Log In Sign Up
Models:
Alyssa Salazar
AlyssaS/
VoltRon
0
Downloads: 1
Diff of /docs/tutorials.html [000000] .. [413088]

Switch to unified view

a b/docs/tutorials.html 

  1
  
<!DOCTYPE html>





  
  

  2
  





  
  

  3
  
<html>





  
  

  4
  





  
  

  5
  
<head>





  
  

  6
  





  
  

  7
  
<meta charset="utf-8" />





  
  

  8
  
<meta name="generator" content="pandoc" />





  
  

  9
  
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />





  
  

  10
  





  
  

  11
  





  
  

  12
  





  
  

  13
  





  
  

  14
  
<title>Tutorials</title>





  
  

  15
  





  
  

  16
  
<script src="site_libs/header-attrs-2.29/header-attrs.js"></script>





  
  

  17
  
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>





  
  

  18
  
<meta name="viewport" content="width=device-width, initial-scale=1" />





  
  

  19
  
<link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />





  
  

  20
  
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>





  
  

  21
  
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>





  
  

  22
  
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>





  
  

  23
  
<style>h1 {font-size: 34px;}





  
  

  24
  
       h1.title {font-size: 38px;}





  
  

  25
  
       h2 {font-size: 30px;}





  
  

  26
  
       h3 {font-size: 24px;}





  
  

  27
  
       h4 {font-size: 18px;}





  
  

  28
  
       h5 {font-size: 16px;}





  
  

  29
  
       h6 {font-size: 12px;}





  
  

  30
  
       code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}





  
  

  31
  
       pre:not([class]) { background-color: white }</style>





  
  

  32
  
<script src="site_libs/navigation-1.1/tabsets.js"></script>





  
  

  33
  
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />





  
  

  34
  
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>





  
  

  35
  
<link href="site_libs/font-awesome-6.5.2/css/all.min.css" rel="stylesheet" />





  
  

  36
  
<link href="site_libs/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet" />





  
  

  37
  





  
  

  38
  
<style type="text/css">





  
  

  39
  
  code{white-space: pre-wrap;}





  
  

  40
  
  span.smallcaps{font-variant: small-caps;}





  
  

  41
  
  span.underline{text-decoration: underline;}





  
  

  42
  
  div.column{display: inline-block; vertical-align: top; width: 50%;}





  
  

  43
  
  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}





  
  

  44
  
  ul.task-list{list-style: none;}





  
  

  45
  
    </style>





  
  

  46
  





  
  

  47
  
<style type="text/css">code{white-space: pre;}</style>





  
  

  48
  
<script type="text/javascript">





  
  

  49
  
if (window.hljs) {





  
  

  50
  
  hljs.configure({languages: []});





  
  

  51
  
  hljs.initHighlightingOnLoad();





  
  

  52
  
  if (document.readyState && document.readyState === "complete") {





  
  

  53
  
    window.setTimeout(function() { hljs.initHighlighting(); }, 0);





  
  

  54
  
  }





  
  

  55
  
}





  
  

  56
  
</script>





  
  

  57
  





  
  

  58
  





  
  

  59
  





  
  

  60
  





  
  

  61
  





  
  

  62
  





  
  

  63
  





  
  

  64
  





  
  

  65
  





  
  

  66
  
<style type = "text/css">





  
  

  67
  
.main-container {





  
  

  68
  
  max-width: 940px;





  
  

  69
  
  margin-left: auto;





  
  

  70
  
  margin-right: auto;





  
  

  71
  
}





  
  

  72
  
img {





  
  

  73
  
  max-width:100%;





  
  

  74
  
}





  
  

  75
  
.tabbed-pane {





  
  

  76
  
  padding-top: 12px;





  
  

  77
  
}





  
  

  78
  
.html-widget {





  
  

  79
  
  margin-bottom: 20px;





  
  

  80
  
}





  
  

  81
  
button.code-folding-btn:focus {





  
  

  82
  
  outline: none;





  
  

  83
  
}





  
  

  84
  
summary {





  
  

  85
  
  display: list-item;





  
  

  86
  
}





  
  

  87
  
details > summary > p:only-child {





  
  

