You can do this by using the Convert Brightness to Opacity function in Clip Studio Paint and SAI or the Alpha Channel function in Photoshop. At times like these, it’s best to extract your line work and convert it into something more suited for digital coloring.
So, you just scanned or took a picture of your hand-drawn line art with your smartphone and, you go to color it to find that it just doesn’t look as ready to color as the original.