Control of image processing is done primarily through the histogram window. The objective is to optimally display channels that have widely different dynamics. Contrast, brightness, and gamma adjust the image into proper display range within the full range.

The image Histogram graphs the tonal distribution of an image. The X axis represents pixel intensity, with 0 is the lowest possible value and 65535 being the highest possible value in a 16 bit image. The Y axis represents the number of pixels at each value. The scale of the x axis can be set to linear, logarithmic or logicle.

Data Range

Adjust the minimum and maximum values displayed in the image by sliding the nodes on the end of the curve or by changing the "Min" and "Max" value at the bottom of the histogram. While this can be done for thresholding, the Data Range checkbox provides a visual by highlighting pixels included in the data range.

Check the "Data Range" box to unlock the bar. Adjust the range by dragging the green (min) and red (max) marks.

Blink Effects

The "Blink" and "Smooth fade" features provide the user with rudimentary animation controls. This is an extremely useful feature when displaying many combinations of channels at once and creating multiple perspective combinations.

Selecting the checkboxes next to the Blink function will control the blink intervals, so you can customize blinking effects when visualizing or creating scenes for a sequencer movie that can later be exported.

The blink intervals function like musical bars, and the 4 checkboxes constitute a 4 beat whole. You can change the duration of the blink by changing the note (checkbox). For example, selecting all 4 checkboxes will create a whole blink (4 beats), and selecting just the 3rd checkbox will create a quarter blink on the 3rd beat.

You can toggle the blink effect for a channel multiple ways:

Note that only in the Histogram and Properties widgets can you customize the blink intervals and toggle the smooth fade transition. Right clicking the channel name in the legend will only apply the blink affect set in place for that channel.

The following are examples of both normal and slow fade blinks:

Normal Blink
Slow Fade Blink


Linear Scale

Linear scales are most effective for displaying datasets with values spread evenly across a given range. It is less practical when data points consume a larger dynamic range. 

Logarithmic Scale

Logarithmic scales are most effective when graphing parameters with a wide dynamic range., which is often the case when plotting fluorescent flowcytometry data to delineate heterogeneous populations of cells.. A log scale is based on exponential differences between values. Consecutive graduations along an axis represent equal changes in ratio.

Logical Scale

The logical scale avoids problems encountered with logarithmic scaling of data, when primary measurements and/or compensated data includes very low and negative values. The inverse hyperbolic sine function (sinh−1) offers attractive features as a scaling function in that it gives a near-linear region above and below data zero, near-logarithmic behavior at high data values, and a narrow but very smooth transition from one to the other.