Accounting for shadows from clouds in creating orthomosaic/point cloud

Hi Patrick, 

Sorry for the delay and thank you for your comments.

First of all, we do not recommend to use Photoshop as some filters/processes can even modify the geometry of the image.

As for your question, I am not sure if I understand it well but I think this other post can help you:

https://community.pix4d.com/t/7112-Questions-about-Ortho-Mosaic- 

Pix4D uses a custom color alignment algorithm. This algorithm accounts for both exposure mismatches between images of a project (global offset and gain per image) and camera-related defects such as vignetting (that result in pixel-varying correction terms). While this problem can seem complex at first, we exploit the results of the geometric computations of step 1 (mandatory) and step 2 (when available) to make it tractable.

I hope this answer helps you.

Regards.