Table 1. Formulae and glossary of terms used by the JIP-test (modified after Strasser et al. 2004).

Data extracted from the recorded fluorescence transient OJIP
Ft	fluorescence at time t after onset of actinic illumination
F50μs or F20μs	minimal reliable recorded fluorescence, at 50 μs with the PEA- or 20 μs with the Handy-PEA-fluorimeter
F300μs	fluorescence intensity at 300μs
FJ ≡ F2ms	fluorescence intensity at the J-step (2 ms) of OJIP
FI ≡ F30ms	fluorescence intensity at the I-step (30 ms) of OJIP
FP	maximal recorded fluorescence intensity, at the peak P of OJIP
tFM	time (ms) to reach the maximal fluorescence intensity FM
Area	total complementary area between the fluorescence induction curve and F = FM
Fluorescence parameters derived from the extracted data
F0 ≅ F50μs or ≅ F20μs	minimal fluorescence (all PSII RCs are assumed to be open)
FM (= FP)	maximal fluorescence, when all PSII RCs are closed (equal to FP when the actinic light intensity is above 500 μmol photons m-2 s-1 and provided that all RCs are active as QA reducing)
Fυ≡ Ft-F0	variable fluorescence at time t
FV ≡ FM-F0	maximal variable fluorescence
Vt ≡ Fυ/FV ≡ (Ft-F0)/(FM-F0)	relative variable fluorescence at time t
M0 ≡ [(ΔF/Δt)0]/(FM-F50μs) ≡ 4 (F300μs-F50μs)/(FM- F50μs)	approximated initial slope (in ms-1) of the fluorescence transient normalised on the maximal variable fluorescence FV
Specific energy fluxes (per Q A -reducing PSII reaction center—RC)
ABS /RC = M0 (1/VJ)(1/φPo)	absorption flux (of antenna Chls) per RC
TR0/RC = M0 (1/VJ)	trapped energy flux (leading to QA reduction) per RC
ET0/ RC = M0 (1/VJ)ψEo	electron transport flux (further than QA ⚿) per RC
RE0/RC = M0 (1/VJ)ψEo δRo	electron flux reducing end electron acceptors at the PSI acceptor side, per RC
Quantum yields and efficiencies
φPt ≡ TRt/ABS = [1-(Ft/FM)] = ΔFt/FM	quantum yield for primary photochemistry at any time t, according to the general equation of Paillotin (1976)
φPo ≡ TR0/ABS = [1-(F0/FM)]	maximum quantum yield for primary photochemistry
ψEo ≡ ET0/TR0 = (1-VJ)	efficiency/probability for electron transport (ET), i.e. efficiency/probability that an electron moves further than QA ⚿
φEo ≡ ET0/ABS = [1-(F0/FM)]ψEo	quantum yield for electron transport (ET)
δRo ≡ RE0/ET0 = (1-VI)/(1-VJ)	efficiency/probability with which an electron from the intersystem electron carriers moves to reduce end electron acceptors at the PSI acceptor side (RE)
φRo ≡ RE0/ABS = [1-(F0/FM)]ψEo δRo	quantum yield for reduction of end electron acceptors at the PSI acceptor side (RE)
γRC = ChlRC/Chltotal = RC/(ABS+RC)	probability that a PSII Chl molecule functions as RC
RC/ABS = γRC/(1-γRC) = φPo (VJ/ M0)	QA-reducing RCs per PSII antenna Chl (reciprocal of ABS/RC)
Phenomenological fluxes
ABS/CS = Fo or ABS/CSM = F M	absorption per excited cross-section
TRo/CS = ΦPo·(ABS/CS)	trapping per excited cross-section
ETo/CS = ΦPo·Ψo·(ABS/CS)	electron transport per excited cross-section
Performance indexes
PIABS ≡ [γRC/(1-γRC)]. [φPo/(1- φPo)].[ψo/(1- ψo]	performance index (potential) for energy conservation from exciton to the reduction of intersystem electron acceptors
PItotal ≡ (PIABS).(δRo/1- δRo)	performance index (potential) for energy conservation from exciton to the reduction of PSI end acceptors