This panel allows you to see and control how image intensities are displayed. When an image is acquired or read from a file, pixels are sampled over a particular area to determine how to scale the intensities for display. The program finds the lower and upper intensities beyond which only a certain small fraction of pixels have intensities, and stretches the contrast to map these limiting intensities to 0 and 255 in an intermediate byte image used for display. This byte image is displayed with a second mapping determined by the Brightness and Contrast sliders; 0 and 255 display as black and white on the screen when these sliders are in the middle position. These limiting values of the first mapping are shown in the Black and White text boxes. You can control the size of the area that will be analyzed, as well as the percent of pixels whose intensities will be saturated at each extreme. You can also simply change the black and white values directly. Nothing you do in this window will affect the pixel values that get saved to a file.
Black and White level sliders and text boxes
The text boxes show the image intensities that map to 0 and 255, and which then display to black and white on the screen with Brightness and Contrast in the middle position. The sliders are tied to these values, and the range of the sliders corresponds to minimum and maximum image intensities estimated by sampling the entire image. Because the sampling can miss bright pixels cause by X-rays, the latter values are typically not the same as the minimum and maximum intensities in the image, which you can determine with the Min/Max/Mean command in the Process menu. You can adjust the sliders or enter new values in the boxes to control the degree of saturation at the extreme values in the image. You can enter values beyond the range of the sliders as well.
Note that these sliders do not correspond to the Black and White sliders in 3dmod; rather, they are similar to the High and Low sliders that appear when 3dmod is opened with the option to store values internally as 16-bit integers.
Brightness and Contrast sliders
Use these sliders to adjust the brightness and contrast settings of the display for the current image. Different images can have different brightness/contrast settings. A newly acquired image will inherit its settings from the previous image in the A buffer. If an image appears saturated at a uniform gray level after adjusting these sliders, you probably need to adjust the Black or White levels to see detail in these regions. If a bright area appears saturated, try raising the White level; if a dark area is saturated, lower the Black level.
Zoom
The text box displays the image zoom and allows a zoom value to be entered directly. The up and down arrows allow you to increase or decrease the zoom. The -/_ and =/+ hot keys and the mouse scroll wheel are more convenient for this purpose.
Cross (Hot key Shift+H)
When this option is selected, the program will always draw a large red cross in the center of the display, not just when shifting with the mouse.
Invert
Use this button to invert the image contrast; the hot key F11 can also be used.
Set Truncation
Use this button to enter new values for the percent of pixels that will have their intensities truncated at the low and the high end of the intensity range, and new values controlling how FFTs are scaled. You will enter four dialog boxes for entering new values. The first two are for entering the percent of pixels truncated at the low and high end of the range. The next one is the mean gray level that FFTs should have at their edges when first displayed. Values in the range of 16 to 64 may be useful, although the actual perceived gray level will depend on how noisy the FFTs are. An entry of 0 here will disable the special scaling of FFTs. The final text box sets the relative diameter of a ring of pixels whose mean magnitude will be displayed as white. Useful values are in the range of 0.002 to 0.025, depending on whether there may be detail at the lowest frequencies that you want to appear in the display. If any of these parameters are changed, the current image will be re-analyzed and displayed with the new settings, which will apply for new images that are acquired. Note that all of these parameters affect the setting of the Black and White levels, which you can change if there is too much or not enough truncation of extreme values.
Set Area Fraction
Use this button to enter a new value for the fraction of image to analyze when determining the Black and White levels. Enter a fraction of the linear extent of the image. For example, if you enter 0.5, then only pixels from 256 to 768 in X and Y in a 1024 x 1024 pixel image will be analyzed, which is actually only one-quarter of the image area.
Extra info (Hot key Shift+X)
Use this button to turn the display of scale bars, min/max/mean, camera name, and dose rate on or off.
Tilt axis
Use this button to turn a display of the tilt axis on all images on or off. With the option off, the tilt axis will be displayed only on Low Dose View or Search images when defining the Trial or Focus area.
Antialiasing
This button controls whether images zoomed down below 0.8 are scaled with a filter that eliminates noise and artifacts from aliased information. Aliasing occurs when an image is zoomed down by simply sub-sampling the pixels; namely, information at frequencies higher than what can appear in the scaled-down image appears as noise at other frequencies in the sub-sampled image. The antialias filter removes frequencies above the new frequency limit in the process of making the scaled down image. This process can take several seconds for very large images; thus this option can be used to turn off the filter. The filter is temporarily turned off when panning an image with the left mouse button.
False color
Use this button to display the current image in false color; the hot key F12 can also be used. Contrast inversion can be used to invert the color ramp.