  88
  
  display: inline;





  
  

  89
  
}





  
  

  90
  
pre code {





  
  

  91
  
  padding: 0;





  
  

  92
  
}





  
  

  93
  
</style>





  
  

  94
  





  
  

  95
  





  
  

  96
  
<style type="text/css">





  
  

  97
  
.dropdown-submenu {





  
  

  98
  
  position: relative;





  
  

  99
  
}





  
  

  100
  
.dropdown-submenu>.dropdown-menu {





  
  

  101
  
  top: 0;





  
  

  102
  
  left: 100%;





  
  

  103
  
  margin-top: -6px;





  
  

  104
  
  margin-left: -1px;





  
  

  105
  
  border-radius: 0 6px 6px 6px;





  
  

  106
  
}





  
  

  107
  
.dropdown-submenu:hover>.dropdown-menu {





  
  

  108
  
  display: block;





  
  

  109
  
}





  
  

  110
  
.dropdown-submenu>a:after {





  
  

  111
  
  display: block;





  
  

  112
  
  content: " ";





  
  

  113
  
  float: right;





  
  

  114
  
  width: 0;





  
  

  115
  
  height: 0;





  
  

  116
  
  border-color: transparent;





  
  

  117
  
  border-style: solid;





  
  

  118
  
  border-width: 5px 0 5px 5px;





  
  

  119
  
  border-left-color: #cccccc;





  
  

  120
  
  margin-top: 5px;





  
  

  121
  
  margin-right: -10px;





  
  

  122
  
}





  
  

  123
  
.dropdown-submenu:hover>a:after {





  
  

  124
  
  border-left-color: #adb5bd;





  
  

  125
  
}





  
  

  126
  
.dropdown-submenu.pull-left {





  
  

  127
  
  float: none;





  
  

  128
  
}





  
  

  129
  
.dropdown-submenu.pull-left>.dropdown-menu {





  
  

  130
  
  left: -100%;





  
  

  131
  
  margin-left: 10px;





  
  

  132
  
  border-radius: 6px 0 6px 6px;





  
  

  133
  
}





  
  

  134
  
</style>





  
  

  135
  





  
  

  136
  
<script type="text/javascript">





  
  

  137
  
// manage active state of menu based on current page





  
  

  138
  
$(document).ready(function () {





  
  

  139
  
  // active menu anchor





  
  

  140
  
  href = window.location.pathname





  
  

  141
  
  href = href.substr(href.lastIndexOf('/') + 1)





  
  

  142
  
  if (href === "")





  
  

  143
  
    href = "index.html";





  
  

  144
  
  var menuAnchor = $('a[href="' + href + '"]');





  
  

  145
  





  
  

  146
  
  // mark the anchor link active (and if it's in a dropdown, also mark that active)





  
  

  147
  
  var dropdown = menuAnchor.closest('li.dropdown');





  
  

  148
  
  if (window.bootstrap) { // Bootstrap 4+





  
  

  149
  
    menuAnchor.addClass('active');





  
  

  150
  
    dropdown.find('> .dropdown-toggle').addClass('active');





  
  

  151
  
  } else { // Bootstrap 3





  
  

  152
  
    menuAnchor.parent().addClass('active');





  
  

  153
  
    dropdown.addClass('active');





  
  

  154
  
  }





  
  

  155
  





  
  

  156
  
  // Navbar adjustments





  
  

  157
  
  var navHeight = $(".navbar").first().height() + 15;





  
  

  158
  
  var style = document.createElement('style');





  
  

  159
  
  var pt = "padding-top: " + navHeight + "px; ";





  
  

  160
  
  var mt = "margin-top: -" + navHeight + "px; ";





  
  

  161
  
  var css = "";





  
  

  162
  
  // offset scroll position for anchor links (for fixed navbar)





  
  

  163
  
  for (var i = 1; i <= 6; i++) {





  
  

  164
  
    css += ".section h" + i + "{ " + pt + mt + "}\n";





  
  

  165
  
  }





  
  

  166
  
  style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;





  
  

  167
  
  document.head.appendChild(style);





  
  

  168
  
});





  
  

