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<!DOCTYPE html>





  
  

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<html>





  
  

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<head>





  
  

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<meta charset="utf-8" />





  
  

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<meta name="generator" content="pandoc" />





  
  

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<title>VoltRon</title>





  
  

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<script src="site_libs/header-attrs-2.29/header-attrs.js"></script>





  
  

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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>





  
  

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<meta name="viewport" content="width=device-width, initial-scale=1" />





  
  

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<link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />





  
  

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<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>





  
  

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<style>h1 {font-size: 34px;}





  
  

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}





  
  

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</style>





  
  

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<script type="text/javascript">





  
  

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// manage active state of menu based on current page





  
  

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$(document).ready(function () {





  
  

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  // active menu anchor





  
  

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  href = window.location.pathname





  
  

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    dropdown.find('> .dropdown-toggle').addClass('active');





  
  

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  } else { // Bootstrap 3





  
  

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  }





  
  

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});





  
  

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</script>





  
  

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}





  
  

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}





  
  

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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {





  
  

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</style>





  
  

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<!-- code folding -->





  
  

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</head>





  
  

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<body>





  
  

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<div class="container-fluid main-container">





  
  

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<div class="navbar navbar-default  navbar-fixed-top" role="navigation">





  
  

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  <div class="container">





  
  

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    <div class="navbar-header">





  
  

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      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">





  
  

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        <span class="icon-bar"></span>





  
  

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        <span class="icon-bar"></span>





  
  

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        <span class="icon-bar"></span>





  
  

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      </button>





  
  

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      <a class="navbar-brand" href="index.html">VoltRon</a>





  
  

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    </div>





  
  

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    <div id="navbar" class="navbar-collapse collapse">





  
  

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      <ul class="nav navbar-nav">





  
  

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        <li>





  
  

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  <a href="tutorials.html">Explore</a>





  
  

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</li>





  
  

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<li class="dropdown">





  
  

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  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

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    Vignette





  
  

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    <span class="caret"></span>





  
  

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  </a>





  
  

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  <ul class="dropdown-menu" role="menu">





  
  

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    <li class="dropdown-submenu">





  
  

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      <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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      <ul class="dropdown-menu" role="menu">





  
  

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        <li>





  
  

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          <a href="registration.html">Spatial Data Alignment</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="multiomic.html">Multi-omic Integration</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="nicheclustering.html">Niche Clustering</a>





  
  

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        </li>





  
  

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      </ul>





  
  

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    </li>





  
  

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    <li class="dropdown-submenu">





  
  

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      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Downstream Analysis</a>





  
  

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      <ul class="dropdown-menu" role="menu">





  
  

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        <li>





  
  

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          <a href="roianalysis.html">ROI Analysis</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="spotanalysis.html">Cell/Spot Analysis</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="moleculeanalysis.html">Molecule Analysis</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="pixelanalysis.html">Pixels (Image Only) Analysis</a>





  
  

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        </li>





  
  

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      </ul>





  
  

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    </li>





  
  

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    <li class="dropdown-submenu">





  
  

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      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Utilities</a>





  
  

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      <ul class="dropdown-menu" role="menu">





  
  

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        <li>





  
  

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          <a href="interactive.html">Interactive Utilities</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="importingdata.html">Importing Spatial Data</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="voltronobjects.html">Working with VoltRon Objects</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="conversion.html">Converting VoltRon Objects</a>





  
  

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        </li>





  
  

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        <li>





  
  

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          <a href="ondisk.html">OnDisk-based Analysis Utilities</a>





  
  

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        </li>





  
  

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      </ul>





  
  

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    </li>





  
  

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  </ul>





  
  

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</li>





  
  

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      </ul>





  
  

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      <ul class="nav navbar-nav navbar-right">





  
  

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        <li class="dropdown">





  
  

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  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

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    <span class="fa fa-envelope-o"></span>





  
  

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    Contact





  
  

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    <span class="caret"></span>





  
  

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  </a>





  
  

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  <ul class="dropdown-menu" role="menu">





