CUDA-Based image processing for single molecule localization microscopy
A C++/CUDA toolbox with python bindings for doing single molecule microscopy image processing.
- Features include:
- Super fast spot detection and extraction on tiff files (~1 KHz on my dell xps laptop)
- Max-Likelihood fitting of various 2D Gaussian models
- (XY with or without fixed sigma, 3D using astigmatism)
- SIMFLUX (https://www.nature.com/articles/s41592-019-0657-7)
- Easy rendering of results: Piccaso Render compatible HDF5 export (https://github.com/jungmannlab/picasso)
- sCMOS-corrected MLE (See https://www.nature.com/articles/nmeth.2488)
- Phasor-based SMLM (https://aip.scitation.org/doi/full/10.1063/1.5005899)
- A C++ templated approach to quickly implement new PSF models as long as the first derivative can be computed.
- Work in progress:
- Drift correction using redundant cross-correlation (needs reliability checks)
- Cubic spline PSFs
Currently compiled for CUDA 10.2 / Windows x64 using Visual Studio 2019
Credits to Willem Melching (@pd0wm) for general debugging and implementation of astigmatic Gaussian PSF models, as well as yet unpublished code.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size photonpy-1.0.6-py3-none-any.whl (3.2 MB)||File type Wheel||Python version py3||Upload date||Hashes View|