UCSDcellTrack

This is a MATLAB toolbox designed for automated cell tracking, analysis, and visualization from sequences of live-cell microscopy images. Author: Brooks Taylor, b4taylor@ucla.edu

Download & Installation

From command line:

$ git clone https://github.com/brookstaylorjr/UCSDcellTrack.git
...
$ cd UCSDcellTrack
$ sh install.sh
...

Basic usage using the GUI

1. Ensure that UCSDcellTrack (and all subfolders) have been added to your MATLAB path.
2. To launch, type UCSDcellTrack at the MATLAB command prompt.
3. A window will open, allowing you to personalize locations for your computer: in order to allow tracking on a computational server, then later analysis of the results on your personal machine, UCSDcellTrack creates composite paths for both the input microscopy images and the output data: you choose the "mount" location for (e.g.) a NAS containing images or data, and then specify a subdirectory under that location. If images or data are stored locally, just specify your system's file root (/ or C:\).
4. Set parameters, then test and initiate tracking/measurement from the UCSDcellTrack GUI. Measured trajectories will be saved to AllMeasurements.mat
5. In order to explore results, a general-purpose tool is included. Launch this by typing UCSDcellQuery at the MATLAB command prompt, then navigate to, and load, your newly-saved AllMeasurements.mat file.

Analyzing experiments from a spreadsheet

1. Establish a set of parameters that works for the set(s) to be tracked using the GUI, and save in the Parameters folder.
2. Publish a Google Spreadsheet like the one here and put the link in the locations.mat file. The essential column headings are in blue (the spreadsheet is parsed by these headings, so yours need to match mine exactly).
3. Run the command (e.g.) runID(1:4) to track and measure the first 4 entries of your spreadsheet.

TODO:

• Make package into a matlab toolbox (e.g.: potterswheel or https://github.com/nwh/matlab)
  • During install, move all the files into /path-to-matlab/toolbox/UCSDcellTrack; make that discoverable during startup
  • It then can be used by any users in the same computer or cluster
• Make a wiki or UCSDcellTrack.github.io pages for better documentation.
  • eg: https://select2.github.io/