Post Analysis¶

There are a few utilities for processing and rendering the results of the analysis included in this project.

Note

The Matlab STORM project also includes a viewer.

Visualization & Rendering¶

Visualizer¶

storm_analysis/visualizer/visualizer.py

You can use this program to evaluate the quality of the analysis and to decide if the analysis parameters are reasonable. It provides a simple GUI viewer in which you can load a STORM movie and a XX.hdf5 or a XX_list.bin file. It will show an overlay of the localizations that were found in the current frame.

Rendering¶

Image can be created from .hdf5 localization files using storm_analysis/sa_utilities/hdf5_to_image.py. This can be used from the command line to create 2D .tif images (32 bit float format). In addition it provides a number of functions that you can use to create 2D or 3D images (returned as numpy arrays).

Clustering¶

DBSCAN¶

storm_analysis/dbscan/dbscan_analysis.py

This is an implementation of the DBSCAN clustering algorithm that works on HDF5 format localization files.

Getting started:

$ python ./dbscan_analysis.py --help

$ python ./cluster_images.py --help

Voronoi¶

storm_analysis/voronoi/voronoi_analysis.py

This is an implementation of the SR-Tesseler clustering algorithm (Levet et al) that works on HDF5 format localization files.

Gettings started:

$ python ./voronoi_analysis.py --help

Note:

This is a pure Python implementation and may be slow when dealing with more than 1M localizations.
The density factor is relative to the median Voronoi polygon area.
Clustering is always done in 2D and the molecules category is always ignored.

Other¶

FRC¶

storm_analysis/frc/frc_calc2d.py

This is an implementation of the FRC method (Nieuwenhuizen et al) for estimating the resolution of a STORM image.