Cancer Imaging Phenomics Toolkit (CaPTk)  1.0.1.20170207
Interaction Details

Image Loading

All the file types are loaded from the File -> Load menu.

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Sliders control the movement across respective axes (the single horizontal slider controls across the temporal axis for Perfusion).

Various basic operations such as adjusting contrast and brightness (right mouse button click + horizontal/vertical drag on the visualization pane), window and level set (bottom panel) are available for the user. The bottom panel also shows basic information about the image and the currently selected coordinate.

Tab Docking

Double clicking on the tab bar will dock/undock the entire section (highlighted in red). This behavior is replicated by single click of the dock/undock button (highlighted in yellow).

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Initializing Seed Points

Below the Seed Points tab, there are two general types of initializations - tumor points and tissue points. The controls to add/remove points are the same as above. The radio buttons control which initialization type is selected and related functions.

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Tumor Points

These are basically seed points that have a coordinate and a radius. These are helpful for applications like tumor growth model simulation. The controls are as follows:

Key Stroke Function
Shift + Space Set initial tumor center
Ctrl + Space Update tumor radius
Space Update tumor center

Tissue Points

These are basically seed points with just coordinate information. They can be used for a multitude of applications where manual initialization(s) are required for a semi-automated algorithm. There are various tissues that can be initialized in this panel:

Tissue Acronym Full Form
CSF Cerebrospinal Fluid
VT Ventricular Cerebrospinal Fluid
GM Gray Matter
WM White Matter
VS Vessels
ED Edema
NCR Necrosis
TU Enhancing Tumor
NE Non-Enhancing Tumor
CB Cerebellum
CAE Enhancing Cavity
CAN Non-Enhancing Cavity
RTN Tumor Recurrence
RTE Enhanced Tumor Recurrence

Application-specific tissue types are automatically enabled when the corresponding application is selected. For example, when trying to initialize tissue points for GLISTR, only CSF, GM, WM, VS, ED, NCR, TU, NE and CB buttons will be enabled and the rest will be disabled. If there are some required tissue types missing for an application, CaPTk will display a warning and not let the user save the incorrect tissue points.

Loading and saving is done via text files in a format consistent with similar applications. Seed-point files are needed for the following applications (and all derivatives): GLISTR, GLISTRBoost (BRATS 2015 Winning Algorithm) and PORTR.

Drawing Regions of Interest (ROI)

ROIs are useful for applications that need a mask as input. There are the following controls underneath the Drawing tab:

Buttons Description
View Mode Switch from drawing mode (which is enabled when either Near or Far ROI drawing is selected) to normal viewing mode
Marker Size A square marker of specific voxel size. Acts as size for Near and Far ROIs and for eraser
Near ROI Highlighted in Red and saved as value 150 in the 0-255 space
Far ROI Highlighted in Green and saved as value 255 in the 0-255 space
Erase Voxels This acts as an eraser for both Near and Far ROIs
Clear Separate buttons to clear Near and Far ROIs
Undo Undos last drawing action