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<h1 class="title toc-ignore">Tutorials</h1>
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<p><br> <!-- <br> --></p>
<!-- ## Spatial Data Analysis with VoltRon -->
<p><br></p>
<div id="spatially-aware-data-integration-and-analysis"
class="section level2">
<h2>Spatially Aware Data Integration and Analysis</h2>
<p><strong>VoltRon</strong> incorporates multiple <strong>data
integration utilities to achieve data transfer</strong> across a diverse
set of spatial data modalities and types. VoltRon utilizes OpenCV to
align and synchronize spatial omic datasets using <strong>computer
vision and image registration</strong>. Users can automaticaly or
manually align a list of microscopy images (<strong>H&E</strong>,
<strong>DAPI</strong> etc) using a <strong>Shiny App</strong>
incorporated within our analysis workflow. Once aligned, feature data
and metadata level information can be transfered across aligned tissue
sections.</p>
<p>In addition, VoltRon provides a number of spatially aware data
analysis methods to detecting niches (i.e. <strong>Niche
Clustering</strong>) within tissues. VoltRon allows estimating niches
associated with each cell by incorporating the cell type level
information around each cell or spot. We either detect cellular
populations/compositions within a spatial neighborhood of a cell to
create these niche level information (e.g. Xenium) or we estimate the
cell type abundances of spots (e.g. Visium, DBIT-Seq) from a reference
single cell data (Seurat, SingleCellExperiment etc.) with already
annotated cell types. VoltRon can also use these spatial neighborhood to
detect hot spots (i.e. <strong>Hot Spot Analysis</strong>) of features,
cell types and even molecular densities.</p>
<div>
<table>
<tbody>
<tr>
<td onclick="location.href='registration.html';">
<p class="tutorial">
Spatial Data Alignment
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/registration.png" class="center">
</div>
<p style="margin-top: 3%">
Automated and manual alignment of spatial data assays
</p>
</td>
<td onclick="location.href='multiomic.html';">
<p class="tutorial">
Multi-omic Integration
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/multiomic.png" class="center">
</div>
<p style="margin-top: 8%">
Integrating data modalities within or across tissue sections
</p>
</td>
<td onclick="location.href='nicheclustering.html';">
<p class="tutorial">
Niche Clustering
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/deconvolution.png" class="center">
</div>
<p style="margin-top: 10%">
Clustering based on ROI/spot deconvolution and Spatial Neighborhood
</p>
</td>
</tr>
</tbody>
</table>
</div>
<p><br> <br></p>
</div>
<div id="additional-downstream-analysis" class="section level2">
<h2>Additional Downstream Analysis</h2>
<p><strong>VoltRon</strong> is also capable of end-to-end analysis of
diverse set of spatial data types (or spatial entities)such as
<strong>ROIs</strong> (regions of interest), <strong>spots</strong>,
<strong>single cells</strong>, <strong>molecules</strong> and even
<strong>images</strong>. Users can set any data type as default at any
time where VoltRon provides minimal set of functions to analyze, process
and visualize each of these modalities.</p>
<table>
<tbody>
<tr>
<td onclick="location.href='roianalysis.html';">
<p class="tutorial">
Region of Interests (ROIs)
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/GeoMx.png" class="center">
</div>
<p style="margin-top: 7%">
Quality control, analysis and visualization of ROI segments
</p>
</td>
<td onclick="location.href='spotanalysis.html';">
<p class="tutorial">
Cells/Spots
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/spotanalysis.png" class="center">
</div>
<p style="margin-top: 3%">
Quality control, analysis and visualization of Cell/Spot datasets
</p>
</td>
<td onclick="location.href='moleculeanalysis.html';">
<p class="tutorial">
Molecules
</p>
<br>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/molecule_visualize.png" class="center">
</div>
<p style="margin-top: 10%">
Analysis and visualization of Molecule datasets <br> <strong> (Under
Development) </strong>
</p>
</td>
</tr>
<tr>
<td onclick="location.href='pixelanalysis.html';">
<p class="tutorial">
Pixels (Image Only)
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/tissue_lowres_image_grid.png" class="center">
</div>
<p style="margin-top: 3%">
Analysis and visualization of Image datasets <br> <strong> (Under
Development) </strong>
</p>
</td>
<td>
</td>
<td>
</td>
</tr>
</tbody>
</table>
<p><br> <br></p>
</div>
<div id="other-utilities" class="section level2">
<h2>Other Utilities</h2>
<p>Here, we provide a group of tutorials to use additional features of
the VoltRon objects as well as further information on how to use
VoltRon. We describe a collection of features that VoltRon package
utilizes such as <strong>interactive annotation/visualization</strong>
and importing spatially aware data from <strong>diverse spatial omic
technologies</strong>. VoltRon is able to convert its objects to a
diverse set of objects/datatypes commonly incorporated spatial data
analysis (<strong>Seurat</strong>, <strong>SpatialExperiment</strong>,
<strong>Giotto</strong>, <strong>AnnData</strong> etc.). Large VoltRon
objects can be <strong>saved ondisk</strong> and efficiently analyzed
without straining memory.</p>
<table>
<tbody>
<tr>
<td onclick="location.href='interactive.html';">
<p class="tutorial">
Interactive Utilities
</p>
<br>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/interactiveannotation.png" class="center">
</div>
<p style="margin-top: 8%">
Interactive annotation and visualization
</p>
</td>
<td onclick="location.href='voltronobjects.html';">
<p class="tutorial">
Working with VoltRon Objects
</p>
<br>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltronobjects.png" class="center">
</div>
<br> <br>
<p style="margin-top: 6%">
Manipulating and configuring VoltRon objects
</p>
</td>
<td onclick="location.href='importingdata.html';">
<p class="tutorial">
Importing Spatial Data
</p>
<div style="margin: 10%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/technologies.png" class="center">
</div>
<p style="margin-top: -3%">
Importing readouts of spatial technologies
</p>
</td>
</tr>
<tr>
<td onclick="location.href='conversion.html';">
<p class="tutorial">
Converting VoltRon Objects
</p>
<br>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/conversion.png" class="center">
</div>
<p style="margin-top: 9%">
Converting VoltRon objects into Seurat, SpatialExperiment and Squidpy
(anndata) etc.
</p>
</td>
<td onclick="location.href='ondisk.html';">
<p class="tutorial">
OnDisk Analysis Utilities
</p>
<div style="margin: 5%">
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk.png" class="center">
</div>
<p style="margin: 5%">
Efficient access to large VoltRon objects
</p>
</td>
</tr>
</tbody>
</table>
<p><br></p>
</div>
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