pamfit : A new R package for spatially resolved analysis of Imaging PAM photosynthesis–irradiance light curve parameters

Imaging Pulse Amplitude Modulation (PAM) fluorometry allows spatially resolved measurements of Photosystem II (PSII) fluorescence kinetics through time without disturbing study organisms or their environments. In particular, the use of photosynthesis–irradiance curves (P–I curves) provides detailed information on PSII quantum efficiency, electron transport rates and the overall photosynthetic performance of samples. Here, we present the R “pamfit” package developed as a Shiny application to significantly extend current analysis capabilities for Imaging PAM P–I curve datasets. Through a sequential Shiny user interface, pamfit allows to (i) import Imaging PAM TIFF P–I curve datasets, assign light levels and employ pixel smoothing; (ii) define a region of interest for subsequent modeling; (iii) derive optimal start parameters and fit one of three P–I curve models—Jassby and Platt, Platt et al., or Eilers and Peeters; and (iv) undertake pixel-wise interrogation of both initial data and derived P–I curve parameters including, light utilization (α) and saturation (Ek) coefficients, maximum electron transport rates (ETRmax), photo-inhibition coefficients (e.g., β when derived), and associated residual mean square error (RMSE) images. Outputs can be saved in GeoTIFF or CSV format and exported to the R global environment for subsequent processing. We present here example applications of pamfit to three P–I curve datasets for the photosynthetic sea slug Elysia timida, a microphytobenthic biofilm, and the coralline seaweed Corallina officinalis, chosen because they exhibit high spatial variability. The flexibility of processing images using free open-source software extends the usefulness of this technique and holds great potential for application in ecophysiological studies.