  169
  
</script>





  
  

  170
  





  
  

  171
  
<!-- tabsets -->





  
  

  172
  





  
  

  173
  
<style type="text/css">





  
  

  174
  
.tabset-dropdown > .nav-tabs {





  
  

  175
  
  display: inline-table;





  
  

  176
  
  max-height: 500px;





  
  

  177
  
  min-height: 44px;





  
  

  178
  
  overflow-y: auto;





  
  

  179
  
  border: 1px solid #ddd;





  
  

  180
  
  border-radius: 4px;





  
  

  181
  
}





  
  

  182
  





  
  

  183
  
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {





  
  

  184
  
  content: "\e259";





  
  

  185
  
  font-family: 'Glyphicons Halflings';





  
  

  186
  
  display: inline-block;





  
  

  187
  
  padding: 10px;





  
  

  188
  
  border-right: 1px solid #ddd;





  
  

  189
  
}





  
  

  190
  





  
  

  191
  
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {





  
  

  192
  
  content: "\e258";





  
  

  193
  
  font-family: 'Glyphicons Halflings';





  
  

  194
  
  border: none;





  
  

  195
  
}





  
  

  196
  





  
  

  197
  
.tabset-dropdown > .nav-tabs > li.active {





  
  

  198
  
  display: block;





  
  

  199
  
}





  
  

  200
  





  
  

  201
  
.tabset-dropdown > .nav-tabs > li > a,





  
  

  202
  
.tabset-dropdown > .nav-tabs > li > a:focus,





  
  

  203
  
.tabset-dropdown > .nav-tabs > li > a:hover {





  
  

  204
  
  border: none;





  
  

  205
  
  display: inline-block;





  
  

  206
  
  border-radius: 4px;





  
  

  207
  
  background-color: transparent;





  
  

  208
  
}





  
  

  209
  





  
  

  210
  
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {





  
  

  211
  
  display: block;





  
  

  212
  
  float: none;





  
  

  213
  
}





  
  

  214
  





  
  

  215
  
.tabset-dropdown > .nav-tabs > li {





  
  

  216
  
  display: none;





  
  

  217
  
}





  
  

  218
  
</style>





  
  

  219
  





  
  

  220
  
<!-- code folding -->





  
  

  221
  





  
  

  222
  





  
  

  223
  





  
  

  224
  





  
  

  225
  
</head>





  
  

  226
  





  
  

  227
  
<body>





  
  

  228
  





  
  

  229
  





  
  

  230
  
<div class="container-fluid main-container">





  
  

  231
  





  
  

  232
  





  
  

  233
  





  
  

  234
  





  
  

  235
  
<div class="navbar navbar-default  navbar-fixed-top" role="navigation">





  
  

  236
  
  <div class="container">





  
  

  237
  
    <div class="navbar-header">





  
  

  238
  
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">





  
  

  239
  
        <span class="icon-bar"></span>





  
  

  240
  
        <span class="icon-bar"></span>





  
  

  241
  
        <span class="icon-bar"></span>





  
  

  242
  
      </button>





  
  

  243
  
      <a class="navbar-brand" href="index.html">VoltRon</a>





  
  

  244
  
    </div>





  
  

  245
  
    <div id="navbar" class="navbar-collapse collapse">





  
  

  246
  
      <ul class="nav navbar-nav">





  
  

  247
  
        <li>





  
  

  248
  
  <a href="tutorials.html">Explore</a>





  
  

  249
  
</li>





  
  

  250
  
<li class="dropdown">





  
  

  251
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  252
  
    Vignette





  
  

  253
  
     





  
  

  254
  
    <span class="caret"></span>





  
  

  255
  
  </a>





  
  

  256
  
  <ul class="dropdown-menu" role="menu">





  
  

  257
  
    <li class="dropdown-submenu">





  
  

  258
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Spatial Data Integration</a>





  
  

  259
  
      <ul class="dropdown-menu" role="menu">





  
  

  260
  
        <li>





  
  

  261
  
          <a href="registration.html">Spatial Data Alignment</a>





  
  

  262
  
        </li>





  
  

  263
  
        <li>





  
  

