The Alpha Channel/Transparency Tool can be used to manually adjust the opacity of individual pixels on a 32-bit picture. The tool may be used either by clicking on specific pixels, or by dragging the mouse to modify multiple pixels along a path. The left mouse button will change the alpha channel to the value on the left side of PixelNEO's Color Box. The right mouse button will  will change the alpha channel to the value on the right side of the Color Box. This tool is most useful when making small corrections or performing precise editing in zoom mode.

With 32-bit pictures, the alpha channel contains opacity information for each pixel. This provides precise control over how the picture's pixels and the screen's existing background are mixed. A value of 255 in the alpha channel results in a completely opaque (solid) pixel, and 0 results in a completely transparent (see through) pixel. Alpha channel values between 0 and 255 result in pixels that are partially transparent. The lower the alpha value, the more of the background will show through.

This tool only works with 32-bit pictures.