  
  

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    <li>





  
  

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      <a href="https://bioinformatics.mdc-berlin.de">Altuna Lab/BIMSB Bioinfo</a>





  
  

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    </li>





  
  

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    <li>





  
  

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      <a href="https://www.mdc-berlin.de/landthaler">Landthaler Lab/BIMSB</a>





  
  

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    </li>





  
  

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  </ul>





  
  

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</li>





  
  

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  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

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    <span class="fa fa-github"></span>





  
  

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    GitHub





  
  

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    <span class="caret"></span>





  
  

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  </a>





  
  

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  <ul class="dropdown-menu" role="menu">





  
  

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    <li>





  
  

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      <a href="https://github.com/BIMSBbioinfo/VoltRon">VoltRon</a>





  
  

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    </li>





  
  

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    <li>





  
  

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      <a href="https://github.com/BIMSBbioinfo">BIMSB Bioinfo</a>





  
  

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    </li>





  
  

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  </ul>





  
  

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</li>





  
  

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      </ul>





  
  

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    </div><!--/.nav-collapse -->





  
  

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</div><!--/.navbar -->





  
  

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<div id="header">





  
  

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<h1 class="title toc-ignore">VoltRon</h1>





  
  

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</div>





  
  

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body {





  
  

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}





  
  

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  font-size: 1.1em;





  
  

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<p><br></p>





  
  

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<!-- ## VoltRon: An R package for Spatial Data Analysis and Integration -->





  
  

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<p><br></p>





  
  

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<div style="width:76%; margin-left: auto; margin-right: auto; ">





  
  

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<p><img width="100%" height="100%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltron_framework_box_io.png" class="center"></p>





  
  

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<p><br></p>





  
  

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<p class="maintext">





  
  

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<strong> VoltRon </strong> is a spatial omic analysis toolbox for





  
  

  401
  
multi-omics integration using spatial image registration. VoltRon is





  
  

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also capable of analyzing multiple types of spatially-aware data





  
  

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modalities.





  
  

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</p>





  
  

  405
  
<ul class="maintext2">





  
  

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<li style="padding-bottom: 10px">





  
  

  407
  
<strong> Unique data structure </strong> of VoltRon allows users to





  
  

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seamlessly define tissue blocks, layers and multiple assay types in one





  
  

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R object.





  
  

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</li>





  
  

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<li style="padding-bottom: 10px">





  
  

  412
  
<strong> End-to-end downstream data analysis </strong> for distinct





  
  

  413
  
spatial biology technologies are supported. VoltRon visualizes and





  
  

  414
  
analyzes regions of interests (ROIs), spots, cells, molecules and tiles





  
  

  415
  
<strong>(under development)</strong>.





  
  

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</li>





  
  

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<li style="padding-bottom: 10px">





  
  

  418
  
<strong> Automated Image Registration </strong> incorporates





  
  

  419
  
<a href="https://opencv.org/">OpenCV</a> (fully embedded into the





  
  

  420
  
package using <a href="https://www.rcpp.org/">Rcpp</a>) to detect common





  
  

  421
  
features across images and achieves registration. Users may interact





  
  

  422
  
with built-in mini shiny apps to change alignment parameters and





  
  

  423
  
validate alignment accuracy.





  
  

  424
  
</li>





  
  

  425
  
<li style="padding-bottom: 10px">





  
  

  426
  
<strong> Manual Image Registration </strong> helps users to select





  
  

  427
  
common features across spatial datasets using reference images stored in





  
  

  428
  
VoltRon objects. In case automated image registration doesn’t work, you





  
  

  429
  
can still align images by manually picking landmark points.





  
  

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</li>





  
  

  431
  
<li style="padding-bottom: 10px">





  
  

  432
  
<p style="padding-bottom: 3px">





  
  

  433
  
<strong> Spatially Aware Analysis </strong> allows detecting spatial





  
  

  434
  
patterns across cells, spots, molecules and other entities.





