This may be a silly question but I cannot find any explanation on the website or the wiki from the Github repo. What exactly do the numbers in the raw traces mean? From some simple tests I have figured out they depend on both brightness and length of the pulses but I don't know what physical quantity is behind these numbers.
My end goal is to calculate the fraction of light that goes through a leaf for different wavelength. Not relative changes in this fraction, but the actual fraction.
The numbers on the y-axis of the trace are the raw adc counts from the photodiode. If you want to calculate transmission through the leaf you will need to output the raw absorbance values from each LED. The "Leaf Photosynthesis MultispeQ v1.0" protocol currently outputs the raw absorbance values from just LED 2 and 6 (light2_raw1, etc). We measure the absorbance of each LED at 3 light intensities to allow us to account for leaf thickness. If you want to output the raw absorbance values for different lights, you can create a copy of the protocol and associate it with a new macro that outputs the raw values for each LED. Help on how to edit and create protocols and macros can be found here.