I have tried using the "automatically place Passpoints" tool on the georeferencing toolbar in ArcGIS 10.3.1 but this only seems to work with Aerial photos which are near to identical. I have many colour infrared aerial photos and normal RGB aerial photos for the same areas which were taken 5 years apart from each other. This tools hardly works at all for these - either because of the colour difference or the fact that there are many discrepencies due to the time interval.

Does anyone know of other software which automates georeferencing? Or is there are way in which I could make it work better in ArcGIS 10.3.1?

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    If you are trying to do this in ArcGIS for Desktop then I think you should focus your question on asking about that. If you are looking for an alternative software recommendation then I think you should consider the Software Recommendations Stack Exchange. Asking about both in the same question makes me think this is too broad. – PolyGeo Feb 4 '16 at 19:58
  • Would the ArcGIS tool work on grayscale versions of your RBG photos? That would eliminate the problem with color differences. – whuber Feb 7 '16 at 14:45
  • as other software comes into consideration, many "drone pilots" i know use agisoft photoscan. But at least you need overlapping pictures and some ground points for georeferencing! – Andreas Müller Feb 7 '16 at 16:30