Download Latest Version vbTRACK_2D_V7 (3).zip (66.3 MB) Get Updates
Home
Name Modified Size InfoDownloads / Week
ReadMe.txt 2021-06-23 2.3 kB
0
vbTRACK_2D_V7 (3).zip 2021-06-23 66.3 MB
0
Totals: 2 Items   66.3 MB 0 
README for running vbTRACK_2D as uploaded to SourceForge on
        June 22, 2021.

The SourceForge project vbTRACK_2D is a folder with subfolders, MATLAB files and input (x,y) data for several particles tracked with Video Spot Tracker (CISMM, UNC-Chapel Hill, NC) within one cell.  On our system, input data, output data, and output figures are on an external HDD (H:\ on our computer).  However, because this HDD has data for hundreds of particles, which you don’t need to see the program run, we have replaced it with a folder with identical directory structure but only one trial on the F:\ drive of our computer. This folder is what has been uploaded to SourceForge as vbTRACK_2D_V7. Use of this program requires familiarity with Matlab; the code is not embalmed in a graphical user interface (GUI).
To run vbTRACK_2D,
1. Download vbTRACK_2D_V7.zip to your computer.
2. unzip the file.
3. Make the directory containing unzipped vbTRACK_2D_V7 folder your starting and working directories for Matlab.
4. Start Matlab.
5. Define the Matlab path as the folder and subfolders containing vbTRACK_2D_V7. 
6. Open run_vbTrack_2D.m 
7. Program should start. It will request user input to choose the Trial data for analysis. There is only one dataset available, with filename = Trial6.vrpn.mat . Select this file. 
8. Program continues by asking you several questions:  First question is framerate. Enter 100->return.  Second question is whether you want to process all the tracked particles in Trial6 or only a single bead. Enter “0” to process all beads or “1”to process only one bead. Enter “1” for quicker results (approx. 1 minute).  Third question is “which bead?”. Enter “5” to work with a particular bead which occupied 3 states. 
9. Program run_vbTRACK_2D should then run to the end in about 1 minute for 1 bead. The program automatically generates and saves several Figures marking its progress in variational Bayesian analysis as well as computation of the msd for each state. The program should also generate and save an Excel spreadsheet with the main results. Several of these figures were used in the our publication in Scientific Reports(2020).
Example Spreadsheet output file Example: 

VSV Matlab Output File Example: 

	
Contact: George Holzwarth gholz@wfu.edu.    June 22, 2021
Source: ReadMe.txt, updated 2021-06-23