Process images acquire from a overhead crane

I am using an overhead crane to acquire photos over an experimental channel in which aquatic grasses have been planted. The base of the overhead crane is visible in the photos. As the overhead crane moves with the camera, part of the scene changes from one photo to the next but part is constant and shows the base of the overhead crane. Does this interfere with the mosaicking process?
If so, is it possible to crop the images (from an altum PT camera) before importing them into Pix4D?
Thank you