  
  

  435
  
</p>





  
  

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<ul class="maintext3">





  
  

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<li style="padding-bottom: 10px padding-top: 12px">





  
  

  438
  
<strong>(Niche Clustering: Spots)</strong> VoltRon allows integration to





  
  

  439
  
single cell RNA datasets using





  
  

  440
  
<a href="https://satijalab.org/seurat/">Seurat</a>,





  
  

  441
  
<a href="https://www.bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SingleCellExperiment</a>





  
  

  442
  
and <a href="https://github.com/dmcable/spacexr">spacexr</a> for spot





  
  

  443
  
deconvolution. Estimated cell type abundances are then used to cluster





  
  

  444
  
spots into groups of cell type niches which are defined as spots with





  
  

  445
  
distinct composition of cell types.





  
  

  446
  
</li>





  
  

  447
  
<li style="padding-bottom: 2px">





  
  

  448
  
<strong>(Niche Clustering: Cells)</strong> VoltRon creates spatial





  
  

  449
  
neighborhoods around cells to cluster local cellular compositions around





  
  

  450
  
all cells which in turn informs users on cell types that are likely





  
  

  451
  
within proximity to each other.





  
  

  452
  
</li>





  
  

  453
  
<li style="padding-bottom: 10px">





  
  

  454
  
<strong>(Hot Spot Detection)</strong> VoltRon detects region of locally





  
  

  455
  
spatial patterns of cells/molecules/spots that are abundant in





  
  

  456
  
biological events and/or features.





  
  

  457
  
</li>





  
  

  458
  
</ul>





  
  

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</li>





  
  

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<li style="padding-bottom: 10px">





  
  

  461
  
<p>





  
  

  462
  
<strong> Support for Big Data </strong> for VoltRon objects enables





  
  

  463
  
storing large feature data matrices and large microscopic images of





  
  

  464
  
tissues on disk without overloading memory, thus allowing analysis on





  
  

  465
  
large datasets with ease. VoltRon stores large images as pyramid





  
  

  466
  
structures to speed up visualization and data retrieval.





  
  

  467
  
</p>





  
  

  468
  
</li>





  
  

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<li style="padding-bottom: 10px">





  
  

  470
  
<p>





  
  

  471
  
<strong> Interoperability across R/Python frameworks </strong> allows





  
  

  472
  
users to convert VoltRon objects to a large number of objects used by





  
  

  473
  
other spatial omic platforms such as Seurat, Squidpy (AnnData),





  
  

  474
  
SpatialExperiment (BioConductor) and Giotto.





  
  

  475
  
</p>





  
  

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</li>





  
  

  477
  
</ul>





  
  

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</div>





  
  

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<div style="width:70%; margin-left: auto; margin-right: auto">





  
  

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<div style="float:left; margin-left: auto; margin-right: auto">





  
  

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<p><br></p>





  
  

  482
  
<div id="staying-up-to-date" class="section level2">





  
  

  483
  
<h2>Staying up-to-date</h2>





  
  

  484
  
<p>To ask questions please use VoltRon discussion forum on google





  
  

  485
  
groups.</p>





  
  

  486
  
<ul>





  
  

  487
  
<li><a href="https://groups.google.com/forum/#!forum/voltron_discussion"





  
  

  488
  
class="uri">https://groups.google.com/forum/#!forum/voltron_discussion</a></li>





  
  

  489
  
</ul>





  
  

  490
  
<p><br></p>





  
  

  491
  
</div>





  
  

  492
  
<div id="installation" class="section level2">





  
  

  493
  
<h2>Installation</h2>





  
  

  494
  
<p>Install from the GitHub repository using devtools (with R version





  
  

  495
  
4.3.0 or higher):</p>





  
  

  496
  
<pre class="r"><code>if (!require(&quot;devtools&quot;, quietly = TRUE))





  
  

  497
  
    install.packages(&quot;devtools&quot;)





  
  

  498
  
devtools::install_github(&quot;BIMSBbioinfo/VoltRon&quot;)</code></pre>





  
  

  499
  
<p>Depending on the number of required dependencies, installation may be





  
  

