Adjusting the Color Scale

Once you have loaded a greyscale image (like, e.g., an intensity map) you might want to adjust the colorscale to better display your data. To do this hit the 'Volumes' button in the main menu and choose the 'Display' tab in the related panel.

Set the 'Active Volume' selector to the dataset for which you want to adjust the color scale. For our example this should be 'IntensityMap'. Then select one of the slice views by clicking into it. If you start adjusting the color scale, changes will be applied immediately to this slice view.

Choosing a Color Palette

The 'Palette' selector allows to choose from a set of color palettes. Set it to your favorite palette.

For our excercise, set the color patette to 'Gray'.

Contrast Adjustment

The 'Win' and 'Lev' sliders control how the data values are transformed into brightness levels on your display. When choosing a black-to-white colorscale ("palette") as an example, with the 'Win' slider you would control over which range in data units the color would turn from black to white. In the same example, and for fixed 'Win' slider, the 'Lev' slider would further control above which data value the color slowly starts to turn from black to grey. Set the 'Window/Level' selector to 'Auto' for an automatic contrast optimization.

The example dataset, e.g., is well displayed when setting 'Win' to 4700 and 'Lev' to 1900. This means that all voxels with a data value below 1900-4700/2=-450 will be displayed black, while those exceeding 1900+4700/2=4250 will be rendered white.

Clipping Data

The 'Lo' and 'Hi' sliders can be used to clip data below or above some threshold. Voxels with data values below the treshold set by the 'Lo' slider, respectively above the value set by the 'Hi' slider, are colored black in the slide views. When activating 2D slides within the 3D scene these slides become transparent where pixels are clipped.

In our specific case, 'Lo' and 'Hi' settings of 400 and 1000, respectively, yield slice views in which all data below a significant level of emission of 400 mK is displayed as black. Also bright areas above 1000 mK are rendered black. Slices projected into the 3D scene (use the 'V' buttons next to the slice views) become transparent in the same areas.

Please reset 'Lo' and 'Hi' to the smallest and largest values possible, respectively, before proceeding to surface creation.