Colors dialog box

The Colors dialog box contains functions for adjusting the data's color properties. To access it, select a data object from the list within the Data controls of a display window, then click the "Colors" button. A dialog box like the following will appear:

Colors dialog box

The dialog's preview display provides a quick view of the consequences of any color changes made. Clicking the OK button will apply those changes to the entire dataset.

Brightness and contrast

Image brightness and contrast can be adjusted with the brightness and contrast sliders, respectively.

Opacity (transparency)

The opacity slider controls how opaque the data is. The rightmost value of 256 is 100% opaque, whereas the leftmost value of 0 is 100% transparent.

The "Constant" transparency model behaves like a layer in Photoshop, with the opacity value uniformly defining how opaque each pixel is.

The "Curved" transparency model maps a transparency curve from the minimum color value to the maximum color value, with the opacity value defining how sharply the curve arcs. An opacity of 128 (the center of the slider) is a straight line from min to max, meaning that pixels with the minimum color value are completely transparent while pixels with the maximum color value are completely opaque, with intermediate values weighted linearly. An opacity of 0 slants the line so that most pixels are nearly completely transparent unless they are at or near the maximum value, while an opacity of 256 slants the line so that most pixels are nearly opaque unless they are at or near the minimum value. (If it sounds complex, don't worry: just play with it a bit while watching the color table on the right and it will make perfect sense.)

The "Curved" model is especially useful when performing volume rendering (see the Data settings topic for more information on volume rendering).

Range components

Data in VisBio has one or more range components. That is, at each pixel, there may be one or more associated values. Often, there will be only one range component (such as intensity, representing the intensity at that pixel), although some data may have three range components (such as red, green and blue, representing the red, green and blue values for that pixel, respectively). Data collected with multi-spectral imaging techniques may even have 32 or more range components.

Color models

VisBio supports three color models: RGB, HSV and Composite. In the RGB color model, the color space is divided into the components Red, Green and Blue, representing the levels of red, green and blue present at each pixel, respectively. In the HSV color model, the color space is divided into the components Hue, Saturation and Value, where hue represents a value along a color continuum (similar to a rainbow), saturation represents how saturated each pixel is with that color (the less saturated, the whiter the pixel will be), and value represents the brightness of each pixel (the less the value, the blacker the pixel will be). The Composite color model maps all color components to a color continuum known as "pseudocolor" and averages them, so that each pixel represents a composite of all its range components.

Range component color mappings

Range components from the data can be mapped to one or more color components. For example, data with one range component, intensity, could have intensity mapped to Red, Green and Blue, producing a standard grayscale image. For data with three range components, the natural mapping is to map the first component to Red, the second to Green and the third to Blue, fully representing the data in the RGB color space.

VisBio will attempt to guess at good range component mappings when data is first loaded, but in some cases, adjustments may be necessary to achieve the desired visualization. In particular, when the data has more than three range components, you will probably want to choose which range components to map to which color components for greatest effectiveness.

To map a range component to a color component, choose the desired range component from the color component's drop-down menu. For example, to map intensity to Red, choose intensity from the drop-down menu labeled Red.

At times, it may be useful to fully saturate a color component, or completely empty a color component. To zero out a color component, choose None from that component's drop-down menu. To max out a color component, choose Full instead.

Lastly, when the Composite color model is selected, the range component drop-down menus will be grayed out, since all components are mapped to pseudocolor.

Range component color tables

Each range component has an associated color table that fully represents its mapping into the color space. To view this color table, choose the desired range component from the drop-down menu above the color table. The displayed color table and color range will change to represent the chosen range component.

By changing brightness, contrast, range component mappings and other options, you will see the changes reflected in that range component's color table. However, complete control over each color table is available if needed. To modify a color table directly, drag the left mouse button across to the table to modify the active color component level at different range values. Click the right mouse button to cycle through active color components, from Red to Green to Blue to Alpha (opacity) and back to Red.

The "Save LUT..." button allows you to preserve the current color table for later use, by storing it on disk as a LUT file (compatible with ImageJ). The "Load LUT..." button reads these LUT files back in and sets the color table accordingly. VisBio also has several preset color tables available from the popup menu accessible with the "LUTs >" button.

Color scaling

Each range component has a range of values. By default, VisBio assumes the minimum value is 0 and the maximum value is 255. That is, a range component value of 0 corresponds to the leftmost color in its color table, whereas a range component value of 255 corresponds to the rightmost color in the table.

Of course, it may not be the case that a particular range component conforms to this assumption. Thus, minimum and maximum range values can be manually specified for each range component by typing them into the appropriate text boxes after checking the "Fixed color range" option. Alternately, VisBio will compute these bounds automatically if "Fixed color range" is unchecked.

See also: