Welcome to PAM’s documentation!

PAM is short for PIE Analysis with MATLAB - it is a GUI-based software package for the analysis of fluorescence experiments and supports a large number of analysis methods. While originally designed for pulsed-interleaved excitation (PIE, [Müller2005]) experiments, it now has a wide support for the most commonly used fluorescence experiments.

Currently implemented:

  • Fluorescence correlation spectroscopy and its derivatives
  • Single-molecule FRET spectroscopy (burst analysis), including:
    • Photon distribution analysis for two- and three-color FRET experiments
    • species-selective filtered fluorescence correlation spectroscopy
  • Image correlation spectroscopy, including:
    • ratser lifetime image correlation spectroscopy (RLICS)
    • support for arbitrary region image correlation spectroscopy (ARICS)
  • Fluorescence lifetime imaging (PhasorFLIM)
  • TCSPC and time-resolved anisotropy analysis
[Lamb2000]Lamb, D. C., Schenk, A., Röcker, C., Scalfi-Happ, C. & Nienhaus, G. U. Sensitivity Enhancement in Fluorescence Correlation Spectroscopy of Multiple Species Using Time-Gated Detection. Biophys J 79, 1129–1138 (2000)
[Müller2005]Müller, B. K., Zaychikov, E., Bräuchle, C. & Lamb, D. C. Pulsed interleaved excitation. Biophys J 89, 3508–3522 (2005)
[Kudryavtsev2012]Kudryavtsev, V. et al. Combining MFD and PIE for Accurate Single-Pair Förster Resonance Energy Transfer Measurements. ChemPhysChem 13, 1060–1078 (2012)
[Hendrix2013]Hendrix, J., Schrimpf, W., Höller, M. & Lamb, D. C. Pulsed Interleaved Excitation Fluctuation Imaging. Biophys J 105, 848–861 (2013)
[Hendrix2016]Hendrix, J., Dekens, T., Schrimpf, W. & Lamb, D. C. Arbitrary-Region Raster Image Correlation Spectroscopy. Biophys J 111, 1785–1796 (2016)