Difference between revisions of "Learn more..."
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COMKAT, which stands for 'COmpartment Model Kinetic Analysis Tool', is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user. | COMKAT, which stands for 'COmpartment Model Kinetic Analysis Tool', is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user. | ||
| + | |||
| + | == What makes COMKAT unique? == | ||
| + | ==== Integration between biomedical imaging and compartment modeling ==== | ||
| + | Although there have been various software packages for processing biomedical imaging, few of them provide the functionalities of compartment modeling. In COMKAT, the COMKAT Image Tool can be used to load images, fuse images and draw volume or region of interest (VOI or ROI). For PET images, time-activity curves can be generated and passed to the COMKAT GUI for modeling analysis. With the enhanced integration for both imaging and modeling, COMKAT is convenient to use for research and data analysis. | ||
| + | ==== Fast model solving with compiled solver ==== | ||
| + | Based on the SUNDIALS package [https://computation.llnl.gov/casc/sundials/main.html] developed by Lawrence Livermore National Laboratory, COMKAT provides a compiled (mex) version of cvodes solver that is much faster than the Matlab built-in solver. | ||
| + | ==== Easy and intuitive model implementation ==== | ||
| + | Compartment models can be easily created, configured and solved in COMKAT using either GUI or command line functions. Parameter estimation and sensitivity is also simple and intuitive using COMKAT. | ||
| + | ==== Extensive analysis tools ==== | ||
| + | We provide many tools in COMKAT, including input function estimation, graphical method analysis, simulation and more! | ||
| + | ==== Friendly user interface ==== | ||
| + | COMKAT provides various command line functions for modeling and imaging needs. Based on those, we also developed graphical user interfaces (GUIs) for modeling, imaging and lots of analysis functionalities. Even for people who are not familiar with Matlab programming COMKAT is friendly and intuitive. | ||
| + | ==== Complete online support ==== | ||
| + | COMKAT website provides complete documentation of manuals, tutorials and examples. The wiki-based website also provides an environment for inputs around the world. | ||
| + | ==== Open source and free non-commercial use ==== | ||
| + | Almost all the functions in COMKAT provide source code. Using COMKAT for non-commercial research use is free. | ||
| + | |||
| + | == Latest version == | ||
| + | The latest version of COMKAT is COMKAT R3, released on January, 2008. | ||
| + | |||
| + | == Latest features == | ||
| + | The latest added functions of COMKAT include: | ||
| + | * '''Input function estimation''' | ||
| + | We have developed a method to estimate the input function from images. It's now a GUI included in COMKAT. | ||
| + | |||
| + | * '''Revised COMKAT Image tool''' | ||
| + | The new COMKAT image tool is more powerful! You can now easily translate and rotate images. Automatic image fusion is within clicks away by mutual information algorithms. | ||
| + | |||
| + | * '''Fast DICOM reading and more image formats supported''' | ||
| + | Our own DICOM reading function written as a mex file speeds up reading DICOM images by a factor of 10 compared to the Matlab built-in functions. | ||
| + | We also support NIFTI images now. | ||
| + | |||
| + | * '''Graphical methods''' | ||
| + | New command line functions for graphical methods of modeling analysis | ||
== COMKAT developers == | == COMKAT developers == | ||
| Line 8: | Line 42: | ||
* '''Command line functions''' | * '''Command line functions''' | ||
| − | The command line functions of COMKAT provides functionalities to both imaging and modeling analysis. You can write a Matlab script to construct a compartment model with as simple as several lines. Models can be solved or used to estimate parameters. These functions are the basis of COMKAT because all the GUIs call underlying functions. | + | The command line functions of COMKAT provides functionalities to both imaging and modeling analysis. You can write a Matlab script to construct a compartment model with as simple as several lines. Models can be solved or used to estimate parameters. These functions are the basis of COMKAT because all the GUIs call underlying functions. |
* '''COMKAT GUI''' | * '''COMKAT GUI''' | ||
| Line 18: | Line 52: | ||
* '''COMKAT Input function GUI''' | * '''COMKAT Input function GUI''' | ||
To load input functions from files or functions, a user can use the input function GUI. | To load input functions from files or functions, a user can use the input function GUI. | ||
| + | |||
{| border = "1" | {| border = "1" | ||
| Line 25: | Line 60: | ||
| COMKAT Image Tool <br> [[Image:Cit screen.JPG]] | | COMKAT Image Tool <br> [[Image:Cit screen.JPG]] | ||
|} | |} | ||
| + | |||
== System requirement == | == System requirement == | ||
=== Available version === | === Available version === | ||
| − | COMKAT was originally designed to run as a Matlab toolbox. | + | COMKAT was originally designed to run as a Matlab toolbox. It is recommended that the users use COMKAT under Matlab. |
| − | |||
| − | It is recommended that the users use COMKAT under Matlab | ||
| − | |||
| − | |||
| − | |||
