Correct workflow for aligning photogrammetry orthomosaics

[ianMc]

Hi,

Context:
- we want to difference two orthomosaics to see where NDVI changes, so we need the orthos to be perfectly aligned. However, this is apparently more difficult than I thought.
- We are using Metashape Pro v2.0.3.16960.

This is my current workflow. I do this separately for each flight.
- load photos and align
- build point cloud
- export point cloud, align to a standard one we have in CloudCompare software
- start a new chunk and re-upload the aligned point cloud as laser scans.
- re-upload the photos and align again (this time I understand it uses the laser scans).
- build a new point cloud
- Build DEM, and then build orthomosaic.

The result is that one side of the study area is almost aligned while the other side is not. I can confirm that the CloudCompare outputs are aligned because I've checked on DSMs created from them and they are perfect.

I have tried the following without success:
- aligning the two flight chunks
- uploading the aligned point clouds as point clouds instead of laser scans, merge to single cloud, then build DEM via extrapolation
- following the tutorial as described here for terrestrial lidar scanning: https://agisoft.freshdesk.com/support/solutions/articles/31000168474-terrestrial-laser-scans-processing-in-metashape-2-1
- building the orthomosaic directly from the laser scans *does* produce aligned orthomosaics, but the resolution is worse and there are many artifacts in the image that make comparison difficult.

My questions:
- am I missing something in my workflow that would help the alignment?
- does anyone have any recommendations for something else to try?

Thanks!

[ianMc]

Bumping this, can anyone either at Agisoft or otherwise verify if the workflow is correct or not?