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| 1 | <!DOCTYPE html> |
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| 2 | |||
| 3 | <html> |
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| 4 | |||
| 5 | <head> |
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| 6 | |||
| 7 | <meta charset="utf-8" /> |
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| 8 | <meta name="generator" content="pandoc" /> |
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| 9 | <meta http-equiv="X-UA-Compatible" content="IE=EDGE" /> |
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| 10 | |||
| 11 | |||
| 12 | |||
| 13 | |||
| 14 | <title>Importing Spatial Data</title> |
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| 15 | |||
| 16 | <script src="site_libs/header-attrs-2.29/header-attrs.js"></script> |
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| 17 | <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script> |
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| 19 | <link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" /> |
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| 20 | <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> |
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| 22 | <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> |
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| 23 | <style>h1 {font-size: 34px;} |
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| 24 | h1.title {font-size: 38px;} |
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| 25 | h2 {font-size: 30px;} |
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| 26 | h3 {font-size: 24px;} |
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| 27 | h4 {font-size: 18px;} |
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| 28 | h5 {font-size: 16px;} |
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| 29 | h6 {font-size: 12px;} |
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| 30 | code {color: inherit; background-color: rgba(0, 0, 0, 0.04);} |
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| 31 | pre:not([class]) { background-color: white }</style> |
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| 69 | <style type = "text/css"> |
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| 132 | .dropdown-submenu.pull-left>.dropdown-menu { |
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| 133 | left: -100%; |
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| 137 | </style> |
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| 138 | |||
| 139 | <script type="text/javascript"> |
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| 140 | // manage active state of menu based on current page |
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| 141 | $(document).ready(function () { |
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| 142 | // active menu anchor |
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| 143 | href = window.location.pathname |
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| 144 | href = href.substr(href.lastIndexOf('/') + 1) |
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| 145 | if (href === "") |
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| 146 | href = "index.html"; |
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| 147 | var menuAnchor = $('a[href="' + href + '"]'); |
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| 148 | |||
| 149 | // mark the anchor link active (and if it's in a dropdown, also mark that active) |
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| 150 | var dropdown = menuAnchor.closest('li.dropdown'); |
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| 151 | if (window.bootstrap) { // Bootstrap 4+ |
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| 152 | menuAnchor.addClass('active'); |
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| 153 | dropdown.find('> .dropdown-toggle').addClass('active'); |
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| 154 | } else { // Bootstrap 3 |
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| 155 | menuAnchor.parent().addClass('active'); |
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| 156 | dropdown.addClass('active'); |
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| 159 | // Navbar adjustments |
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| 160 | var navHeight = $(".navbar").first().height() + 15; |
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| 162 | var pt = "padding-top: " + navHeight + "px; "; |
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| 169 | style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css; |
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| 170 | document.head.appendChild(style); |
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| 172 | </script> |
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| 174 | <!-- tabsets --> |
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| 176 | <style type="text/css"> |
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| 177 | .tabset-dropdown > .nav-tabs { |
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| 178 | display: inline-table; |
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| 182 | border: 1px solid #ddd; |
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| 183 | border-radius: 4px; |
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| 186 | .tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { |
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| 191 | border-right: 1px solid #ddd; |
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| 194 | .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { |
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| 205 | .tabset-dropdown > .nav-tabs > li > a:focus, |
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| 206 | .tabset-dropdown > .nav-tabs > li > a:hover { |
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| 209 | border-radius: 4px; |
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| 210 | background-color: transparent; |
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| 212 | |||
| 213 | .tabset-dropdown > .nav-tabs.nav-tabs-open > li { |
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| 214 | display: block; |
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| 215 | float: none; |
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| 216 | } |
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| 217 | |||
| 218 | .tabset-dropdown > .nav-tabs > li { |
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| 219 | display: none; |
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| 221 | </style> |
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| 222 | |||
| 223 | <!-- code folding --> |
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| 227 | <style type="text/css"> |
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| 228 | |||
| 229 | #TOC { |
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| 230 | margin: 25px 0px 20px 0px; |
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| 231 | } |
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| 232 | @media (max-width: 768px) { |
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| 233 | #TOC { |
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| 234 | position: relative; |
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| 235 | width: 100%; |
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| 237 | } |
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| 238 | |||
| 239 | @media print { |
