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+} +body { + text-align: justify +} +.center { + display: block; + margin-left: auto; + margin-right: auto; +} +table, th, td { + border-collapse: collapse; + align-self: center; + padding-right: 10px; + padding-left: 10px; +} +</style> +<style type="text/css"> +.watch-out { + color: black; +} +</style> +<p><br></p> +<div id="analyzing-image-datasets" class="section level1"> +<h1>Analyzing Image Datasets</h1> +<p>VoltRon is a spatial omic analysis platform that allows storing a +large amount of spatially resolved datasets. As opposed to datasets with +either supracellular (spot-level) or cellular resolutions, one might +analyze image datasets and pixels to characterize the morphology of a +tissue section. Here, images can also be used to build VoltRon objects +where pixels (or tiles) are defined as spatial points, and then can also +be used for multiple downstream analysis purposes.</p> +<p><br></p> +<div id="analysis-of-he-images" class="section level2"> +<h2>Analysis of H&E images</h2> +<p>In this use case, we will analyze the H&E image derived from a +tissue section that was first analyzed by The 10x Genomics <a +href="https://www.10xgenomics.com/platforms/xenium">Xenium In Situ</a> +platform. Three tissue sections were cut from a single formalin-fixed, +paraffin-embedded (FFPE) breast cancer tissue block. A 5 <span +class="math inline">\(\mu\)</span>m section was used to generate a +single Xenium replicate.</p> +<p>More information on the Xenium and the study can be also be found on +the <a +href="https://www.biorxiv.org/content/10.1101/2022.10.06.510405v1">BioArxiv +preprint</a>. You can download the H&E image from the <a +href="https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast">10x +Genomics website</a> as well (specifically, import the +<strong>Post-Xenium H&E image (TIFF)</strong> data).</p> +<p>We incorporate <strong>importImageData</strong> to convert an image +into a pixel-based spatial dataset.</p> +<pre class="r watch-out"><code>Xen_R1_image <- importImageData("Xenium_FFPE_Human_Breast_Cancer_Rep1_he_image.tif", + sample_name = "XeniumR1image", + image_name = "H&E") +Xen_R1_image</code></pre> +<pre><code>VoltRon Object +XeniumR1image: + Layers: Section1 +Assays: ImageData(Main) </code></pre> +<pre class="r watch-out"><code>vrImages(Xen_R1_image, scale.perc = 2)</code></pre> +<p><img width="70%" height="70%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/importdata_HE.png" class="center"></p> +<p></br></p> +<p>This VoltRon object stores the metadata information and localization +of all pixels in the image.</p> +<pre class="r watch-out"><code>head(Metadata(Xen_R1_image))</code></pre> +<pre><code> id assay_id Assay Layer Sample id + <char> <char> <char> <char> <char> <char> +1: tile1_3adf0a Assay1 ImageData Section1 XeniumR1image tile1 +2: tile2_3adf0a Assay1 ImageData Section1 XeniumR1image tile2 +3: tile3_3adf0a Assay1 ImageData Section1 XeniumR1image tile3 +4: tile4_3adf0a Assay1 ImageData Section1 XeniumR1image tile4 +5: tile5_3adf0a Assay1 ImageData Section1 XeniumR1image tile5 +6: tile6_3adf0a Assay1 ImageData Section1 XeniumR1image tile6</code></pre> +<pre class="r watch-out"><code>nrow(Metadata(Xen_R1_image))</code></pre> +<pre><code>[1] 5656658</code></pre> +</div> +</div> + + + +</div> +</div> + +</div> + +<script> + +// add bootstrap table styles to pandoc tables +function bootstrapStylePandocTables() { + $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed'); +} +$(document).ready(function () { + bootstrapStylePandocTables(); +}); + + +</script> + +<!-- tabsets --> + +<script> +$(document).ready(function () { + window.buildTabsets("TOC"); +}); + +$(document).ready(function () { + $('.tabset-dropdown > .nav-tabs > li').click(function () { + $(this).parent().toggleClass('nav-tabs-open'); + }); +}); +</script> + +<!-- code folding --> + +<script> +$(document).ready(function () { + + // temporarily add toc-ignore selector to headers for the consistency with Pandoc + $('.unlisted.unnumbered').addClass('toc-ignore') + + // move toc-ignore selectors from section div to header + $('div.section.toc-ignore') + .removeClass('toc-ignore') + .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); + + // establish options + var options = { + selectors: "h1,h2,h3,h4", + theme: "bootstrap3", + context: '.toc-content', + hashGenerator: function (text) { + return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_'); + }, + ignoreSelector: ".toc-ignore", + scrollTo: 0 + }; + options.showAndHide = false; + options.smoothScroll = false; + + // tocify + var toc = $("#TOC").tocify(options).data("toc-tocify"); +}); +</script> + +<!-- dynamically load mathjax for compatibility with self-contained --> +<script> + (function () { + var script = document.createElement("script"); + script.type = "text/javascript"; + script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; + document.getElementsByTagName("head")[0].appendChild(script); + })(); +</script> + +</body> +</html>