CUDA-Based image processing for single molecule localization microscopy
Project description
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 (~1k frames/s on my dell xps laptop)
- Max-Likelihood fitting of various 2D Gaussian models
(XY with or without fixed sigma, 3D using astigmatism)
Easy rendering of results: Piccaso Render compatible HDF5 export (https://github.com/jungmannlab/picasso)
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.
Drift correction using entropy minimization (SAME) and redundant cross correlation (RCC)
- Work in progress:
Cubic spline PSFs
Currently compiled for CUDA 10.1 update 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to Willem Melching (@pd0wm) for general debugging and implementation of astigmatic Gaussian PSF models, as well as yet unpublished code.
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