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Problems georeferencing images taken in succession

We are conducting a study of a field. There are control markers placed on the field to enable us to line the images up. We flew the field daily for a week and created a mosaic image for each day. We then imported the image into ArcMap and georeferenced using the same point file and the control markers. The first day, we digitized the rows. When we applied the digitization to the next day’s image, it was not lined up correctly. The rows for the second day were digitized. The third day didn’t line up with either of the first 2.

Is there something about the mosaic process that could cause this issue? I’m not familiar with how Pix4d works in detail. Does the mosaicing stretch or condense the images, so the rows would be off? I have searched for similar problems with ESRI, but have found nothing.

Thank you for your time.

Dear Jason,

Is this issue solved? 

If we understand correctly the issue, the orthomosaics of the different days are not perfectly aligned. Do you have GCPs for the project? What is the accuracy of the GCPs? How much is the misalignment? 

Can you please send some screenshots that illustrate the issue?

Best regards,