  264
  
          <a href="multiomic.html">Multi-omic Integration</a>





  
  

  265
  
        </li>





  
  

  266
  
        <li>





  
  

  267
  
          <a href="nicheclustering.html">Niche Clustering</a>





  
  

  268
  
        </li>





  
  

  269
  
      </ul>





  
  

  270
  
    </li>





  
  

  271
  
    <li class="dropdown-submenu">





  
  

  272
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Downstream Analysis</a>





  
  

  273
  
      <ul class="dropdown-menu" role="menu">





  
  

  274
  
        <li>





  
  

  275
  
          <a href="roianalysis.html">ROI Analysis</a>





  
  

  276
  
        </li>





  
  

  277
  
        <li>





  
  

  278
  
          <a href="spotanalysis.html">Cell/Spot Analysis</a>





  
  

  279
  
        </li>





  
  

  280
  
        <li>





  
  

  281
  
          <a href="moleculeanalysis.html">Molecule Analysis</a>





  
  

  282
  
        </li>





  
  

  283
  
        <li>





  
  

  284
  
          <a href="pixelanalysis.html">Pixels (Image Only) Analysis</a>





  
  

  285
  
        </li>





  
  

  286
  
      </ul>





  
  

  287
  
    </li>





  
  

  288
  
    <li class="dropdown-submenu">





  
  

  289
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Utilities</a>





  
  

  290
  
      <ul class="dropdown-menu" role="menu">





  
  

  291
  
        <li>





  
  

  292
  
          <a href="interactive.html">Interactive Utilities</a>





  
  

  293
  
        </li>





  
  

  294
  
        <li>





  
  

  295
  
          <a href="importingdata.html">Importing Spatial Data</a>





  
  

  296
  
        </li>





  
  

  297
  
        <li>





  
  

  298
  
          <a href="voltronobjects.html">Working with VoltRon Objects</a>





  
  

  299
  
        </li>





  
  

  300
  
        <li>





  
  

  301
  
          <a href="conversion.html">Converting VoltRon Objects</a>





  
  

  302
  
        </li>





  
  

  303
  
        <li>





  
  

  304
  
          <a href="ondisk.html">OnDisk-based Analysis Utilities</a>





  
  

  305
  
        </li>





  
  

  306
  
      </ul>





  
  

  307
  
    </li>





  
  

  308
  
  </ul>





  
  

  309
  
</li>





  
  

  310
  
      </ul>





  
  

  311
  
      <ul class="nav navbar-nav navbar-right">





  
  

  312
  
        <li class="dropdown">





  
  

  313
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  314
  
    <span class="fa fa-envelope-o"></span>





  
  

  315
  
     





  
  

  316
  
    Contact





  
  

  317
  
     





  
  

  318
  
    <span class="caret"></span>





  
  

  319
  
  </a>





  
  

  320
  
  <ul class="dropdown-menu" role="menu">





  
  

  321
  
    <li>





  
  

  322
  
      <a href="https://bioinformatics.mdc-berlin.de">Altuna Lab/BIMSB Bioinfo</a>





  
  

  323
  
    </li>





  
  

  324
  
    <li>





  
  

  325
  
      <a href="https://www.mdc-berlin.de/landthaler">Landthaler Lab/BIMSB</a>





  
  

  326
  
    </li>





  
  

  327
  
  </ul>





  
  

  328
  
</li>





  
  

  329
  
<li class="dropdown">





  
  

  330
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  331
  
    <span class="fa fa-github"></span>





  
  

  332
  
     





  
  

  333
  
    GitHub





  
  

  334
  
     





  
  

  335
  
    <span class="caret"></span>





  
  

  336
  
  </a>





  
  

  337
  
  <ul class="dropdown-menu" role="menu">





  
  

  338
  
    <li>





  
  

  339
  
      <a href="https://github.com/BIMSBbioinfo/VoltRon">VoltRon</a>





  
  

  340
  
    </li>





  
  

  341
  
    <li>





  
  

  342
  
      <a href="https://github.com/BIMSBbioinfo">BIMSB Bioinfo</a>





  
  

  343
  
    </li>





  
  

  344
  
  </ul>





  
  

