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<h1 class="title toc-ignore">Importing Spatial Data</h1>
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<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>
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Datasets
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