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Jian Tay edited this page Mar 8, 2022 · 3 revisions

User Guide

This document will get you up and running with the CyAn toolbox.

Installation

  1. Download the latest version of the toolbox from the Releases page

  2. Download the following dependencies:

  3. Double-click on the toolbox file (.mltbx) and open it with MATLAB, then click Install.

    If MATLAB does not start automatically:

    1. Launch MATLAB
    2. In MATLAB, navigate to the folder where the downloaded toolbox is saved
    3. Open the toolbox by double-clicking the file in the Current Folder panel

  4. During the installation, you should also be prompted to install the following MATLAB products (if not already installed):

    1. Curve Fitting Toolbox
    2. Image Processing Toolbox
    3. Parallel Computing Toolbox

    For more instructions on how to install these Add-Ons, please consult MATLAB's documentation. Please note that you will need an appropriate license to access these Toolboxes.

Checking if toolboxes are installed

To check if the toolboxes were installed correctly, open the Add-On Manager: In the Home tab, select Add-Ons > Manage Add-Ons. The toolboxes should be listed.

Uninstalling

To uninstall the toolbox:

  1. Open the Add-Ons manager by clicking on Add-Ons > Manage Add-Ons in the Home tab
  2. Find the toolbox, and click on ⋮ (vertical ellipsis) to show more options. Select open folder and note the folder location.
  3. Again, click on ⋮ (vertical ellipsis) to show more options and select uninstall.

(Optional) If you encounter a message saying the some files remain after uninstalling, remove the remaining files by:

  1. Closing MATLAB
  2. Navigate to the Add-Ons/Toolboxes folder (the parent folder from step 2 above) and delete the folder containing the remaining files. The folder should be named after the toolbox.

The default location of the Add-Ons directory is listed here. Alternatively, you can look up the location by clicking on Preferences in the home tab, and then selecting MATLAB > Add-Ons.

Basic usage

This toolbox defines two main classes:

  • CyTracker - This is the main class used to process movies
  • DataAnalyzer - This is a class that can be used to develop data analysis

This is the general workflow:

   graph LR;
      Movie -- Cytracker --> TrackArray -- DataAnalyzer --> Data!;
Loading

Processing movies

To start tracking cells, create a CyTracker object by assigning it to a variable:

CT = CyTracker;

Tracker settings

You can check the current settings of the object by retrieving the variable:

>> CT

CT = 

  CyTracker with properties:

            FrameRange: Inf
           SeriesRange: Inf
           OutputMovie: 1
              UseMasks: 0
              ... %truncated

To change the value of a particular setting, simply assign a new value to the object property. For example, to change the FrameRange to process only frames 1 through 10:

>> CT.FrameRange = 1:10;

To stop producing output movies:

>> CT.OutputMovie = false;

Processing movies

Once the tracker options have been set, call the function process on the CyTracker object.

Examples:

Calling the function process without any additional arguments will cause a dialog box to pop up, allowing the user to select the file(s) to process:

>> process(CT)

Alternatively, supply the filename and output directory path (useful for repeated processing commands):

>> process(CT, 'movie.nd2', 'C:\path\to\output')

Using the online help

You can get additional help by using the help command: help CyTracker.<function name>. For example, to get more information about the process command:

>> help CyTracker.process
 process  Run segmentation and tracking on ND2 files
 
   process(OBJ) will run the segmentation and tracking
   operations using the current settings in CObj. A dialog box
   will appear prompting the user to select ND2 file(s) to
   process, as well as the output directory.
 
   process(OBJ, FILE1, ..., FILEN, OUTPUTDIR) will run the
   processing on the file(s) specified. Note that the files do
   not need to be in the same directory. The output files will
   be written to OUTPUTDIR.

Next steps

User Guide

Algorithms

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