logo PAMtools

What is PAMtools?

PAMtools is a set of helper functions written in Matlab and Python to export and plot single-molecule data that has been processed using PIE Analysis with Matlab (PAM) software for single-molecule fluorescence spectroscopy. The Matlab functions (MatPAM) are used to extract data from PAM’s BurstBrowser and FCSfit, while the Python functionality (PyPAM) is dedicated to visualizing the extracted data for example in a jupyter notebook.

Download and install

  1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed).

  2. Install [PAM](https://gitlab.com/PAM-PIE/PAM)

  3. Clone or download PAMtools into a directory of your choice.

    git clone https://github.com/fdsteffen/PAMtools.git

  • Add the MatPAM folder to the Matlab search path

  • Install the PyPAM module via pip

    pip install <path/to/PAMtools>

  1. Copy the file in matpam/profiles/profile PIE.mat` into the profiles directory in PAM.

  2. Copy the FCS models in matpam/models to the Models directory in PAM

Dependencies

  • MatPAM uses the function jsonencode() and therefore requires Matlab 2016b (9.1) or newer

  • PyPAM depends on the following Python packages:

    • numpy

    • scipy

    • pandas

    • matplotlib

    • seaborn

    • uncertainties

    • naturalcolors (get it from here)