Stack Contrast

Background

When viewing any image on a monitor, contrast settings are incredibly important. If the contrast is not set properly you may NOT see elements or structures in an image that ARE actually there.

Each stack is made up of pixels. Each pixel has an intensity (brightness) value in a range of possible intensity values. The range of possible intensity values is determined by the pixels bit-depth. A Pixels bit-depth is the number of binary digits that make up the number which represents the pixels intensity. Common bit depths (used in Map Tracker and biological imaging in general) are 8-bit, 11-bit, 16-bit, and 32-bit.

Here are the intensity ranges for each of these bit-depths:

  • 8-bit:      0..255
  • 11-bit:     0..2047
  • 16-bit:     0..65535
  • 32-bit:     0..4294967295

So why is this a problem? Why will I sometimes NOT see structures that ARE actually in an image?

Your monitor has a limited range of intensities it can display. Most monitors are limited to displaying a range of 8-bit intensities (from 0 to 255). If you view an 11-bit image (from 0 to 2047) the monitor is only able to display a range 256 values. Most monitors will display the full intensity range by grouping pixels with similar intensity values into the same intensity. The result is that you will not see some detail as these similar pixel intensities are being grouped into one intensity value.

Solution

Your monitor is going to display 256 intensity values, no matter what the bit-depth of the image displayed. We specify a low and a high intensity value such that any pixels with an intensity value  less than the low value will be displayed as a black pixel (intensity=0). Any pixel above the high value will become white (intensity=255). The monitor then fills in the remaining range (between the low and the high intensity values) with the remaining 255 intensity values.

Put another way, by specifying a low and high intensity value (a clipping window) you are expanding the range of intensities used to display the remaining intensities between these values. The result is that you can see more detail in this range than if the full range of the actual image was used.

How to do this in Map Tracker

The same 11-bit image plane at three different contrast setting.

Here is the same image plane from an 11-bit stack at three different contrast settings. Remember, the image data is not changing here, just the display. The three images correspond to different [low,high] clipping levels as follows:

  • Left: [0, 2047]
  • Middle [100, 1100]
  • Right [20, 800]

You can set these low/high values using three different interfaces:

  • Histogram (keyboard ‘h’ from a stack).
  • Process Panel.
  • Using a stacks contrast toolbar (keybord ‘c’ from a stack window).

histogram

When viewing a stack, open its histogram window (keyboard ‘h’) and you can interactively set the low (upper slider) and high (lower slider) values interactively. The image displayed in the stack will update in real-time as you adjust the low/high sliders.

When viewing a stack, switch to the process window, set the low/high values and click ‘Set’. Each stack will be displaying a channel, either Channel 1 or Channel 2 (Ch1 and Ch2 respectively).

In both cases (process panel or histogram) you can select low/high default values with the ‘Default Contrast’ popup.

Note: The bit-depth of the stack you are viewing is displayed in the upper left of the image.

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