preferred method to align outputs from multiple cameras

I fly an ag field several times throughout the growing season using a Mavic 3 Multispectral and Mavic 3 Thermal. I’m also using a D-RTK 2 on all flights. This produces 3 sets of data - rgb, multispec and thermal images. I’m currently processing the 3 sets of images separately, Pix4Dmapper steps 1 - 3. Individually, the outputs look as expected. When performing post-processing in GIS software using all Pix4D output orthomosaics/indices I can see that there is a slight shift between the geo positions of various images. This skew between images is causing issues. What is plant material in one index, is soil in another, etc…

Reading more, I found others recommended creating a merged project. I created 3 sub-projects and ran only step 1 processing. I added 5 MTPs (field markers used to assist with GIS processing) to each sub-project, manually marking several images in each band, including each of the 4 multispec bands. I created a merged project using the 3 sub-projects. All 6 cameras were detected, but only rgb indices were available to select in step 3. Not sure what happened to the multispec and thermal indices, but I ran it anyway to see how the outputs looked, but it failed during step 3 processing…

I’m now trying to decide if it is worth troubleshooting the merged processing. If I can get it working, will it provide indices for all bands? (3 rgb, 4 multispec, and 1 thermal) And most importantly, will the images be spatially aligned with each other? Would I be able to accomplish the same thing by running each set of images as a separate project (steps 1 - 3, which works well, no errors) and using my existing, anchored field markers as GCPs? I haven’t done so, but imagine I could get their positions using the D-RTK 2 or maybe even pull values from an existing orthomosaic. If I include the same GCPs in each project will that generate outputs with better alignment with each other?

This seems like a common problem, but I only do this type of work a few times a year. I’m hoping someone with more experience can point me in the right direction.

Hello, The best approach would be having GCPs on your project so that all the project algin and you can process them separately.