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\mainpage Overview

<b>THIS VERSION WAS USED FOR BRATS 2016 TESTING AND CONTAINS EXTREMELY BASIC FUNCTIONALITY.</b>

The Cancer And Phenomics Toolkit (<b>CapTk</b>) showcases some of the highlight applications from the <a href="https://www.cbica.upenn.edu/">Center for Biomedical Image Computing and Analytics (CBICA)</a>.<br><br>

<b>NOTES:</b><br>

- Our application has been optimized for monitors with 16:9 resolution, especially 1920x1080 at 100% scaling. More resolutions and scaling options are being actively tested and support will increase in subsequent releases.

- The CapTk software family (which includes the interactive framework and available applications) incorporates 3rd party libraries and toolkits. All rights to these components are subject to the terms and licenses of their respective owners. All trademarks are the property of their respective owners. The libraries include but are not limited to:

  -# <a href="https://www.qt.io/">Qt</a>
  -# <a href="https://www.itk.org/">ITK</a>
  -# <a href="http://www.vtk.org/">VTK</a>
  -# <a href="http://www.opencv.org/">OpenCV</a>
  
- CapTk comes in various variants. Each variant caters to a particular usage scenario. When requesting for download, ensure you provide which variant you want, otherwise the default will get downloaded. Some of the envisioned variants are highlighted below:

  -# <b>Viewer</b>: This is meant to be used as a light-weight medical image viewer. It provides capabilities of adding seed points, drawing regions of interest, etc. and saving them in open formats to be used in other applications.
  -# <b>Neuro</b>: Viewer + neuro-imaging applications like EGFRvIII prediction, Recurrence estimation, Geodesic segmentation, etc.
  -# <b>Torso</b>: Viewer + breast and lung imaging applications like LIBRA, SBRT, etc.
  -# <b>Full</b>: Viewer + Neuro + Torso.

- CapTk does the visualization based on the physical coordinate system of the image (i.e., it takes the origin and direction information into account while doing the rendering). In practice, this means that images that are shifted (have different origins), appear mis-aligned, as they rightly should be. However, this behaviour has not been seen in other neuro-imaging visualization software packages, who do rendering based on the cartesian coordinate information in the image.

This page serves as a basic landing page for anyone who wants to read the documentation of CapTk. There are various topics in this documentation and they are covered in a sequential manner as follows: 

- Download - This section gives download instructions for CapTk.
- Installation - This section provides details instructions on building CapTk from its source code.
- Usage - This section caters to information related to using the various functions in CapTk.
- ForDevelopers - This section has technical information related to APIs using which developers can integrate their application(s) into the CapTk framework are highlighted here.
- People - This section lists the people involved in this project.
- Publications - This section lists the publications related to CapTk.
- Changelog - This section records the changes with respect to the previous release(s).
- License - Copy of the <a href="https://www.cbica.upenn.edu/sbia/software/license.html">SBIA license</a>, which covers the source code of CapTk but not its dependencies.


Though we have tried to make the documentation for CapTk as comprehensive as possible, if users need any details, feel free to contact <a href="mailto:software@cbica.upenn.edu">CBICA Software</a> with details of the issue/question.
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