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| 242 | float: right; |
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| 243 | } |
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| 244 | } |
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| 245 | |||
| 246 | .toc-content { |
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| 247 | padding-left: 30px; |
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| 248 | padding-right: 40px; |
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| 249 | } |
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| 250 | |||
| 251 | div.main-container { |
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| 252 | max-width: 1200px; |
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| 253 | } |
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| 254 | |||
| 255 | div.tocify { |
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| 256 | width: 20%; |
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| 257 | max-width: 260px; |
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| 258 | max-height: 85%; |
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| 259 | } |
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| 260 | |||
| 261 | @media (min-width: 768px) and (max-width: 991px) { |
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| 262 | div.tocify { |
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| 263 | width: 25%; |
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| 264 | } |
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| 265 | } |
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| 266 | |||
| 267 | @media (max-width: 767px) { |
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| 268 | div.tocify { |
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| 269 | width: 100%; |
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| 270 | max-width: none; |
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| 271 | } |
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| 272 | } |
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| 273 | |||
| 274 | .tocify ul, .tocify li { |
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| 275 | line-height: 20px; |
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| 276 | } |
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| 277 | |||
| 278 | .tocify-subheader .tocify-item { |
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| 279 | font-size: 0.90em; |
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| 280 | } |
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| 281 | |||
| 282 | .tocify .list-group-item { |
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| 283 | border-radius: 0px; |
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| 284 | } |
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| 285 | |||
| 286 | .tocify-subheader { |
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| 287 | display: inline; |
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| 288 | } |
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| 289 | .tocify-subheader .tocify-item { |
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| 290 | font-size: 0.95em; |
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| 291 | } |
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| 292 | |||
| 293 | </style> |
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| 294 | |||
| 295 | |||
| 296 | |||
| 297 | </head> |
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| 298 | |||
| 299 | <body> |
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| 300 | |||
| 301 | |||
| 302 | <div class="container-fluid main-container"> |
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| 303 | |||
| 304 | |||
| 305 | <!-- setup 3col/9col grid for toc_float and main content --> |
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| 306 | <div class="row"> |
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| 307 | <div class="col-xs-12 col-sm-4 col-md-3"> |
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| 308 | <div id="TOC" class="tocify"> |
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| 309 | </div> |
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| 310 | </div> |
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| 311 | |||
| 312 | <div class="toc-content col-xs-12 col-sm-8 col-md-9"> |
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| 313 | |||
| 314 | |||
| 315 | |||
| 316 | |||
| 317 | <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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| 318 | <div class="container"> |
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| 319 | <div class="navbar-header"> |
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| 320 | <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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| 321 | <span class="icon-bar"></span> |
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| 322 | <span class="icon-bar"></span> |
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| 323 | <span class="icon-bar"></span> |
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| 324 | </button> |
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| 325 | <a class="navbar-brand" href="index.html">VoltRon</a> |
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| 326 | </div> |
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| 327 | <div id="navbar" class="navbar-collapse collapse"> |
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| 328 | <ul class="nav navbar-nav"> |
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| 329 | <li> |
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| 330 | <a href="tutorials.html">Explore</a> |
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| 331 | </li> |
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| 332 | <li class="dropdown"> |
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| 333 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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| 334 | Vignette |
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| 335 | |||
| 336 | <span class="caret"></span> |
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| 337 | </a> |
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| 338 | <ul class="dropdown-menu" role="menu"> |
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| 339 | <li class="dropdown-submenu"> |
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| 340 | <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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| 341 | <ul class="dropdown-menu" role="menu"> |
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| 342 | <li> |
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| 343 | <a href="registration.html">Spatial Data Alignment</a> |
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| 344 | </li> |
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| 345 | <li> |
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| 346 | <a href="multiomic.html">Multi-omic Integration</a> |
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| 347 | </li> |
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| 348 | <li> |
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| 349 | <a href="nicheclustering.html">Niche Clustering</a> |
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| 350 | </li> |
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| 351 | </ul> |
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| 352 | </li> |
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| 353 | <li class="dropdown-submenu"> |
