fit3Dcspline is a GPU based 3D single molecule fitter for arbitrary, experimental point spread functions (PSF). The fitting speeds achieves more than 10^5 fits/s on a consumer graphic card GTX 1070. The implmentation of the fitting algorithm is based on maximum likelihood estimation and employs Levenberg-Marquardt optimization routine, which reaches theoretical minimum uncertainty. Both the EMCCD and sCMOS noise model are included. The softare package also includes tools to robustly model beads based experimental PSFs of different modality and correct for depth induce aberrations.
- Matlab R2016a or newer
The GPU fitter requires:
- Microsoft Windows 7 or newer, 64-bit
- CUDA capable graphics card, minimum Compute Capability 3.0
- CUDA 8 compatible graphics driver (for GeForce products 378.66 or later)
The CPU version runs on macOS and Microsoft Windows 7 or newer, 64-bit
Example code is avalible in file example_3D_fit.m. The required 3D image stacks for the demo code can be found in the folder data.
For any questions / comments about this software, please contact Ries Lab.
Copyright (c) 2017 Ries Lab, European Molecular Biology Laboratory, Heidelberg.
fit3Dcspline also includes OME Bio-Formats package for reading and converting biological file formats in folder bfmatlab which comes with a separate copyright.
The fit3Dcspline is licenced under the GNU GPL.