    <li class="dropdown-submenu">
+      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Utilities</a>
+      <ul class="dropdown-menu" role="menu">
+        <li>
+          <a href="interactive.html">Interactive Utilities</a>
+        </li>
+        <li>
+          <a href="importingdata.html">Importing Spatial Data</a>
+        </li>
+        <li>
+          <a href="voltronobjects.html">Working with VoltRon Objects</a>
+        </li>
+        <li>
+          <a href="conversion.html">Converting VoltRon Objects</a>
+        </li>
+        <li>
+          <a href="ondisk.html">OnDisk-based Analysis Utilities</a>
+        </li>
+      </ul>
+    </li>
+  </ul>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <span class="fa fa-envelope-o"></span>
+     
+    Contact
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="https://bioinformatics.mdc-berlin.de">Altuna Lab/BIMSB Bioinfo</a>
+    </li>
+    <li>
+      <a href="https://www.mdc-berlin.de/landthaler">Landthaler Lab/BIMSB</a>
+    </li>
+  </ul>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <span class="fa fa-github"></span>
+     
+    GitHub
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="https://github.com/BIMSBbioinfo/VoltRon">VoltRon</a>
+    </li>
+    <li>
+      <a href="https://github.com/BIMSBbioinfo">BIMSB Bioinfo</a>
+    </li>
+  </ul>
+</li>
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+<div id="header">
+
+
+
+<h1 class="title toc-ignore">Tutorials</h1>
+
+</div>
+
+
+<style>
+.title{
+  display: none;
+}
+body {
+  text-align: justify
+}
+table, th, td, tr{
+  empty-cells:hide;
+  border-spacing: 25px;
+  border-collapse: separate;
+}
+td{
+  filter:drop-shadow(0 0 10px rgba(0,0,0,0.3));
+  padding: 10px;
+  background:white;
+  text-align:center;
+  width:33%;
+  vertical-align: text-top;
+}
+td:hover, td:active{
+  filter:drop-shadow(0 0 10px rgba(0,0,0,0.3));
+  transform: scale(1.02);
+  cursor: pointer;
+}
+.main-container {
+  max-width: 1200px;
+  margin-left: auto;
+  margin-right: auto;
+}
+<!-- .main-container { -->
+<!--   margin-left: %5; -->
+<!--   margin-right: auto; -->
+<!-- } -->
+p.tutorial {
+  text-decoration: none!important;
+  font-size: 1.5em;
+  color: #23803A;
+  margin: 3%
+}
+</style>
+<p><br> <!-- <br> --></p>
+<!-- ## Spatial Data Analysis with VoltRon -->
+<p><br></p>
+<div id="spatially-aware-data-integration-and-analysis"
+class="section level2">
+<h2>Spatially Aware Data Integration and Analysis</h2>
+<p><strong>VoltRon</strong> incorporates multiple <strong>data
+integration utilities to achieve data transfer</strong> across a diverse
+set of spatial data modalities and types. VoltRon utilizes OpenCV to
+align and synchronize spatial omic datasets using <strong>computer
+vision and image registration</strong>. Users can automaticaly or
+manually align a list of microscopy images (<strong>H&amp;E</strong>,
+<strong>DAPI</strong> etc) using a <strong>Shiny App</strong>
+incorporated within our analysis workflow. Once aligned, feature data
+and metadata level information can be transfered across aligned tissue
+sections.</p>
+<p>In addition, VoltRon provides a number of spatially aware data
+analysis methods to detecting niches (i.e. <strong>Niche
+Clustering</strong>) within tissues. VoltRon allows estimating niches
+associated with each cell by incorporating the cell type level
+information around each cell or spot. We either detect cellular
+populations/compositions within a spatial neighborhood of a cell to
+create these niche level information (e.g. Xenium) or we estimate the
+cell type abundances of spots (e.g. Visium, DBIT-Seq) from a reference
+single cell data (Seurat, SingleCellExperiment etc.) with already
+annotated cell types. VoltRon can also use these spatial neighborhood to
+detect hot spots (i.e. <strong>Hot Spot Analysis</strong>) of features,
+cell types and even molecular densities.</p>
+<div>
+<table>
+<tbody>
+<tr>
+<td onclick="location.href=&#39;registration.html&#39;;">
+<p class="tutorial">
+Spatial Data Alignment
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/registration.png" class="center">
+</div>
+<p style="margin-top: 3%">
+Automated and manual alignment of spatial data assays
+</p>
+</td>
+<td onclick="location.href=&#39;multiomic.html&#39;;">
+<p class="tutorial">
+Multi-omic Integration
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/multiomic.png" class="center">
+</div>
+<p style="margin-top: 8%">
+Integrating data modalities within or across tissue sections
+</p>
+</td>
+<td onclick="location.href=&#39;nicheclustering.html&#39;;">
+<p class="tutorial">
+Niche Clustering
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/deconvolution.png" class="center">
+</div>
+<p style="margin-top: 10%">
+Clustering based on ROI/spot deconvolution and Spatial Neighborhood
+</p>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<p><br> <br></p>
+</div>
+<div id="additional-downstream-analysis" class="section level2">
+<h2>Additional Downstream Analysis</h2>
+<p><strong>VoltRon</strong> is also capable of end-to-end analysis of
+diverse set of spatial data types (or spatial entities)such as