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| 354 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Downstream Analysis</a> |
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| 355 | <ul class="dropdown-menu" role="menu"> |
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| 356 | <li> |
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| 357 | <a href="roianalysis.html">ROI Analysis</a> |
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| 358 | </li> |
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| 359 | <li> |
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| 360 | <a href="spotanalysis.html">Cell/Spot Analysis</a> |
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| 361 | </li> |
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| 362 | <li> |
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| 363 | <a href="moleculeanalysis.html">Molecule Analysis</a> |
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| 364 | </li> |
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| 365 | <li> |
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| 366 | <a href="pixelanalysis.html">Pixels (Image Only) Analysis</a> |
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| 367 | </li> |
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| 368 | </ul> |
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| 369 | </li> |
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| 370 | <li class="dropdown-submenu"> |
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| 371 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Utilities</a> |
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| 372 | <ul class="dropdown-menu" role="menu"> |
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| 373 | <li> |
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| 374 | <a href="interactive.html">Interactive Utilities</a> |
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| 375 | </li> |
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| 376 | <li> |
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| 377 | <a href="importingdata.html">Importing Spatial Data</a> |
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| 378 | </li> |
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| 379 | <li> |
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| 380 | <a href="voltronobjects.html">Working with VoltRon Objects</a> |
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| 381 | </li> |
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| 382 | <li> |
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| 383 | <a href="conversion.html">Converting VoltRon Objects</a> |
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| 384 | </li> |
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| 385 | <li> |
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| 386 | <a href="ondisk.html">OnDisk-based Analysis Utilities</a> |
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| 387 | </li> |
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| 388 | </ul> |
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| 389 | </li> |
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| 390 | </ul> |
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| 391 | </li> |
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| 392 | </ul> |
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| 393 | <ul class="nav navbar-nav navbar-right"> |
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| 394 | <li class="dropdown"> |
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| 395 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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| 396 | <span class="fa fa-envelope-o"></span> |
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| 397 | |||
| 398 | Contact |
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| 399 | |||
| 400 | <span class="caret"></span> |
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| 401 | </a> |
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| 402 | <ul class="dropdown-menu" role="menu"> |
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| 403 | <li> |
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| 404 | <a href="https://bioinformatics.mdc-berlin.de">Altuna Lab/BIMSB Bioinfo</a> |
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| 405 | </li> |
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| 406 | <li> |
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| 407 | <a href="https://www.mdc-berlin.de/landthaler">Landthaler Lab/BIMSB</a> |
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| 408 | </li> |
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| 409 | </ul> |
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| 410 | </li> |
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| 411 | <li class="dropdown"> |
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| 412 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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| 413 | <span class="fa fa-github"></span> |
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| 414 | |||
| 415 | GitHub |
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| 416 | |||
| 417 | <span class="caret"></span> |
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| 418 | </a> |
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| 419 | <ul class="dropdown-menu" role="menu"> |
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| 420 | <li> |
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| 421 | <a href="https://github.com/BIMSBbioinfo/VoltRon">VoltRon</a> |
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| 422 | </li> |
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| 423 | <li> |
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| 424 | <a href="https://github.com/BIMSBbioinfo">BIMSB Bioinfo</a> |
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| 425 | </li> |
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| 426 | </ul> |
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| 427 | </li> |
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| 428 | </ul> |
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| 429 | </div><!--/.nav-collapse --> |
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| 430 | </div><!--/.container --> |
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| 431 | </div><!--/.navbar --> |
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| 432 | |||
| 433 | <div id="header"> |
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| 434 | |||
| 435 | |||
| 436 | |||
| 437 | <h1 class="title toc-ignore">Importing Spatial Data</h1> |
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| 438 | |||
| 439 | </div> |
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| 440 | |||
| 441 | |||
| 442 | <style> |
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| 443 | .title{ |
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| 444 | display: none; |
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| 445 | } |
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| 446 | body { |
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| 447 | text-align: justify |
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| 448 | } |
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| 449 | .center { |
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| 450 | display: block; |
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| 451 | margin-left: auto; |
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| 452 | margin-right: auto; |