  345
  
</li>





  
  

  346
  
      </ul>





  
  

  347
  
    </div><!--/.nav-collapse -->





  
  

  348
  
  </div><!--/.container -->





  
  

  349
  
</div><!--/.navbar -->





  
  

  350
  





  
  

  351
  
<div id="header">





  
  

  352
  





  
  

  353
  





  
  

  354
  





  
  

  355
  
<h1 class="title toc-ignore">Tutorials</h1>





  
  

  356
  





  
  

  357
  
</div>





  
  

  358
  





  
  

  359
  





  
  

  360
  
<style>





  
  

  361
  
.title{





  
  

  362
  
  display: none;





  
  

  363
  
}





  
  

  364
  
body {





  
  

  365
  
  text-align: justify





  
  

  366
  
}





  
  

  367
  
table, th, td, tr{





  
  

  368
  
  empty-cells:hide;





  
  

  369
  
  border-spacing: 25px;





  
  

  370
  
  border-collapse: separate;





  
  

  371
  
}





  
  

  372
  
td{





  
  

  373
  
  filter:drop-shadow(0 0 10px rgba(0,0,0,0.3));





  
  

  374
  
  padding: 10px;





  
  

  375
  
  background:white;





  
  

  376
  
  text-align:center;





  
  

  377
  
  width:33%;





  
  

  378
  
  vertical-align: text-top;





  
  

  379
  
}





  
  

  380
  
td:hover, td:active{





  
  

  381
  
  filter:drop-shadow(0 0 10px rgba(0,0,0,0.3));





  
  

  382
  
  transform: scale(1.02);





  
  

  383
  
  cursor: pointer;





  
  

  384
  
}





  
  

  385
  
.main-container {





  
  

  386
  
  max-width: 1200px;





  
  

  387
  
  margin-left: auto;





  
  

  388
  
  margin-right: auto;





  
  

  389
  
}





  
  

  390
  
<!-- .main-container { -->





  
  

  391
  
<!--   margin-left: %5; -->





  
  

  392
  
<!--   margin-right: auto; -->





  
  

  393
  
<!-- } -->





  
  

  394
  
p.tutorial {





  
  

  395
  
  text-decoration: none!important;





  
  

  396
  
  font-size: 1.5em;





  
  

  397
  
  color: #23803A;





  
  

  398
  
  margin: 3%





  
  

  399
  
}





  
  

  400
  
</style>





  
  

  401
  
<p><br> <!-- <br> --></p>





  
  

  402
  
<!-- ## Spatial Data Analysis with VoltRon -->





  
  

  403
  
<p><br></p>





  
  

  404
  
<div id="spatially-aware-data-integration-and-analysis"





  
  

  405
  
class="section level2">





  
  

  406
  
<h2>Spatially Aware Data Integration and Analysis</h2>





  
  

  407
  
<p><strong>VoltRon</strong> incorporates multiple <strong>data





  
  

  408
  
integration utilities to achieve data transfer</strong> across a diverse





  
  

  409
  
set of spatial data modalities and types. VoltRon utilizes OpenCV to





  
  

  410
  
align and synchronize spatial omic datasets using <strong>computer





  
  

  411
  
vision and image registration</strong>. Users can automaticaly or





  
  

  412
  
manually align a list of microscopy images (<strong>H&amp;E</strong>,





  
  

  413
  
<strong>DAPI</strong> etc) using a <strong>Shiny App</strong>





  
  

  414
  
incorporated within our analysis workflow. Once aligned, feature data





  
  

  415
  
and metadata level information can be transfered across aligned tissue





  
  

  416
  
sections.</p>





  
  

  417
  
<p>In addition, VoltRon provides a number of spatially aware data





  
  

  418
  
analysis methods to detecting niches (i.e. <strong>Niche





  
  

  419
  
Clustering</strong>) within tissues. VoltRon allows estimating niches





  
  

  420
  
associated with each cell by incorporating the cell type level





  
  

  421
  
information around each cell or spot. We either detect cellular





  
  

  422
  
populations/compositions within a spatial neighborhood of a cell to





  
  

  423
  
create these niche level information (e.g. Xenium) or we estimate the





  
  

