Reproducability

The position of objects in the s and p image is easily messed up by little angles, or by the crystals changing position. I've done lots of tests to figure out the best way to position them to keep the stable and I've learned to do image registration, taking two images and getting them to overlap correctly. It was a lot harder than I thought it would be, and I ended up learning how to do it both in Fiji Image and in MATLAB. 

In this first image, I realized I hadn't taken into account that the s and p images mirrored each other. So even when they "overlapped" the computer had a difficult time lining everything up. 

This is just before I implemented my image registration into the other code I am using. Gray represents overlapping pixels and green and pink represent image 1 and image 2 when they don't overlap well. The registration code is finished and I wanted to see how accurately I could position the crystals in the same place over and over again. Since they move in their 3D printed case, it didn't work out very well. That's not great, but important to know going forward.