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Dynamic Bioimaging Lab

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SOFTWARE

Most of our ensemble, single-molecule and imaging data analysis we do with PAM, an open source software package we developed together with Prof. Don C. Lamb and co-workers at LMU Munich [Schrimpf et al., 2018].

PAM can read many TCSPC/TTTR data types (custom read-in routines can easily be implemented) and converts them to a unified data structure. Although PAM was originally designed for TCSPC/time resolved data, currently different image formats can be directly read in too.

The PAM software is available as source code, requiring MATLAB to run, or as pre-compiled standalone distributions for Windows or MacOS hosted in Git repositories under http://www.gitlab.com/PAM-PIE/PAM and http://www.gitlab.com/PAM-PIE/PAMcompiled. Sample data is provided under http://www.gitlab.com/PAM-PIE/PAM-sampledata.

A detailed manual is found under http://pam.readthedocs.io.

We advocate for open source software and happily refer to others packages:

  • SOFI analysis in Localizer
  • PALM/STORM analysis in Thunderstorm, RapidSTORM and Localizer
  • SIM analysis in fairSIM¬†