  424
  
cell type abundances of spots (e.g. Visium, DBIT-Seq) from a reference





  
  

  425
  
single cell data (Seurat, SingleCellExperiment etc.) with already





  
  

  426
  
annotated cell types. VoltRon can also use these spatial neighborhood to





  
  

  427
  
detect hot spots (i.e. <strong>Hot Spot Analysis</strong>) of features,





  
  

  428
  
cell types and even molecular densities.</p>





  
  

  429
  
<div>





  
  

  430
  
<table>





  
  

  431
  
<tbody>





  
  

  432
  
<tr>





  
  

  433
  
<td onclick="location.href=&#39;registration.html&#39;;">





  
  

  434
  
<p class="tutorial">





  
  

  435
  
Spatial Data Alignment





  
  

  436
  
</p>





  
  

  437
  
<div style="margin: 5%">





  
  

  438
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/registration.png" class="center">





  
  

  439
  
</div>





  
  

  440
  
<p style="margin-top: 3%">





  
  

  441
  
Automated and manual alignment of spatial data assays





  
  

  442
  
</p>





  
  

  443
  
</td>





  
  

  444
  
<td onclick="location.href=&#39;multiomic.html&#39;;">





  
  

  445
  
<p class="tutorial">





  
  

  446
  
Multi-omic Integration





  
  

  447
  
</p>





  
  

  448
  
<div style="margin: 5%">





  
  

  449
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/multiomic.png" class="center">





  
  

  450
  
</div>





  
  

  451
  
<p style="margin-top: 8%">





  
  

  452
  
Integrating data modalities within or across tissue sections





  
  

  453
  
</p>





  
  

  454
  
</td>





  
  

  455
  
<td onclick="location.href=&#39;nicheclustering.html&#39;;">





  
  

  456
  
<p class="tutorial">





  
  

  457
  
Niche Clustering





  
  

  458
  
</p>





  
  

  459
  
<div style="margin: 5%">





  
  

  460
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/deconvolution.png" class="center">





  
  

  461
  
</div>





  
  

  462
  
<p style="margin-top: 10%">





  
  

  463
  
Clustering based on ROI/spot deconvolution and Spatial Neighborhood





  
  

  464
  
</p>





  
  

  465
  
</td>





  
  

  466
  
</tr>





  
  

  467
  
</tbody>





  
  

  468
  
</table>





  
  

  469
  
</div>





  
  

  470
  
<p><br> <br></p>





  
  

  471
  
</div>





  
  

  472
  
<div id="additional-downstream-analysis" class="section level2">





  
  

  473
  
<h2>Additional Downstream Analysis</h2>





  
  

  474
  
<p><strong>VoltRon</strong> is also capable of end-to-end analysis of





  
  

  475
  
diverse set of spatial data types (or spatial entities)such as





  
  

  476
  
<strong>ROIs</strong> (regions of interest), <strong>spots</strong>,





  
  

  477
  
<strong>single cells</strong>, <strong>molecules</strong> and even





  
  

  478
  
<strong>images</strong>. Users can set any data type as default at any





  
  

  479
  
time where VoltRon provides minimal set of functions to analyze, process





  
  

  480
  
and visualize each of these modalities.</p>





  
  

  481
  
<table>





  
  

  482
  
<tbody>





  
  

  483
  
<tr>





  
  

  484
  
<td onclick="location.href=&#39;roianalysis.html&#39;;">





  
  

  485
  
<p class="tutorial">





  
  

  486
  
Region of Interests (ROIs)





  
  

  487
  
</p>





  
  

  488
  
<div style="margin: 5%">





  
  

  489
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/GeoMx.png" class="center">





  
  

  490
  
</div>





  
  

  491
  
<p style="margin-top: 7%">





  
  

  492
  
Quality control, analysis and visualization of ROI segments





  
  

  493
  
</p>





  
  

  494
  
</td>





  
  

  495
  
<td onclick="location.href=&#39;spotanalysis.html&#39;;">





  
  

  496
  
<p class="tutorial">





  
  

  497
  
Cells/Spots





  
  

  498
  
</p>





  
  

