An Automated Photosynthetic Characterization Method With Fluorescence v1

We’re interested in characterizing photosynthetic machinery to better predict how plants will fare under changing climate and learn a bit about the world. In the long term, we hope to scale up and standardize precise measurement of plant mechanics. This protocol documents the approach we ran as a pilot experiment in summer 2026: an automated program for the LI-6800 built on the dynamic assimilation method. We added low-CO2 holding periods between ramps and frequent fluorometry flashes. The program outputs a detailed 3D surface of carbon assimilation (A), intercellular carbon dioxide concentration (Ci), and light levels (Q), and takes about 3 hours to run. This method is not perfect and remains under development: we link to some further discussion below. Technical report: https://github.com/RileyLeff/aciq-surfaces#readme.