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+---
+title: "Tutorials"
+---
+
+<style>
+.title{
+  display: none;
+}
+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>
+
+```{r setup, include=FALSE}
+# use rmarkdown::render_site(envir = knitr::knit_global())
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+<br>
+<!-- <br> -->
+
+<!-- ## Spatial Data Analysis with VoltRon -->
+
+<br>
+
+## Spatially Aware Data Integration and Analysis
+
+**VoltRon** incorporates multiple **data integration utilities to achieve data transfer** across a diverse set of spatial data modalities and types. VoltRon utilizes OpenCV to align and synchronize spatial omic datasets using **computer vision and image registration**. Users can automaticaly or manually align a list of microscopy images (**H&E**, **DAPI** etc) using a **Shiny App** incorporated within our analysis workflow. Once aligned, feature data and metadata level information can be transfered across aligned tissue sections. 
+
+In addition, VoltRon provides a number of spatially aware data analysis methods to detecting niches (i.e. **Niche Clustering**) 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. **Hot Spot Analysis**) of features, cell types and even molecular densities.
+
+<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>
+
+<br>
+<br>
+
+## Additional Downstream Analysis
+
+**VoltRon** is also capable of end-to-end analysis of diverse set of spatial data types (or spatial entities)such as **ROIs** (regions of interest), **spots**, **single cells**,  **molecules** and even **images**. 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. 
+
+<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>
+
+<br>
+<br>
+
+##  Other Utilities
+
+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 **interactive annotation/visualization** and importing spatially aware data from **diverse spatial omic technologies**. VoltRon is able to convert its objects to a diverse set of objects/datatypes commonly incorporated spatial data analysis (**Seurat**, **SpatialExperiment**, **Giotto**, **AnnData** etc.). Large VoltRon objects can be **saved ondisk** and efficiently analyzed without straining memory.
+
+<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>
+
+<br>