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+} +body { + text-align: justify +} +table, th, td, tr{ + empty-cells:hide; + border-spacing: 25px; + border-collapse: separate; +} +td{ + filter:drop-shadow(0 0 10px rgba(0,0,0,0.3)); + padding: 10px; + background:white; + text-align:center; + width:33%; + vertical-align: text-top; +} +td:hover, td:active{ + filter:drop-shadow(0 0 10px rgba(0,0,0,0.3)); + transform: scale(1.02); + cursor: pointer; +} +.main-container { + max-width: 1200px; + margin-left: auto; + margin-right: auto; +} +<!-- .main-container { --> +<!-- margin-left: %5; --> +<!-- margin-right: auto; --> +<!-- } --> +p.tutorial { + text-decoration: none!important; + font-size: 1.5em; + color: #23803A; + margin: 3% +} +</style> +<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> + + + + +</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 --> + + +<!-- 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>