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+      <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>
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+  <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>
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+        <li>
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+        </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>
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+        <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>
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+     
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+  <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>
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+    <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 -->
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+<h1 class="title toc-ignore">VoltRon</h1>
+
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+</style>
+<p><br></p>
+<!-- ## VoltRon: An R package for Spatial Data Analysis and Integration -->
+<p><br></p>
+<div style="width:76%; margin-left: auto; margin-right: auto; ">
+<p><img width="100%" height="100%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltron_framework_box_io.png" class="center"></p>
+<p><br></p>
+<p class="maintext">
+<strong> VoltRon </strong> is a spatial omic analysis toolbox for
+multi-omics integration using spatial image registration. VoltRon is
+also capable of analyzing multiple types of spatially-aware data
+modalities.
+</p>
+<ul class="maintext2">
+<li style="padding-bottom: 10px">
+<strong> Unique data structure </strong> of VoltRon allows users to
+seamlessly define tissue blocks, layers and multiple assay types in one
+R object.
+</li>
+<li style="padding-bottom: 10px">
+<strong> End-to-end downstream data analysis </strong> for distinct
+spatial biology technologies are supported. VoltRon visualizes and
+analyzes regions of interests (ROIs), spots, cells, molecules and tiles
+<strong>(under development)</strong>.
+</li>
+<li style="padding-bottom: 10px">
+<strong> Automated Image Registration </strong> incorporates
+<a href="https://opencv.org/">OpenCV</a> (fully embedded into the
+package using <a href="https://www.rcpp.org/">Rcpp</a>) to detect common
+features across images and achieves registration. Users may interact
+with built-in mini shiny apps to change alignment parameters and
+validate alignment accuracy.
+</li>
+<li style="padding-bottom: 10px">
+<strong> Manual Image Registration </strong> helps users to select
+common features across spatial datasets using reference images stored in
+VoltRon objects. In case automated image registration doesn’t work, you
+can still align images by manually picking landmark points.
+</li>
+<li style="padding-bottom: 10px">
+<p style="padding-bottom: 3px">
+<strong> Spatially Aware Analysis </strong> allows detecting spatial
+patterns across cells, spots, molecules and other entities.
+</p>
+<ul class="maintext3">
+<li style="padding-bottom: 10px padding-top: 12px">
+<strong>(Niche Clustering: Spots)</strong> VoltRon allows integration to
+single cell RNA datasets using
+<a href="https://satijalab.org/seurat/">Seurat</a>,
+<a href="https://www.bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SingleCellExperiment</a>
+and <a href="https://github.com/dmcable/spacexr">spacexr</a> for spot
+deconvolution. Estimated cell type abundances are then used to cluster
+spots into groups of cell type niches which are defined as spots with
+distinct composition of cell types.
+</li>
+<li style="padding-bottom: 2px">
+<strong>(Niche Clustering: Cells)</strong> VoltRon creates spatial
+neighborhoods around cells to cluster local cellular compositions around
+all cells which in turn informs users on cell types that are likely
+within proximity to each other.
+</li>
+<li style="padding-bottom: 10px">
+<strong>(Hot Spot Detection)</strong> VoltRon detects region of locally
+spatial patterns of cells/molecules/spots that are abundant in
+biological events and/or features.
+</li>
+</ul>
+</li>
+<li style="padding-bottom: 10px">
+<p>
+<strong> Support for Big Data </strong> for VoltRon objects enables
+storing large feature data matrices and large microscopic images of
+tissues on disk without overloading memory, thus allowing analysis on
+large datasets with ease. VoltRon stores large images as pyramid
+structures to speed up visualization and data retrieval.
+</p>
+</li>
+<li style="padding-bottom: 10px">
+<p>
+<strong> Interoperability across R/Python frameworks </strong> allows
+users to convert VoltRon objects to a large number of objects used by
+other spatial omic platforms such as Seurat, Squidpy (AnnData),
+SpatialExperiment (BioConductor) and Giotto.
