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.
Getting started:
$python ./frc_calc2d.py --help
Note:
- Results are plotted using matplotlib and also saved in the output text file.
- This is the un-corrected FRC, so repeated localizations of the same molecule could artificially increase the apparent resolution.