---
title: "Tutorials"
---

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```{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>
