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Research Projects


Project Leader(s): Jean-Baptiste Sibarita

PALMTracer is an all-in-one software package for the analysis of Single Molecule Localization Microscopy (SMLM) data. Low-resolution stacks of single emitters can be segmented, localized, and stored as a list of coordinates and metadata in a human-readable file format. Individual single molecule localizations can be spatiotemporally reconnected to create single molecule trajectories, from which the mean squared diffusion (MSD) parameters can be extracted. PALMTracer includes a breadth of visualization options for both localization and trajectories, including density maps, 3D projections and Z-stacks, imaging plane, and multi-plane stacks.

This new version of PALMTracer includes a revamped user interface and supports importing WaveTracer online localization files, better batch support, new visualization options including better 3D support, live filtering previews, custom file format export for common third-party applications like ThunderSTORM and VISP, chromatic aberration correction for 2-color imaging, custom graphs, better fiducial marker handling, and more.

PALMTracer is designed to work hand-in-hand with SR-Tesseler.


PALMTracer requires a 64-bit installation of MetaMorph, 7.10.2 or later

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Check out our YouTube channel for tutorials on how to configure and use PALMTracer:



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