  499
  
<div style="margin: 5%">





  
  

  500
  
<img  src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/spotanalysis.png" class="center">





  
  

  501
  
</div>





  
  

  502
  
<p style="margin-top: 3%">





  
  

  503
  
Quality control, analysis and visualization of Cell/Spot datasets





  
  

  504
  
</p>





  
  

  505
  
</td>





  
  

  506
  
<td onclick="location.href=&#39;moleculeanalysis.html&#39;;">





  
  

  507
  
<p class="tutorial">





  
  

  508
  
Molecules





  
  

  509
  
</p>





  
  

  510
  
<br>





  
  

  511
  
<div style="margin: 5%">





  
  

  512
  
<img  src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/molecule_visualize.png" class="center">





  
  

  513
  
</div>





  
  

  514
  
<p style="margin-top: 10%">





  
  

  515
  
Analysis and visualization of Molecule datasets <br> <strong> (Under





  
  

  516
  
Development) </strong>





  
  

  517
  
</p>





  
  

  518
  
</td>





  
  

  519
  
</tr>





  
  

  520
  
<tr>





  
  

  521
  
<td onclick="location.href=&#39;pixelanalysis.html&#39;;">





  
  

  522
  
<p class="tutorial">





  
  

  523
  
Pixels (Image Only)





  
  

  524
  
</p>





  
  

  525
  
<div style="margin: 5%">





  
  

  526
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/tissue_lowres_image_grid.png" class="center">





  
  

  527
  
</div>





  
  

  528
  
<p style="margin-top: 3%">





  
  

  529
  
Analysis and visualization of Image datasets <br> <strong> (Under





  
  

  530
  
Development) </strong>





  
  

  531
  
</p>





  
  

  532
  
</td>





  
  

  533
  
<td>





  
  

  534
  
</td>





  
  

  535
  
<td>





  
  

  536
  
</td>





  
  

  537
  
</tr>





  
  

  538
  
</tbody>





  
  

  539
  
</table>





  
  

  540
  
<p><br> <br></p>





  
  

  541
  
</div>





  
  

  542
  
<div id="other-utilities" class="section level2">





  
  

  543
  
<h2>Other Utilities</h2>





  
  

  544
  
<p>Here, we provide a group of tutorials to use additional features of





  
  

  545
  
the VoltRon objects as well as further information on how to use





  
  

  546
  
VoltRon. We describe a collection of features that VoltRon package





  
  

  547
  
utilizes such as <strong>interactive annotation/visualization</strong>





  
  

  548
  
and importing spatially aware data from <strong>diverse spatial omic





  
  

  549
  
technologies</strong>. VoltRon is able to convert its objects to a





  
  

  550
  
diverse set of objects/datatypes commonly incorporated spatial data





  
  

  551
  
analysis (<strong>Seurat</strong>, <strong>SpatialExperiment</strong>,





  
  

  552
  
<strong>Giotto</strong>, <strong>AnnData</strong> etc.). Large VoltRon





  
  

  553
  
objects can be <strong>saved ondisk</strong> and efficiently analyzed





  
  

  554
  
without straining memory.</p>





  
  

  555
  
<table>





  
  

  556
  
<tbody>





  
  

  557
  
<tr>





  
  

  558
  
<td onclick="location.href=&#39;interactive.html&#39;;">





  
  

  559
  
<p class="tutorial">





  
  

  560
  
Interactive Utilities





  
  

  561
  
</p>





  
  

  562
  
<br>





  
  

  563
  
<div style="margin: 5%">





  
  

  564
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactiveannotation.png" class="center">





  
  

  565
  
</div>





  
  

  566
  
<p style="margin-top: 8%">





  
  

  567
  
Interactive annotation and visualization





  
  

  568
  
</p>





  
  

  569
  
</td>





  
  

  570
  
<td onclick="location.href=&#39;voltronobjects.html&#39;;">





  
  

  571
  
<p class="tutorial">





  
  

  572
  
Working with VoltRon Objects





  
  

  573
  
</p>





  
  

  574
  
<br>





  
  

  575
  
<div style="margin: 5%">





  
  

  576
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltronobjects.png" class="center">





