Working with false-color images

Single-layer False-color Image

When viewing image-data such as scores of a PCA model built on an image, the scores are formatted with accordance to the original image-data. When displaying the scores of a single component (as a single layer image), the results are displayed in false-colors. Shown in the figure below, is the original image in the Image Manager window (on the left, for reference), and the scores of the first component of a PCA model built on the data (right), note that the colormap for the scores is set to ‘jet’.

Adjusting the Colormap

The colormap may be changed by clicking on the ‘Insert Colorbar’ button, right-clicking on the generated colorbar, select ‘standard colormaps’ and select one of predefined colormaps (such as ‘jet’ or ‘hot’).

When right clicking on the colormap, you may choose ‘open colormap editor’ to create and customize your own colormap. Note that in this false-color mode, the color corresponds to the magnitude of the scores at each pixel.

You may also choose to interactively adjust the colormap by right clicking on it and select ‘Interactive Colormap Shift’, then at the top and the bottom of the colormap you can click & drag to adjust the colormap as desired.

Selecting Variables by Threshold

To select variables based in their respective values, right click on the image and select ‘Image Histogram’, a window will pop-up displaying a histogram of the pixel values in the image. Click on the ‘Select Pixels From Histogram’ in the upper left corner and select a desired region in the histogram (click & drag).

Two/Three-layer False-color Image Overlay

When displaying two or three images in an overlay (such as scores of multiple components in a PCA model), the false-color mode changes from colormap to “RGB mode” in order to accommodate the multiple layers. In “RGB mode”, the colors displayed in the image reflect the magnitude of each overlay/score. The data cursor tool can be used to view these "RGB" values at a specified location/index.

Changing the Color Order in RGB Mode

To Change the Color order, in the Plot Controls window: View -> Settings. A setting window will open, and under ‘Image settings’ there is a field called ‘imagegunorder’ with several number (default: 1 2 3) clicking on these numbers will open a drop down selection for reordering the false-color overlays which results in changing their respective colors. Meaning, 1 2 3: first layer is colored red, second is colored green, and third is colored blue. Likewise, 3 2 1: third layer is colored red, second is colored green, and the first is colored blue.

Multi-layer (4+) False-color Image Overlay

When displaying more than three overlays the color mode changes to correspond to standard plot color order (so they correspond to overlaid scores plots, for example). The false-colors displayed correspond to the component with the highest score/value.