A light attenuating filter is introduced between a light source and a light sensor in a calibration region of a transparency scanner. The transparency scanner includes a carriage for supporting the light source, a transparent platen, and a housing for supporting the transparent platen. The light attenuating filter is placed in the calibration region either as part of a template resting on the transparent platen, as part of housing, or as part of the carriage. Light from the light source is directed through the light attenuating filter and onto the light sensor. The transparency scanner is calibrated to compensate for the attenuation of light by the light attenuating filter. Calibrating the transparency scanner includes adjusting one or more parameters for controlling the transparency scanner. Examples of parameters used for controlling the transparency scanner include light source intensity, light source exposure time, and analog and digital gain of a signal produced by the light sensor. In order to achieve a color balance in the calibration, the light attenuating filter may attenuate light of one color more than light of another color. When the transparency scanner is calibrated using this filter, color balance of the transparency scanner is adjusted.