Difference between revisions of "Getting started with COMKAT"

Revision as of 17:47, 13 April 2009

(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:

GUI: Graphical user interface
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.
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.
COMKAT Image Tool: The imaging GUI for COMKAT. You can load images with it, draw ROI, display and fuse multiple image data sets.
COMKAT Input Function GUI: This GUI is called by COMKAT GUI for specifying the input function.
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.
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.
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:

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.
Image processing
If you only need to load images and draw ROI, you can simply use COMKAT Image Tool as an independent suite.
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.
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.
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].

Prepare your data

Examine your environment

Operating sytem

MATLAB version

Distributed computing

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

COMKAT Standalone Application

Validation

Why do you need to validate COMKAT on your computer?

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.

Command line functions

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

Other COMKAT functions

Please refer to .... to xxxx topics.

@@ Line 4: / Line 4: @@
 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:
+# GUI: Graphical user interface
+# 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.
+# 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.
+# COMKAT Image Tool: The imaging GUI for COMKAT. You can load images with it, draw ROI, display and fuse multiple image data sets.
+# COMKAT Input Function GUI: This GUI is called by COMKAT GUI for specifying the input function.
+# 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]].
+# 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.
+# 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:
+# Parameter estimation for image quantification<br>You have some image data that you would like to draw a region (or regions) of interest and estimate parameters.
+## ROI data<br>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.
+## Parameter estimation with COMKAT GUI<br>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.
+## Parameter estimation with scripts and COMKAT command-line functions<br>For advanced users that can program MATLAB scripts, using COMKAT command-line functions may sometimes provide more flexibilities and advanced functionality.
+# Image processing<br>If you only need to load images and draw ROI, you can simply use COMKAT Image Tool as an independent suite.
+# Model development<br>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.
+## COMKAT GUI: You can create new models with graphical interfaces without programming.
+## 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.
+# 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.
+# 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].
 == Prepare your data ==