Python code and example data to resolve the contributions of photosystem II, photosystem I, and phycobilisomes to the in vivo fluorescence yield

The workflow to resolve the contributions of photosystem II, photosystem I, and phycobilisomes to the in vivo fluorescence yield is performed by running the Python code in the following order (with explanations): Step_1_NMF_and_LS_PSIPBSvarFixed.py – Constrained NMF of fluorescence induction curves, followed by least squares (LS) fitting of variable fluorescence data with fixed Fv/Fm and ΔF/Fm' values for PSI and PBS. (Alternatively, Suppl_Step_1_NMF_and_LS_PSIPBSvarExcluded.py [LS excluding Fv/Fm and ΔF/Fm' values for PSI and PBS] or Suppl_Step_1_NMF_and_LS_PSIPBSvarVariable.py [LS with fixed Fv/Fm and variable ΔF/Fm' values for PSI and PBS] can be used.) Step_2_Clustering_kinetics.py – Clustering of the extracted features from the resolved kinetics of ΦPSII, and relative fluorescence yields of PSII, PSI, and PBS. (The following steps are presented without a prescribed order.) Step_3_Grouped_scatter_interactive_plot_ratios.py – Scatter plots of the relative fluorescence amplitudes of PSII, PSI, and PBS across detection wavebands, obtained from the clustering results. Step_3_Redrawn_OJIP_from_target_column.py – Redrawing the resolved fluorescence induction curves of PSII, PSI, and PBS per cluster (or supercluster) obtained from the clustering results. Step_3_Redrawn_kinetics_from_target_column.py – Redrawing the resolved kinetics of ΦPSII, and relative fluorescence yields of PSII, PSI, and PBS per cluster (or supercluster) obtained from the clustering results. Example data that can be used for executing the above code are described as follows: NMF_background_435ex.csv – Background signal profile during the fluorescence induction curve under blue excitation. NMF_background_590ex.csv – Background signal profile during the fluorescence induction curve under amber excitation. 0702_Cm10DBlue.csv – Fluorescence induction curves recorded under blue excitation. 0702_Cm10DAmber.csv – Fluorescence induction curves recorded under amber excitation. dFFmNPQ_1.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under a series of saturating light pulses using blue measuring light. dFFmNPQ_2.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under a series of saturating light pulses using amber measuring light. dFFmNPQ_3.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under blue illumination followed by darkness using blue measuring light. dFFmNPQ_4.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under blue illumination followed by darkness using amber measuring light. dFFmNPQ_5.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under red illumination followed by darkness using blue measuring light. dFFmNPQ_6.csv – ΔF/Fm' (Fv/Fm) and NPQ kinetics data under red illumination followed by darkness using amber measuring light.