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to Willem Melching (@pd0wm) for general debugging and implementation of astigmatic Gaussian PSF models, as well as yet unpublished code.
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