We are running an experiment to observe time to germination and growth in potato plants in a greenhouse. To that end we have built a gantry system equipped with an RGB camera to capture the plants which are placed on a bench 1.8m wide by 6.5m long (distance from bench to camera approximately 2m). In Pix4D I mosaic the images, but because this experiment is so large-scale, the geolocation tags are discarded and the resulting mosaics have no projection, are therefore not aligned in space, and are not measureable. It is possible to add scale in Pix using "scale constraints", however, this resamples and therefore lowers the quality of the mosaic, and still doesn't solve the projection issue.
In ArcMap, my initial solution was to define a custom projection for the first mosaic, and georeference/resample/snap the rest so the pixels of each aligned as they should (pixel size should all have been the same from the beginning). But, my projection was simply a Transverse Mercator and I did not fiddle with the parameters. Although this aligned the mosaics, they are still not measureable and the metadata does not truly reflect pixel size.
I also tried co-registration in ENVI, but this does not precisely align pixels nor does it allow measurements.
Is there another, more precise solution out there so that I have a time series of perfectly aligned mosaics that I can measure on the mm-cm scale, and that exist in the space that they should?