PAM - PIE Analysis with MATLAB

PAM is a software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with a focus on experiments using pulsed interleaved excitation. PAM combines many advanced fluorescence methods, including:

• Fluorescence fluctuation spectroscopy techniques (FCS, FCCS, Pair-Correlation)
• Single-molecule Förster resonance energy transfer (smFRET) of freely-diffusing molecules in solution with or without multiparameter fluorescence detection (MFD)
• Fluorescence lifetime imaging microscopy (FLIM) using the phasor approach
• Image analysis and fluctuation imaging (ICS, RICS, tICS, N&B)

For details, please the the associated publication:

Schrimpf, W., Barth, A., Hendrix, J. & Lamb, D. C. PAM: A framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data. Biophysical journal 114, 1518-1528 (2018)

The program can be downloaded from the homepage of Prof. Don C. Lamb - http://www.cup.uni-muenchen.de/pc/lamb/ - or through GitLab - https://gitlab.com/PAM-PIE.

The manual can be found at http://pam.readthedocs.io.

This GitLab group contains frour projects:

• PAM: The open-source version of PAM used with MATLAB.
• PAMcompiled: A compiled stand-alone version that does not require MATLAB.
• PAM-sampledata: Some example data the user can use to try out the PAM functionalities.
• PAMdocs: Project that contains files for the delevopers to update the PAM documentation and manual.

Installing the stand-alone version of PAM

1. Verify the correct MATLAB Runtime is installed (currently v9.1/ Matlab 2016b).

   You can download the MATLAB Runtime from the MathWorks Web site by navigating to

   http://www.mathworks.com/products/compiler/mcr/index.html

   For more information about the MATLAB Runtime and the MATLAB Runtime installer, see Package and Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center.

2. Download the compiled version of PAM for your Operating system (MacOS or WIN) from

   https://gitlab.com/PAM-PIE/PAMcompiled

3. Unpack the files.

4. Run the PAM.exe (Windows) or run_PAM.command (MacOS) to start the program. For MacOS, consult the readme.txt and how_to_create_shortcut.txt for additional information.

Installing and updating the open-source version of PAM

The open source version of PAM requires a valid licence for MATLAB (2014b or newer). Certain features further need access to tool boxes (curve fitting, optimization, image processing, statistics and machine learning, parallel computing) to work.

You can obtain and update PAM either through direct download from Gitlab, using the command line through Git, or by using the MATLAB Git integration.

Downloading from the repository

1. Download the open source version of PAM from https://gitlab.com/PAM-PIE/PAM
2. Unpack the files.
3. Start Matlab and navigate to the PAM folder.
4. Type PAM into the Matlab command line to start the program.
5. To update, simply download the newest version and overwrite your files.

Using Git

Installing Git

Updating of PAM requires the installation of Git.

• MacOS:

  MacOS has Git pre-installed since version 10.9. Try to run git from the terminal. If the command fails, you can download Git from https://git-scm.com.

• Windows:

  Download and install Git from https://git-for-windows.github.io.

Downloading and updating using Git

• To clone the repository, type git clone https://gitlab.com/PAM-PIE/PAM.git PAM to create a local copy of the repository in the folder PAM.
  • By default, you are checkout on the branch master, containing the stable version of PAM.
  • Should you need the newest updates, switch to the develop branch by typing git checkout develop.
  • To switch back, type git checkout master.
• To update, simply type git pull to obtain the newest changes. Note that this will only update the branch that you are currently on.

Via MATLAB Git Integration

To use all features of the MATLAB Git integration, it is recommended to install Git as described above.

1. Create a folder for PAM.
2. Start Matlab and navigate to the PAM folder.
3. Right click the 'Current Folder' panel in Matlab and select 'Source Control' and 'Manage Files...'.
4. Set the 'Source control integration' to 'Git' and enter for the 'Repository path' https://gitlab.com/PAM-PIE/PAM.git.
5. Click 'Retrieve' to download the files automatically.
6. To update the PAM Git repository to the latest version, simply type !git pull into the MATLAB command line.

To update, you can alternatively use the MATLAB Git integration, however the !git pull method is easier and quicker.

1. Right click the 'Current Folder' panel in Matlab and select 'Source Control' and 'Fetch'.
2. Right click the 'Current Folder' panel in Matlab and select 'Source Control' and 'Manage Branches'.
3. Select the current branch form the remote repository, called 'origin'. If you work on branch master, select origin/master (or refs/remotes/origin/master).
4. Click 'Merge' to merge the changes from the remote into you local repository.

Modification and development of PAM

Users are encouraged to modify the code of PAM for their individual needs and help with the development of new and the improvement of existing functionalities.

To report bugs or suggest improvements and bugfixes, please use the 'Issues' function of GitLab. For this, a free GitLab account is required.

To contribute to PAM, please consult the contribution guide.

List of contributors

We are thankful to all who contributed to the ongoing development of PAM. If you contributed but do not see your name below, please don't hesitate to contact us.

Thanks go to:

• Simon Wanninger
• Chen Qian
• Nader Danaf
• Ivan Maslov
• Lucy van Pelt
• Philip Messer