README

This is the official source code repository of CellOrganizer.

Pre-requisites

• Matlab 2018b or newer
• Bioinformatics Toolbox
• Computer Vision System Toolbox
• Control System Toolbox
• Curve Fitting Toolbox
• Image Processing Toolbox
• Mapping Toolbox
• Optimization Toolbox
• Robust Control Toolbox
• Signal Processing Toolbox
• Simulink
• Simulink Design Optimization
• Statistics and Machine Learning Toolbox
• System Identification Toolbox
• Wavelet Toolbox

Installation

To install CellOrganizer

1. Download the latest distribution from http://www.cellorganizer.org or http://murphylab.web.cmu.edu/software/CellOrganizer.

2. Unzip the distribution into a folder of your choice.

3. Start Matlab and change the default directory to the folder chosen above.

4. Run setup

Using CellOrganizer from the Matlab command line

Type setup() at the Matlab command prompt to add the relevant paths. The main CellOrganizer commands are

img2slml

which trains a model from a set of images

and

slml2img

which synthesizes one or more image(s) from a trained model.

Examples

There are a numbers of demo files that illustrate how to use CellOrganizer from the command line. Type

demoinfo

to get a listing of available demos.