Installation

Click here to download Shape Space Explorer:

Unzip the downloaded folder and add it to your MATLAB path.

The Shape Space Explorer package requires the following toolboxes:

  • Image Processing
  • MATLAB Coder
  • MATLAB Compiler
  • Statistics and Machine Learning
  • Deep Learning (optional, only required for group analysis of regions)

For more detailed instructions see New to MATLAB.

Terminology

To make the documentation easy to read, some terms are introduced:

  • Movie folder: the folder containing your microscopy data
  • Analysis folder: your folder containing the complete set of analysis files generated using the Shape Space Explorer package described in this tutorial. For this tutorial it is important to save all outputs in this folder unless stated otherwise.
  • Run a “specificMatlabFile.m”: navigate to the specified file, select and run it to execute the script. Should these instructions feel unfamiliar, read the next Section New to MATLAB
  • MATLAB: The program has been tested on Matlab R2022b and 2024b on Windows 10.

All figures produced by the scripts are automatically saved in the folder Analysis > Figures unless otherwise stated.

New to MATLAB

If you have never used MATLAB before, you should install the program and obtain a license first. Most universities offer free licenses for staff and students. A comprehensive guide can be found at Mathworks. During the installation process you will be asked to choose which toolboxes to install, make sure you select the four mentioned in the Terminology section With a valid MATLAB license, previous releases can also be downloaded from the Mathworks Download Page.

To run the program, you need the folder Shape Space Explorer containing all files. Within the Matlab program go to the folder Shape Space Explorer.

Then, right click on Shape Space Explorer folder, and select Add to Path > Selected Folders and Subfolders

This adds the Shape Space Explorer to the MATLAB path, so the scripts are easy to execute. The Shape Space Explorer folder should appear as active

To run a script, open Shape Space Explorer > 1-ImageSegmentationFull and select the File Run_CellSegmentation.m with a double click. Then click on the Run button in the Toolbar. The first line in the MATLAB command window should then contain the line

>> Run_CellSegmentation

Once a script has finished properly, the Command Line shows a new line:

>>