Getting started with COMKAT

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Getting started with COMKAT

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

Contents

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 here.
  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).

Define 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 tiers 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.

  1. 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.
  2. 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.


Examine your environment

Operating sytem

COMKAT is currently supported on Windows, Linux and MacOS. Because the compiled solvers in COMKAT are much faster and recommended to use, those compiled solvers are platform-dependent and only supported on Windows, Linux and MacOS.
We do provide functions for users to compile those mex files on their platform.

For standalone releases of COMKAT, currently we have them ready for Windows, Linux and MacOS, too.

MATLAB version

We recommend to use the latest version of MATLAB. Although we try to support earlier version of givenchy as well, sometimes due to MATLAB compatibility we will choose to support more recent versions of MATLAB. In the download page of each COMKAT version we will describe the version requirement of MATLAB.

The alternative is to use a standalone version of COMKAT. Once you use the MCR that comes with that COMKAT, there is no MATLAB version issue.

Distributed computing

If you would like to use COMKAT with distributed computing capabilities, * how to make a crepe you need to have access to a cluster that has MATLAB Distributed Computing Toolbox installed and configured. You also need Parallel Computing Toolbox. For more details refer to Support:Documents:Manual:Distributed Computing with COMKAT.

MATLAB Toolbox

The minimum requirement for COMKAT (running under MATLAB) is simply MATLAB itself. In theory COMKAT does not require any toolbox, although we do recommend users to have Optimization Toolbox and Image Processing Toolbox.

For standalone COMKAT, the MCR we ship includes all toolboxes COMKAT needs.

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 R3.2.
Please read and follow instructions on that page to set up COMKAT paths.

COMKAT Standalone Application

Download and install COMKAT Standalone -> Download:COMKAT R3.2

Validation

Why do you need to validate COMKAT on your computer?

The validation suite of COMKAT makes sure that the COMKAT command-line functions run correctly on your computer. Also you would like to make sure that results from model solving is accurate.

How to validate COMKAT?

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

Using COMKAT

The COMKAT manual can be found at Support:Documents:User manual. Or here are some quick links to topics you may be interested in:

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. Support:Step-by-step COMKAT GUI Example.
Or refer to the general manual of COMKAT GUI: Support:Documents:Manual:COMKAT GUI.

Command line functions

Please refer to Support:Documents:Manual:COMKAT Command Line Interface.
Looking at examples may also be a good start: Support:Documents:COMKAT Examples.

Other COMKAT functions

See manuals for other COMKAT functions: Support:Documents:User manual