+<strong>ROIs</strong> (regions of interest), <strong>spots</strong>,
+<strong>single cells</strong>, <strong>molecules</strong> and even
+<strong>images</strong>. Users can set any data type as default at any
+time where VoltRon provides minimal set of functions to analyze, process
+and visualize each of these modalities.</p>
+<table>
+<tbody>
+<tr>
+<td onclick="location.href=&#39;roianalysis.html&#39;;">
+<p class="tutorial">
+Region of Interests (ROIs)
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/GeoMx.png" class="center">
+</div>
+<p style="margin-top: 7%">
+Quality control, analysis and visualization of ROI segments
+</p>
+</td>
+<td onclick="location.href=&#39;spotanalysis.html&#39;;">
+<p class="tutorial">
+Cells/Spots
+</p>
+<div style="margin: 5%">
+<img  src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/spotanalysis.png" class="center">
+</div>
+<p style="margin-top: 3%">
+Quality control, analysis and visualization of Cell/Spot datasets
+</p>
+</td>
+<td onclick="location.href=&#39;moleculeanalysis.html&#39;;">
+<p class="tutorial">
+Molecules
+</p>
+<br>
+<div style="margin: 5%">
+<img  src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/molecule_visualize.png" class="center">
+</div>
+<p style="margin-top: 10%">
+Analysis and visualization of Molecule datasets <br> <strong> (Under
+Development) </strong>
+</p>
+</td>
+</tr>
+<tr>
+<td onclick="location.href=&#39;pixelanalysis.html&#39;;">
+<p class="tutorial">
+Pixels (Image Only)
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/tissue_lowres_image_grid.png" class="center">
+</div>
+<p style="margin-top: 3%">
+Analysis and visualization of Image datasets <br> <strong> (Under
+Development) </strong>
+</p>
+</td>
+<td>
+</td>
+<td>
+</td>
+</tr>
+</tbody>
+</table>
+<p><br> <br></p>
+</div>
+<div id="other-utilities" class="section level2">
+<h2>Other Utilities</h2>
+<p>Here, we provide a group of tutorials to use additional features of
+the VoltRon objects as well as further information on how to use
+VoltRon. We describe a collection of features that VoltRon package
+utilizes such as <strong>interactive annotation/visualization</strong>
+and importing spatially aware data from <strong>diverse spatial omic
+technologies</strong>. VoltRon is able to convert its objects to a
+diverse set of objects/datatypes commonly incorporated spatial data
+analysis (<strong>Seurat</strong>, <strong>SpatialExperiment</strong>,
+<strong>Giotto</strong>, <strong>AnnData</strong> etc.). Large VoltRon
+objects can be <strong>saved ondisk</strong> and efficiently analyzed
+without straining memory.</p>
+<table>
+<tbody>
+<tr>
+<td onclick="location.href=&#39;interactive.html&#39;;">
+<p class="tutorial">
+Interactive Utilities
+</p>
+<br>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactiveannotation.png" class="center">
+</div>
+<p style="margin-top: 8%">
+Interactive annotation and visualization
+</p>
+</td>
+<td onclick="location.href=&#39;voltronobjects.html&#39;;">
+<p class="tutorial">
+Working with VoltRon Objects
+</p>
+<br>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltronobjects.png" class="center">
+</div>
+<br> <br>
+<p style="margin-top: 6%">
+Manipulating and configuring VoltRon objects
+</p>
+</td>
+<td onclick="location.href=&#39;importingdata.html&#39;;">
+<p class="tutorial">
+Importing Spatial Data
+</p>
+<div style="margin: 10%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/technologies.png" class="center">
+</div>
+<p style="margin-top: -3%">
+Importing readouts of spatial technologies
+</p>
+</td>
+</tr>
+<tr>
+<td onclick="location.href=&#39;conversion.html&#39;;">
+<p class="tutorial">
+Converting VoltRon Objects
+</p>
+<br>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/conversion.png" class="center">
+</div>
+<p style="margin-top: 9%">
+Converting VoltRon objects into Seurat, SpatialExperiment and Squidpy
+(anndata) etc.
+</p>
+</td>
+<td onclick="location.href=&#39;ondisk.html&#39;;">
+<p class="tutorial">
+OnDisk Analysis Utilities
+</p>
+<div style="margin: 5%">
+<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk.png" class="center">
+</div>
+<p style="margin: 5%">
+Efficient access to large VoltRon objects
+</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p><br></p>
+</div>
+
+
+
+
+</div>
+
+<script>
+
+// add bootstrap table styles to pandoc tables
+function bootstrapStylePandocTables() {
+  $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
+}
+$(document).ready(function () {
+  bootstrapStylePandocTables();
+});
+
+
+</script>
+
+<!-- tabsets -->
+
+<script>
+$(document).ready(function () {
+  window.buildTabsets("TOC");
+});
+
+$(document).ready(function () {
+  $('.tabset-dropdown > .nav-tabs > li').click(function () {
+    $(this).parent().toggleClass('nav-tabs-open');
+  });
+});
+</script>
+
+<!-- code folding -->
+
+
+<!-- dynamically load mathjax for compatibility with self-contained -->
+<script>
+  (function () {
+    var script = document.createElement("script");
+    script.type = "text/javascript";
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