Transparency is used to set the Gif and Icon transparency colors..

To set Transparency click on the “Transparency” button under the settings menu and then select “Define Custom Colors”,

Transparency in settings

Enter in the Red, Green, Blue values of the color that you want to make transparent.

NOTE: Neomesh Image Converter uses near color matching, it will try to get the closest color to the one that you have selected, since Gif colors only have 256 colors it may not find a match. You should use block colors for your transparency, eg 128, 128, 255 etc…
Icon images are not effected by this.