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 the single-molecule software package "PIE Analysis with MATLAB" (PAM) (https://gitlab.com/PAM-PIE).¹ The Matlab functions (MatPAM) are used to extract data from PAM's BurstBrowser and FCSfit, while the Python API (PyPAM) is used to visualize and plot the extracted data for example in a jupyter notebook.

Documentation

PAMtools is documented here.

Download and install

1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed). MatPAM uses the function jsonencode() and therefore requires Matlab 2016b (9.1) or newer

2. Install PAM

3. Clone 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 .

4. Copy the file in src/pamtools/matpam/profiles/profile PIE.mat into the profiles directory in PAM.

5. Copy the FCS models in src/pamtools/matpam/models to the Models directory in PAM

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¹ W. Schrimpf, A. Barth, J. Hendrix, D.C. Lamb, Biophys. J. 2018, 114, 1518–1528.