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I am working on fixing up my criss cross portion of my program. However first I had to get rid of that breakpoint that was bugging me for so long. With Koch's help we figured it was a bug so I just removed the while loop and put a new one in. By suggestion of the doc I put in my new one before removing the faulty while loop. This allowed me to make sure all shift registers were correct before removing the bad one..
OK now with that done--The biggest problem I am seeing so far is in that video from yesterday for like two frames the software tracks the wrong microtubule before getting it right. I am gonna try to stop this from happening. I suspect it happens because my algorithm is to find the brightest pixel in the rectangle, and I am guessing that pixel is in the other MT. So maybe more criteria will stop this from happening.