  500
  
completed under a minute or may take a few minutes.</p>





  
  

  501
  
<p>On <strong>Windows</strong> and <strong>MacOS</strong>, OpenCV will





  
  

  502
  
be downloaded automatically upon installation. However, <a





  
  

  503
  
href="https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html">Rtools</a>





  
  

  504
  
may be required to be downloaded too, hence this may take some time!</p>





  
  

  505
  
<p>On <strong>Ubuntu</strong> we provide a set of instructions that may





  
  

  506
  
help users to build OpenCV with necessary headers [here](<a





  
  

  507
  
href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md"





  
  

  508
  
class="uri">https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md</a>.</p>





  
  

  509
  
<p>On <strong>Fedora</strong> you may need <a





  
  

  510
  
href="https://src.fedoraproject.org/rpms/opencv"><code>opencv-devel</code></a>:</p>





  
  

  511
  
<pre class="sh"><code>yum install opencv-devel</code></pre>





  
  

  512
  
<p><br></p>





  
  

  513
  
</div>





  
  

  514
  
<div id="dependencies" class="section level2">





  
  

  515
  
<h2>Dependencies</h2>





  
  

  516
  
<p>VoltRon incorporates <code>RBioformats</code> package to import





  
  

  517
  
images from <code>ome.tiff</code> files, which requires <a





  
  

  518
  
href="https://www.oracle.com/java/technologies/downloads/?er=221886">Java





  
  

  519
  
JDK</a> to be available in your system:</p>





  
  

  520
  
<p>See <a





  
  

  521
  
href="https://cran.r-project.org/web/packages/rJava">https://cran.r-project.org/web/packages/rJava</a>





  
  

  522
  
for more information.</p>





  
  

  523
  
<p><br></p>





  
  

  524
  
</div>





  
  

  525
  
<div id="docker-hub" class="section level2">





  
  

  526
  
<h2>Docker Hub</h2>





  
  

  527
  
<p>You can also run VoltRon from a container already available in <a





  
  

  528
  
href="https://hub.docker.com/repository/docker/amanukyan1385/rstudio-voltron/general">Docker





  
  

  529
  
Hub</a>. The docker image is based on the <a





  
  

  530
  
href="https://rocker-project.org/">Rocker Project</a> and can be run





  
  

  531
  
from the terminal like below:</p>





  
  

  532
  
<pre><code>docker run --rm -ti -e PASSWORD=&lt;yourpassword&gt; -p 8787:8787 amanukyan1385/rstudio-voltron:main</code></pre>





  
  

  533
  
<p>Then, start the RStudio session from the browser at





  
  

  534
  
<code>http://localhost:8787/</code> and enter <code>rstudio</code> as





  
  

  535
  
username and <code>&lt;yourpassword&gt;</code> as password.</p>





  
  

  536
  
<p>See <a





  
  

  537
  
href="https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/docker_desktop_instructions.md">here</a>





  
  

  538
  
for more instructions on how to run the container using <a





  
  

  539
  
href="https://www.docker.com/products/docker-desktop/">Docker





  
  

  540
  
Desktop</a>.</p>





  
  

  541
  
<p><br></p>





  
  

  542
  
</div>





  
  

  543
  
<div id="references" class="section level2">





  
  

  544
  
<h2>References</h2>





  
  

  545
  
<p>Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A.,





  
  

  546
  
Plumbom, I., … &amp; Akalin, A. (2023). <a





  
  

  547
  
href="https://www.biorxiv.org/content/10.1101/2023.12.15.571667v1">VoltRon:





  
  

  548
  
A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics





  
  

  549
  
Integration using Image Registration</a>. bioRxiv, 2023-12. d</p>





  
  

  550
  
<p>To ask questions please use VoltRon discussion forum on <a





  
  

  551
  
href="https://groups.google.com/forum/#!forum/voltron_discussion">Google





  
  

  552
  
groups</a>.</p>





  
  

  553
  
</div>





  
  

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</div>





  
  

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