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| 453 | } |
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| 454 | table, th, td { |
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| 455 | border-collapse: collapse; |
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| 456 | align-self: center; |
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| 457 | padding-right: 10px; |
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| 458 | padding-left: 10px; |
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| 459 | } |
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| 460 | </style> |
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| 461 | <style type="text/css"> |
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| 462 | .watch-out { |
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| 463 | color: black; |
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| 464 | } |
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| 465 | </style> |
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| 466 | <p><br></p> |
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| 467 | <div id="analyzing-image-datasets" class="section level1"> |
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| 468 | <h1>Analyzing Image Datasets</h1> |
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| 469 | <p>VoltRon is a spatial omic analysis platform that allows storing a |
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| 470 | large amount of spatially resolved datasets. As opposed to datasets with |
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| 471 | either supracellular (spot-level) or cellular resolutions, one might |
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| 472 | analyze image datasets and pixels to characterize the morphology of a |
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| 473 | tissue section. Here, images can also be used to build VoltRon objects |
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| 474 | where pixels (or tiles) are defined as spatial points, and then can also |
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| 475 | be used for multiple downstream analysis purposes.</p> |
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| 476 | <p><br></p> |
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| 477 | <div id="analysis-of-he-images" class="section level2"> |
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| 478 | <h2>Analysis of H&E images</h2> |
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| 479 | <p>In this use case, we will analyze the H&E image derived from a |
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| 480 | tissue section that was first analyzed by The 10x Genomics <a |
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| 481 | href="https://www.10xgenomics.com/platforms/xenium">Xenium In Situ</a> |
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| 482 | platform. Three tissue sections were cut from a single formalin-fixed, |
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| 483 | paraffin-embedded (FFPE) breast cancer tissue block. A 5 <span |
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| 484 | class="math inline">\(\mu\)</span>m section was used to generate a |
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| 485 | single Xenium replicate.</p> |
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| 486 | <p>More information on the Xenium and the study can be also be found on |
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| 487 | the <a |
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| 488 | href="https://www.biorxiv.org/content/10.1101/2022.10.06.510405v1">BioArxiv |
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| 489 | preprint</a>. You can download the H&E image from the <a |
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| 490 | href="https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast">10x |
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| 491 | Genomics website</a> as well (specifically, import the |
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| 492 | <strong>Post-Xenium H&E image (TIFF)</strong> data).</p> |
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| 493 | <p>We incorporate <strong>importImageData</strong> to convert an image |
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| 494 | into a pixel-based spatial dataset.</p> |
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| 495 | <pre class="r watch-out"><code>Xen_R1_image <- importImageData("Xenium_FFPE_Human_Breast_Cancer_Rep1_he_image.tif", |
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| 496 | sample_name = "XeniumR1image", |
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| 497 | image_name = "H&E") |
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| 498 | Xen_R1_image</code></pre> |
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| 499 | <pre><code>VoltRon Object |
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| 500 | XeniumR1image: |
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| 501 | Layers: Section1 |
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| 502 | Assays: ImageData(Main) </code></pre> |
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| 503 | <pre class="r watch-out"><code>vrImages(Xen_R1_image, scale.perc = 2)</code></pre> |
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| 504 | <p><img width="70%" height="70%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/importdata_HE.png" class="center"></p> |
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| 505 | <p></br></p> |
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| 506 | <p>This VoltRon object stores the metadata information and localization |
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| 507 | of all pixels in the image.</p> |
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| 508 | <pre class="r watch-out"><code>head(Metadata(Xen_R1_image))</code></pre> |
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| 509 | <pre><code> id assay_id Assay Layer Sample id |
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| 510 | <char> <char> <char> <char> <char> <char> |
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| 511 | 1: tile1_3adf0a Assay1 ImageData Section1 XeniumR1image tile1 |
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| 512 | 2: tile2_3adf0a Assay1 ImageData Section1 XeniumR1image tile2 |
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| 513 | 3: tile3_3adf0a Assay1 ImageData Section1 XeniumR1image tile3 |
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| 514 | 4: tile4_3adf0a Assay1 ImageData Section1 XeniumR1image tile4 |
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| 515 | 5: tile5_3adf0a Assay1 ImageData Section1 XeniumR1image tile5 |
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| 516 | 6: tile6_3adf0a Assay1 ImageData Section1 XeniumR1image tile6</code></pre> |
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| 517 | <pre class="r watch-out"><code>nrow(Metadata(Xen_R1_image))</code></pre> |
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| 518 | <pre><code>[1] 5656658</code></pre> |
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| 519 | </div> |
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| 520 | </div> |
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| 521 | |||
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| 523 | |||
| 524 | </div> |
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| 525 | </div> |
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