vbSPT is a program suite for analysis of single particle diffusion trajectories, where the diffusion constants switch randomly according to a discrete Markov process. The program runs on Matlab, but uses compiled C-code to speed up the most computer intensive loops. The latest version of the software as well as a forum for discussion and questions can be found at 'sourceforge.net/projects/vbspt/'.

E-mail: bmelinden@gmail.com, freddie.persson@gmail.com, johan.elf@gmail.com

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

If you use vbSPT please cite: "Person F,Lindén M, Unoson C, Elf J, Extracting intracellular reaction rates from single molecule tracking data, Nature Methods 10, 265–269 (2013). doi:10.1038/nmeth.2367"

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

This product includes software developed by Martin Lindén (in HMMcore/), by Jan-Willem van de Meent (in external/), and by Erik A.~Johnson (Tools/displayHMMmodel/private/arrow.m). See copyright in individual files.

updated arrow.m for compatibility with R2014b and later (2020-01-30)

v 1.1.4 (bugfix, 2017-04-11): - changed vbSPTstart so that it can be called from any folder. - new function to plot model+bootstrap s.e.m: VB3_printModel.m - adopt displayHMMTrajs.m to current trajectory format

v 1.1.3 (2015-12-08): - VB3_getResult.m handles calls with runinput files in different folders - changed how parallellization in handled, to adhere to the new set of commands (parpool, gcp) in matlab R2015b. Users with old matlab versions might wish to stick with 1.1.2.

v 1.1.2 (2014-11-19): minor bugfix, mainly to satisfy new mex compiler - removed C++ style comments in HMMcore*.c files to please the mex compiler. - recompiled 64bit mex binaries for linux, mac, and windows 7 - corrected handling of aggregation indices in VB3_removeState.m (not relevant for standard usage) - corrected typo in Eq S69 of vbSPT manual (n_j -> \tilde n_j in the first KL term for \gamma). Note that the code was correct all the time, so computational results are not affected.

v 1.1.1 (2014-10-11): minor bugfix release - corrected a sign error in the KL divergence of the initial state vector (the faulty terms was gammaln of the total prior weight, and so very unlikely to make any practical difference). - corrected some internal function names to be consistent with file names. - made VB3_readData handle input files without the .m ending

v 1.1 (2013-11-12): code speed-up - better representation of data leads to a significantly faster execution (~10-fold on our test data). - A new parameterization of the transition rates, allowing more flexible priors for advanced users (See manual). For non-advanced users, the old priors (Nat. Meth 2013 paper) are still default. - updated VB3_displayHMMmodel and VB3_getTrjStats to the new model format. - deleted VB3_reorder.m (obsolete, replaced by VB3_sortModel.m)

v 1.0.1 (2013-05-31): bugfix release - getDwellTRJ.m : consistent function name in m-file, and better handling trajectories with not all states present. - VB3_HMManalysis.m : added functionaly to create non-existent target folders. - VBviterbi_log.c : fixed bug in viterbi algorithm.

bmelinden / vbSPT

readme

E-mail: bmelinden@gmail.com, freddie.persson@gmail.com, johan.elf@gmail.com

This product includes software developed by Martin Lindén (in HMMcore/), by Jan-Willem van de Meent (in external/), and by Erik A.~Johnson (Tools/displayHMMmodel/private/arrow.m). See copyright in individual files.

updated arrow.m for compatibility with R2014b and later (2020-01-30)

v 1.1.4 (bugfix, 2017-04-11): - changed vbSPTstart so that it can be called from any folder. - new function to plot model+bootstrap s.e.m: VB3_printModel.m - adopt displayHMMTrajs.m to current trajectory format

v 1.1.3 (2015-12-08): - VB3_getResult.m handles calls with runinput files in different folders - changed how parallellization in handled, to adhere to the new set of commands (parpool, gcp) in matlab R2015b. Users with old matlab versions might wish to stick with 1.1.2.

v 1.0.1 (2013-05-31): bugfix release - getDwellTRJ.m : consistent function name in m-file, and better handling trajectories with not all states present. - VB3_HMManalysis.m : added functionaly to create non-existent target folders. - VBviterbi_log.c : fixed bug in viterbi algorithm.