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===Threshold Comparison=== <gallery widths=400px heights=400px perrow=3 caption="RNA FISH Gallery FOXP2-594 (yellow) and CUX2-647 (magenta)"> File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_BestThreshold_ch00.jpg|Field 1, Best threshold File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_NoThreshold_ch00.jpg|Field 1, no thresholding File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_NoZeroThreshold_ch00.jpg|Field 1, no zero threshold </gallery> This gallery brings up an interesting comparison for thresholding. What role does the threshold play? The three images are of the same field, same image, just with different thresholds. The first is the "best threshold", which uses what I determine to be an appropriate level of zero thresholding with the max threshold set such that all remaining pixels are very bright. The second is the image alone, with no thresholding performed at all. The third brings the max threshold down so that the pixels are bright, but has no zero threshold, meaning even pixels with value 10 and under show up. The "no zero" image shows that there is a considerable amount of overlap between the two channels, as almost all large spots of FOXP2 are also seen with CUX2, but at a much lower intensity. Why?
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