The output of the script is three additional channels in the source image sets. These channels are named for the dye signal that has been extracted and can be used in any pipeline as any regular image channel for segmentation etc. In cases of dual staining (e.g. H&E), the third channel essentially contains only the signal that could not be reliably attached to either of the other two. this means that this third channel can essentially be used as some form of quality control for the output since in a perfect deconvolution this third channel would ideally be empty. If there is still a strong signal in the third channel this usually indicates that the deconvolution parameters do not perfectly match  the staining in the image. This could be caused by white balancing issues or extreme staining (either too weak or too strong). 

For more information on the process of the deconvolution, please refer to the published literature on which this is based, linked above.