Are there data about the effect of light leaking into the chamber during measurement? If the sun is shining right on the gap, there could be variable amounts reaching the light guide. I was thinking about attaching a little black felt skirt that blocked at least the direct sunlight from hitting the gap. But maybe the light guides are not sensitive to light coming from the side?
I know we talked about this over Hangout Chris, but I thought I'd get it on public record :)
Yes, in theory the light coming through the side is unwanted, but in practice it is a really really small amount of light which is unlikely to significantly impact your measurement. The light leakage is only relevant to the photosystem II efficiency (phi2) measurement, which is trying to keep a constant and controlled light intensity level within the chamber. Light leakage would provide variability to that level from sample and sample and add light in all samples over what is desired.
However, it's important to note that this light leakage does not affect the signal itself, because we are using pulse modulation (search pulse modulated fluorescence in google for more info) which filters out the fluorescence signal of any static light source.
So - yes light leakage will affect the biology of the plant and therefore your results, but no the light leakage will directly change the signal intensity because it is pulse modulated and constant light sources are filtered out.
This discussion actually played into some design on the next device (v1.0), in which we will have a thin rubber or silicone skirt!