Cancer Imaging Phenomics Toolkit (CaPTk)  1.3.0
Interaction Details

Overview | Pre-Processing | Interaction | Segmentation | Quantitative Imaging Feature Panel | Specialized Applications | Stand Alone CLIs


Contents:

  • Image Loading
  • Tab Docking
  • Coordinate definition (Seedpoint initialization): seed and tumor points
  • Annotation of Regions of Interest (ROIs) & Drawing


Image Loading

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

1_loading_resize.png
Loading images for visualization/processing
Sliders control the movement across respective axes (the single horizontal slider controls across the temporal axis for Perfusion).

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

For every loaded image, the modality is automatically assigned using the header information (for DICOM) or the file name (for NIfTI). In case of discrepancy, the user can use the drop-down modality switcher (see below) to change accordingly. This is needed for further using the images in the Specialized Analysis applications.

5_modalities_resize.png
Modality switching for individual images

Tab Docking (Windows-only)

Double clicking on the tab bar will dock/undock the entire section. This behavior is replicated by single click of the dock/undock button at the end of the section as well.

2_dock_comparison_resize.png
Left is while dock is active and right is undocked behavior

Coordinate definition (Seedpoint initialization)

The Seed Points tab includes two general types of initialization - 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.

3_seeds_resize.png
Seed point initialization

Tumor Points

These are seedpoints used to approximate a tumor by a parametric spherical model, using a seedpoint for its center and another for its 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 seedpoints with coordinate information. They can be used for a multitude of applications where manual initialization(s) are required for a semi-automated algorithm, e.g, segmentation. 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/GLISTRboost, 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.

NOTE: Initial points (tumor center and tissue point) can be added using Double Click of the mouse.



Loading and saving is done via text files in a format consistent with similar applications. Seedpoint files are needed for the following applications (and all derivatives): GLISTR, GLISTRboost (BRATS 2015 top-ranked algorithm) and PORTR.

Annotation of Regions of Interest (ROIs)

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

4_drawing_resize.png
Drawing functions
Button/Box Description
View Mode Switch from drawing mode (which is enabled when either Near or Far ROI drawing is selected) to normal viewing mode
Line Draw a line of selected label color and size
Rectangle Draw a rectangle of selected label color and size
Circle Draw a circle of selected label color and size
Free-Hand Draw selected label using brush of specified size using mouse left button drag
Fill Fill a closed boundary with selected label - uses ITK's connected component filter
Eraser Erases all labels using brush of specified size
Label Selector Label selector between 1-5
Marker Size A square marker of specific voxel size
Marker Opacity Sets the opacity of the marker between 0.0 (transparent) - 1 (opaque)
Clear Selected Label Remove selected label completely from the mask
Clear All Labels Remove all labels completely from the mask
Undo undoes last drawing action


Next (Building from source)