+</p>
+</li>
+</ul>
+</div>
+<div style="width:70%; margin-left: auto; margin-right: auto">
+<div style="float:left; margin-left: auto; margin-right: auto">
+<p><br></p>
+<div id="staying-up-to-date" class="section level2">
+<h2>Staying up-to-date</h2>
+<p>To ask questions please use VoltRon discussion forum on google
+groups.</p>
+<ul>
+<li><a href="https://groups.google.com/forum/#!forum/voltron_discussion"
+class="uri">https://groups.google.com/forum/#!forum/voltron_discussion</a></li>
+</ul>
+<p><br></p>
+</div>
+<div id="installation" class="section level2">
+<h2>Installation</h2>
+<p>Install from the GitHub repository using devtools (with R version
+4.3.0 or higher):</p>
+<pre class="r"><code>if (!require(&quot;devtools&quot;, quietly = TRUE))
+    install.packages(&quot;devtools&quot;)
+devtools::install_github(&quot;BIMSBbioinfo/VoltRon&quot;)</code></pre>
+<p>Depending on the number of required dependencies, installation may be
+completed under a minute or may take a few minutes.</p>
+<p>On <strong>Windows</strong> and <strong>MacOS</strong>, OpenCV will
+be downloaded automatically upon installation. However, <a
+href="https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html">Rtools</a>
+may be required to be downloaded too, hence this may take some time!</p>
+<p>On <strong>Ubuntu</strong> we provide a set of instructions that may
+help users to build OpenCV with necessary headers [here](<a
+href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md"
+class="uri">https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md</a>.</p>
+<p>On <strong>Fedora</strong> you may need <a
+href="https://src.fedoraproject.org/rpms/opencv"><code>opencv-devel</code></a>:</p>
+<pre class="sh"><code>yum install opencv-devel</code></pre>
+<p><br></p>
+</div>
+<div id="dependencies" class="section level2">
+<h2>Dependencies</h2>
+<p>VoltRon incorporates <code>RBioformats</code> package to import
+images from <code>ome.tiff</code> files, which requires <a
+href="https://www.oracle.com/java/technologies/downloads/?er=221886">Java
+JDK</a> to be available in your system:</p>
+<p>See <a
+href="https://cran.r-project.org/web/packages/rJava">https://cran.r-project.org/web/packages/rJava</a>
+for more information.</p>
+<p><br></p>
+</div>
+<div id="docker-hub" class="section level2">
+<h2>Docker Hub</h2>
+<p>You can also run VoltRon from a container already available in <a
+href="https://hub.docker.com/repository/docker/amanukyan1385/rstudio-voltron/general">Docker
+Hub</a>. The docker image is based on the <a
+href="https://rocker-project.org/">Rocker Project</a> and can be run
+from the terminal like below:</p>
+<pre><code>docker run --rm -ti -e PASSWORD=&lt;yourpassword&gt; -p 8787:8787 amanukyan1385/rstudio-voltron:main</code></pre>
+<p>Then, start the RStudio session from the browser at
+<code>http://localhost:8787/</code> and enter <code>rstudio</code> as
+username and <code>&lt;yourpassword&gt;</code> as password.</p>
+<p>See <a
+href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/docker_desktop_instructions.md">here</a>
+for more instructions on how to run the container using <a
+href="https://www.docker.com/products/docker-desktop/">Docker
+Desktop</a>.</p>
+<p><br></p>
+</div>
+<div id="references" class="section level2">
+<h2>References</h2>
+<p>Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A.,
+Plumbom, I., … &amp; Akalin, A. (2023). <a
+href="https://www.biorxiv.org/content/10.1101/2023.12.15.571667v1">VoltRon:
+A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics
+Integration using Image Registration</a>. bioRxiv, 2023-12. d</p>
+<p>To ask questions please use VoltRon discussion forum on <a
+href="https://groups.google.com/forum/#!forum/voltron_discussion">Google
+groups</a>.</p>
+</div>
+</div>
+</div>
+
+
+
+
+</div>
+
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