Getting started with COMKAT

(UNDER construction; should be completed by the weekend)

Getting started with COMKAT

Please carefully read through this document for instructions of setting up and using COMKAT for your specific needs of analysis.

Glossary

Here are some terms you may first need to know about COMKAT:

1. GUI: Graphical user interface
2. COMKAT GUI: Modeling GUI of COMKAT. The central GUI for kinetic modeling and parameter estimation. COMKAT GUI does not require you to do MATLAB programming.
3. COMKAT command-line functions: Functions to call from MATLAB command window or MATLAB scripts and functions. You need to write MATLAB code to call those functions.
4. COMKAT Image Tool: The imaging GUI for COMKAT. You can load images with it, draw ROI, display and fuse multiple image data sets.
5. COMKAT Input Function GUI: This GUI is called by COMKAT GUI for specifying the input function.
6. Standalone application: COMKAT has two types of releases now. It can run under MATLAB or run independently as a executable file. If you do not have a MATLAB license, you will need this COMKAT standalone application. However, some functionality is limited in the standalone application mode as listed in Support:Limitations of COMKAT standalone application.
7. MATLAB path: You need to set up MATLAB path so that it knows where to find COMKAT functions when needed. Therefore, if you use COMKAT under MATLAB you will have to set up your MATLAB path for COMKAT. For standalone applications, COMKAT does not need this process.
8. ROI: region of interest. Sometimes in COMKAT we call it 'Volume of interest' (VOI).

Identify your task

First thing you do is to analyze this: How would you like to use COMKAT? Application can be categorized into the following:

1. Parameter estimation for image quantification
   You have some image data that you would like to draw a region (or regions) of interest and estimate parameters.
   1. ROI data
      You may use COMKAT Image Tool to draw ROI. Or you may use other software to draw ROI, save data as files and load it into COMKAT GUI.
   2. Parameter estimation with COMKAT GUI
      Using COMKAT GUI is the most straight forward method. It has some built-in kinetic models, and you may add new compartment models to COMKAT GUI.
   3. Parameter estimation with scripts and COMKAT command-line functions
      For advanced users that can program MATLAB scripts, using COMKAT command-line functions may sometimes provide more flexibilities and advanced functionality.
2. Image processing
   If you only need to load images and draw ROI, you can simply use COMKAT Image Tool as an independent suite.
3. Model development
   If you don't have experimental data and simply wish to evaluate a kinetic model, you can either do it with COMKAT GUI or COMKAT command-line functions.
   1. COMKAT GUI: You can create new models with graphical interfaces without programming.
   2. COMKAT command-line function: You can create new models with scripts. This is more appropriate for advanced users and does provide more powerful functions and special kinetics.
4. Parametric imaging
   You can now use COMKAT GUI to calculate the parametric imaging. If you have access to a cluster and MATLAB distributed computing, you can use distributed computing to accelerate this computation.
5. Input function estimation
   COMKAT Input Function GUI now incorporates a GUI for estimating input functions based on our publications for input function estimation for small animal [1].

Prepare your data

Here lists the data requirement for COMKAT GUI. For scripting with COMKAT command-line functions, data requirement is more flexible and therefore not described here.

Input Function

You may either have a measured input function or a simulated input function. For the measured input function, refer to Support:Documents:Manual:COMKAT GUI for requirement of file format and storage. By simulated input function, the input function is generated from a equation (such as a Feng input function or exponential function) or some interpolation. You may use the COMKAT Input Function GUI for simulating the input function.

Experimental data

The experimental data may be either from ROI on images or files. Refer to Support:Documents:Manual:COMKAT GUI for requirement of file format and storage.

Install COMKAT

We currently offer two types of COMKAT distribution:
COMKAT on MATLAB runs under standard MATLAB and requires MATLAB licensing.
COMKAT Standalone Application does not require MATLAB license and runs as an executable file. (It does, though, require installation of MATLAB Compiler Runtime, or MCR) You may request MCR from us. Go to MATLAB Compiler Runtime for details and instructions of MCR request.

COMKAT on MATLAB

Download and install COMKAT -> Download:COMKAT R3.1

Validation

How to validate COMKAT?

Validate COMKAT on your computer -> Support:Documents:Validation

Using COMKAT

COMKAT GUI

We have a complete page that goes through all necessary steps to load a complete data set into COMKAT GUI for data analysis.
Or refer to the general manual of COMKAT GUI: Support:Documents:Manual:COMKAT GUI.

Command line functions

Please refer to .... for guidance on this topic.

Other COMKAT functions

Please refer to .... to xxxx topics.