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private fit3Dcspline integrated in SMAP Sep 11, 2019
source fit3Dcspline integrated in SMAP Sep 11, 2019
Licence.txt fit3Dcspline integrated in SMAP Sep 11, 2019
README.md fit3Dcspline integrated in SMAP Sep 11, 2019
User_guide_Ries.pdf fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate3D_GUI_g.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate3D_g.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate3Daberrations.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate_4pi.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate_4pi_v2.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate_4pi_v3.m fit3Dcspline integrated in SMAP Sep 11, 2019
calibrate_globalworkflow.m fit3Dcspline integrated in SMAP Sep 11, 2019
correct_3Daberrations.m fit3Dcspline integrated in SMAP Sep 11, 2019
evalSpline.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_3D_fit.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_3D_fit_NM.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_calibration.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_depth_aberration.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_fit_2DPSF.m fit3Dcspline integrated in SMAP Sep 11, 2019
example_fit_astig.m fit3Dcspline integrated in SMAP Sep 11, 2019
settings_3D.txt fit3Dcspline integrated in SMAP Sep 11, 2019
simSplinePSF.m fit3Dcspline integrated in SMAP Sep 11, 2019
simplefitter_GUI.m fit3Dcspline integrated in SMAP Sep 11, 2019
simplefitter_GUI.prj fit3Dcspline integrated in SMAP Sep 11, 2019
simplefitter_cspline.m fit3Dcspline integrated in SMAP Sep 11, 2019
simulate2c.m fit3Dcspline integrated in SMAP Sep 11, 2019
sxsy2z.m

README.md

fit3Dcspline

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.

Requirements

  • Matlab R2016a or newer
    • Curve Fitting Toolbox
    • Optimization Toolbox

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

How to run

Example code for 3D PSF calibration based on beads on coverglass is avalible in file example_3D_fit.m. Example code for depth dependent PSF calibration based on beads in gel is avalible in file example_depth_aberration.m. The required 3D image stacks for the demo code can be found in the folder by following this link. A full instruction guide can be found in User_guide_Ries.pdf.

Contact

For any questions / comments about this software, please contact Ries Lab.

Copyright and Software License

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.

How to cite fit3Dcspline

If you use fit3Dcspline to process your data, please, cite our paper:

  • Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries. Real-time 3D single-molecule localization using experimental point spread functions. Nat. Methods 15, 367–369 (2018).
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