  
  

  577
  
</div>





  
  

  578
  
<br> <br>





  
  

  579
  
<p style="margin-top: 6%">





  
  

  580
  
Manipulating and configuring VoltRon objects





  
  

  581
  
</p>





  
  

  582
  
</td>





  
  

  583
  
<td onclick="location.href=&#39;importingdata.html&#39;;">





  
  

  584
  
<p class="tutorial">





  
  

  585
  
Importing Spatial Data





  
  

  586
  
</p>





  
  

  587
  
<div style="margin: 10%">





  
  

  588
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/technologies.png" class="center">





  
  

  589
  
</div>





  
  

  590
  
<p style="margin-top: -3%">





  
  

  591
  
Importing readouts of spatial technologies





  
  

  592
  
</p>





  
  

  593
  
</td>





  
  

  594
  
</tr>





  
  

  595
  
<tr>





  
  

  596
  
<td onclick="location.href=&#39;conversion.html&#39;;">





  
  

  597
  
<p class="tutorial">





  
  

  598
  
Converting VoltRon Objects





  
  

  599
  
</p>





  
  

  600
  
<br>





  
  

  601
  
<div style="margin: 5%">





  
  

  602
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/conversion.png" class="center">





  
  

  603
  
</div>





  
  

  604
  
<p style="margin-top: 9%">





  
  

  605
  
Converting VoltRon objects into Seurat, SpatialExperiment and Squidpy





  
  

  606
  
(anndata) etc.





  
  

  607
  
</p>





  
  

  608
  
</td>





  
  

  609
  
<td onclick="location.href=&#39;ondisk.html&#39;;">





  
  

  610
  
<p class="tutorial">





  
  

  611
  
OnDisk Analysis Utilities





  
  

  612
  
</p>





  
  

  613
  
<div style="margin: 5%">





  
  

  614
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk.png" class="center">





  
  

  615
  
</div>





  
  

  616
  
<p style="margin: 5%">





  
  

  617
  
Efficient access to large VoltRon objects





  
  

  618
  
</p>





  
  

  619
  
</td>





  
  

  620
  
</tr>





  
  

  621
  
</tbody>





  
  

  622
  
</table>





  
  

  623
  
<p><br></p>





  
  

  624
  
</div>





  
  

  625
  





  
  

  626
  





  
  

  627
  





  
  

  628
  





  
  

  629
  
</div>





  
  

  630
  





  
  

  631
  
<script>





  
  

  632
  





  
  

  633
  
// add bootstrap table styles to pandoc tables





  
  

  634
  
function bootstrapStylePandocTables() {





  
  

  635
  
  $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');





  
  

  636
  
}





  
  

  637
  
$(document).ready(function () {





  
  

  638
  
  bootstrapStylePandocTables();





  
  

  639
  
});





  
  

  640
  





  
  

  641
  





  
  

  642
  
</script>





  
  

  643
  





  
  

  644
  
<!-- tabsets -->





  
  

  645
  





  
  

  646
  
<script>





  
  

  647
  
$(document).ready(function () {





  
  

  648
  
  window.buildTabsets("TOC");





  
  

  649
  
});





  
  

  650
  





  
  

  651
  
$(document).ready(function () {





  
  

  652
  
  $('.tabset-dropdown > .nav-tabs > li').click(function () {





  
  

  653
  
    $(this).parent().toggleClass('nav-tabs-open');





  
  

  654
  
  });





  
  

  655
  
});





  
  

  656
  
</script>





  
  

  657
  





  
  

  658
  
<!-- code folding -->





  
  

  659
  





  
  

  660
  





  
  

  661
  
<!-- dynamically load mathjax for compatibility with self-contained -->





  
  

  662
  
<script>





  
  

  663
  
  (function () {





  
  

  664
  
    var script = document.createElement("script");





  
  

  665
  
    script.type = "text/javascript";





  
  

  666
  
    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";





  
  

  667
  
    document.getElementsByTagName("head")[0].appendChild(script);





  
  

  668
  
  })();





  
  

  669
  
</script>





  
  

  670
  





  
  

  671
  
</body>





  
  

  672
  
</html>