Alpha Controls group
The Alpha Control group lets you make adjustments to the matte to achieve a superior composite. The interface is comprised of two sections, Gamma and Alpha Cleaner.

Gamma group
The Gamma group lightens, darkens or adjusts the gamma curve of the matte using a standard Levels interface. The controls in Gamma are identical to those found in the standard After Effects Levels filter.
You can use the Input/Output sliders to convert completely opaque or completely transparent areas of a matte to be semi-transparent, or to convert semitransparent areas to be completely opaque or completely transparent. Because transparency is based on the monochrome alpha channel, the controls for this effect refer to complete transparency as black and complete opacity as white.

Histogram
Shows the number of pixels with each luminance value in an image.
Numerics> Input White, Output White
Input White and Output White Pixels in the matte with a luminance value equal to the Input White value are given the Output White value as their new luminance value. The Input White value is represented by the upper right triangle below the histogram. The Output White value is represented by the lower right triangle below the histogram.
Use Output White Level of 1.0 and Input White Level less than 1.0 to convert a range of semitransparent areas to be completely opaque. Use Output White Level less than 1.0 to convert a range of completely opaque areas to be semitransparent.
Numerics> Gamma
The exponent of the power curve that determines the distribution of luminance values in the matte. The Gamma value is represented by the middle triangle below the histogram.
Numerics> Input Black, Output Black
Input Black and Output Black Pixels in the matte with a luminance value equal to the Input Black value are given the Output Black value as their new luminance value. The Input Black value is represented by the upper left triangle below the histogram. The Output Black value is represented by the lower left triangle below the histogram.
Use Output Black Level of 0 and Input Black Level greater than 0 to convert a range of semi-transparent areas to be completely transparent. Use Output Black Level greater than 0 to convert a range of completely transparent areas to be semi-transparent.
Alpha Cleaner group
A big part of getting a successful key involves having good source footage. Unfortunately, this doesn't always happen. Quite often your source image has wrinkles, discoloration, uneven lighting or other problems, all of which can create a problem key. Primatte is able to handle many of these problems but you will still run into issues. Alpha Cleaner is designed to help in these situations. Read a great example in Keying Difficult Footage.
Alpha Cleaner zaps grain or noise, fills holes in the foreground matte, and fixes other problems that would otherwise require a separate matte touch-up in a paint program. Alpha Cleaner works by applying a clean-up pass to your matte and identifying dirt and other artifacts based upon a combination of values like their size, alpha level, and proximity to the principle element in your matte.
There are six Threshold controls for the threshold values for controlling the operations of Alpha Cleaner. These are broken into three pairs of operations, with each pair treating specks or holes or both.

Alpha Cleaner> Cleaning Mode pop-up
Designates which cleaning operation you wish Alpha Cleaner to perform.

Alpha Cleaner> Size Threshold
Determines which pixels will be removed based upon their proximity to each noise or chatter area. The value controls the size of the clean-up area, with 100% representing the largest area of cleanup (roughly 1/5 of the image size) and 0% representing no cleanup. Increase this value to get rid of larger areas of noise, such as larger specks in the black areas or larger holes in the white areas. Noise outside of the Threshold range is left unaffected.
Alpha Cleaner> Level or Alpha Threshold
Determines which pixels will be removed based upon the pixel’s luminance value. Noise pixels with a luminance value below the Level/Alpha Threshold will be set to 0 (black) or 100 (white), depending on whether you are removing specks or filling holes. The higher the Level/Alpha Threshold value, the more pixels will be set to either solid white or solid black.
When you look at your matte, if you have areas of your background or foreground (pixels which should be 100% black or 100% white) which appear gray, this control will allow you to remove them. However, if you have any areas of your matte that are supposed to be semi-transparent, such as hair, smoke, or motion-blurred edges, this operation will remove the transparency in these areas also. In these situations, you should first isolate the areas that need to be cleaned with a garbage matte, then using Alpha Cleaner only on those areas.
Note that only pixels within the range of the Size Threshold value will be affected by Level/Alpha Threshold.
Alpha Cleaner> Connection Threshold
Determines which pixels to remove based on their proximity to major objects in the alpha. The higher this value, the more non-essential pixels will be removed. Increase this value if you find your alpha growing 'tendrils' after cleaning.