SMALL-LABS-pSMLM
The manuscript describing pSMLM-exotic PSF and integration in SMALL-LABS can be found at https://www.sciencedirect.com/science/article/pii/S1046202320301250 (Martens et al., "Integrating engineered point spread functions into the phasor-based single-molecule localization microscopy framework", Methods, 2020); the original phasor-based localization algorithm is described at https://aip.scitation.org/doi/full/10.1063/1.5005899 (Martens et al., "Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): an algorithm for MHz localization rates using standard CPUs", Journal of Chemical Physics, 2018). Please cite accordingly.
SMALL-LABS-pSMLM is an extension of SMALL-LABS, software written by Benjamin P Isaacoff at the University of Michigan. The extension contains pSMLM-based localization, along with an extensive GUI.
The SMALL-LABS (Single-Molecule Accurate Localization by Local Background Subtraction) algorithm, accurately locates and measures the intensity of single molecules, regardless of the shape or brightness of the background.
The SMALL-LABS algorithm is described in B.P. Isaacoff, Y. Li, S.A. Lee and J.S. Biteen, “SMALL-LABS: An algorithm for measuring single-molecule intensity and position in the presence of obscuring backgrounds,” Biophysical Journal, in press (2019). https://doi.org/10.1016/j.bpj.2019.02.006
The pSMLM- and GUI-addition of SMALL-LABS is written by Koen J.A. Martens at the University of Wageningen: https://www.sciencedirect.com/science/article/pii/S1046202320301250.
Installation
Download the entire folder. Change the working directory in Matlab to this folder and open 'GUI_main.m' to open the GUI.
Usage
Please see Quick start guide GUI.pdf for a quick-start guide.
Briefly, one should select the file(s) for localization at the top, choose the appropriate settings, and press 'Start Analysis'.
Credits
All individual programs should have all their individual attributions in place including authors.
The SMALL-LABS code was developed with support from the National Science Foundation (NSF grant CHE-1252322).
The development of this code is greatly indebted to the work of David J Rowland (often referred to as DJR in the code). In addition to containing some functions written by him, I’ve borrowed a lot of code snippets from his programs.
SMALL-LABS uses a number of open-source codes and algorithms:
TiffStack by DR Muir and BM Kampa
DR Muir and BM Kampa. 2015. FocusStack and StimServer: A new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data, Frontiers in Neuroinformatics 8 85. DOI:10.3389/fninf.2014.00085
TIFFStack by Dylan Muir is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Based on a work at http://github.com/DylanMuir/TIFFStack
saveastiff by YoonOh Tak
Copyright (c) 2012, YoonOh Tak All rights reserved. Available at https://www.mathworks.com/matlabcentral/fileexchange/35684-multipage-tiff-stack
bpass by John C. Crocker and David G. Grier
Copyright (c) 1997, John C. Crocker and David G. Grier Available at http://www.physics.emory.edu/faculty/weeks//idl/
MLEwG by KI Mortensen, LS Churchman, JA Spudich, H Flyvbjerg
K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, Nat. Methods 7, 377 (2010) doi:10.1038/nmeth.1447
gaussFit by David J Rowland
David J.Rowland, Julie S.Biteen. Measuring molecular motions inside single cells with improved analysis of single-particle trajectories. Chemical Physics Letters, 674, 173-178, 2017. DOI:10.1016/j.cplett.2017.02.052
The code 'gaussFit.m' should be considered 'freeware'- and may be distributed freely in its original form when properly attributed.
Track_3D2 by David J Rowland
David J.Rowland, Julie S.Biteen. Measuring molecular motions inside single cells with improved analysis of single-particle trajectories. Chemical Physics Letters, 674, 173-178, 2017. DOI:10.1016/j.cplett.2017.02.052
The code 'Track_3D2.m' should be considered 'freeware'- and may be distributed freely in its original form when properly attributed
hungarian by Yi Cao
Available at https://www.mathworks.com/matlabcentral/fileexchange/20652-hungarian-algorithm-for-linear-assignment-problems-v2-3
gpufit by Adrian Przybylski, Björn Thiel, Jan Keller-Findeisen, Bernd Stock, and Mark Bates
Gpufit: An open-source toolkit for GPU-accelerated curve fitting Adrian Przybylski, Björn Thiel, Jan Keller-Findeisen, Bernd Stock, and Mark Bates Scientific Reports, vol. 7, 15722 (2017); doi: https://doi.org/10.1038/s41598-017-15313-9
MIT License. Copyright (c) 2017 Mark Bates, Adrian Przybylski, Björn Thiel, and Jan Keller-Findeisen
License
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
See LICENSE.txt