=== Operating system === | === Operating system === | ||
| Line 43: | Line 74: | ||
== License == | == License == | ||
| − | COMKAT is free for non-commercial use. Please contact us [mailto:muzic. | + | COMKAT is free for non-commercial use. Please contact us [mailto:muzic@case.edu] if you are considering using it in commercial purposes. |
Terms of Usage for registering for a user on COMKAT website: | Terms of Usage for registering for a user on COMKAT website: | ||
| − | <br>1. I have registered (free for noncommercial use) as a user at comkat. | + | <br>1. I have registered (free for noncommercial use) as a user at comkat.case.edu and agree to use COMKAT for non-commercial research. I will not share my copy of COMKAT with others who have not registered as COMKAT users. Note: Commercial use requires written permission of Ray Muzic (muzic@case.edu) |
| − | <br>2. Via citation, I will properly acknowledge use of COMKAT in grant applications, proposals, manuscripts, etc.... | + | <br>2. Via citation, I will properly acknowledge use of <span class="plainlinks">[http://www.makecrepes.net<span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">make a crepe</span>] COMKAT in grant applications, proposals, manuscripts, etc.... |
| − | <br>3. I will inform Ray Muzic (muzic@ | + | <br>3. I will inform Ray Muzic (muzic@case.edu) of citations to COMKAT in my publications so that he can use this information to seek support for COMKAT. |
<br>4. If I modify COMKAT for my own use, I will clearly identify in publications, grant applications, etc...., that I have used a customized version of COMKAT. (I will consider sharing my modifications with Ray Muzic. If they are of general interest, and all parties agree, modifications might be made available to others (with proper acknowledgement for efforts). | <br>4. If I modify COMKAT for my own use, I will clearly identify in publications, grant applications, etc...., that I have used a customized version of COMKAT. (I will consider sharing my modifications with Ray Muzic. If they are of general interest, and all parties agree, modifications might be made available to others (with proper acknowledgement for efforts). | ||
<br>5. I have read and understand the Disclaimer which essentially states: COMKAT IS NOT INTENDED FOR CLINICAL / DIAGNOSTIC USE. USER ASSUMES ALL RISK. | <br>5. I have read and understand the Disclaimer which essentially states: COMKAT IS NOT INTENDED FOR CLINICAL / DIAGNOSTIC USE. USER ASSUMES ALL RISK. | ||
| + | |||
| + | == Publication == | ||
| + | |||
| + | === Reference === | ||
| + | To cite COMKAT , please refer to the following: | ||
| + | Muzic RF, Jr., Cornelius S. COMKAT: compartment model kinetic analysis tool. J Nucl Med. Apr 2001;42(4):636-645. [http://jnm.snmjournals.org/cgi/content/full/42/4/636] | ||
| + | |||
| + | === Papers using COMKAT from our group === | ||
| + | # Muzic RF, Jr., Nelson AD, Saidel GM, Miraldi F. Optimal Experiment Design for PET Quantification of Receptor Concentration. IEEE Trans.Med.Imag. 1996;15:2-12. | ||
| + | # Muzic, RF, Jr., Saidel GM, Zhu N*, Nelson, AD, Zheng, L, and Berridge MS. Iterative Optimal Design of PET Experiments for Estimating b-Adrenergic Receptor Concentration. Med. & Biol. Engr. & Comput.. 2000;38(6):593-602. | ||
| + | # Muzic, RF, Jr., Saidel GM. Distributed Vs. Compartment Models for PET Receptor Studies, IEEE Trans.Med.Imag., 2003; 21(1):11-21. | ||
| + | # Salinas CA, Pagel MD, Muzic Jr RF. Measurement of arterial input functions in rats. Paper presented at: 2004 Society for Molecular Imaging Annual Meeting, 2004; St. Louis. | ||
| + | # Muzic RF, Jr., Christian BT. Evaluation of objective functions for estimation of kinetic parameters. Med Phys. Feb 2006;33(2):342-353. | ||
| + | # Salinas C, Muzic Jr RF, Berridge M, Ernsberger P. PET Imaging of Myocardial [beta]-Adrenergic Receptors with Fluorocarazolol: Lack of Interference by Endogenous Catecholamines. Journal of Cardiovascular Pharmacology. 2005;46(2):222-231. | ||
| + | # CA Salinas, RF Muzic Jr, GM Saidel. Validity of model approximations for receptor-ligand kinetics in nuclear medicine. Medical Physics, 2007. | ||
| + | # Salem N, MacLennan GT, Kuang Y, et al. Quantitative Evaluation of 2-Deoxy-2 [F-18] fluoro-d-glucose-Positron Emission Tomography Imaging on the Woodchuck Model of Hepatocellular Carcinoma with Histological Correlation. Molecular Imaging and Biology. 2007;9(3):135-143. | ||
| + | |||
| + | === Papers using COMKAT outside our group === | ||
| + | Find papers citing COMKAT through Google scholar: [http://scholar.google.com/scholar?hl=en&lr=&cites=http://jnm.snmjournals.org/cgi/content/abstract/42/4/636] | ||
| + | |||
| + | '''Selected citation''' | ||
| + | |||
| + | # Morris ED, Christian BT, Yoder KK, Muzic RF Jr. Estimation of Local Receptor Density, B'(max), and Other Parameters via Multiple-Injection Positron Emission Tomography Experiments Methods Enzymol. 2004;385:184-213. | ||
| + | # K. K. Yoder, C. Wang, and E. D. Morris. Change in Binding Potential as a Quantitative Index of Neurotransmitter Release Is Highly Sensitive to Relative Timing and Kinetics of the Tracer and the Endogenous Ligand. J. Nucl. Med., May 1, 2004; 45(5): 903 - 911. | ||
| + | # F. Pain, P. Laniece, R. Mastrippolito, P. Gervais, P. Hantraye, and L. Besret. Arterial Input Function Measurement Without Blood Sampling Using a {beta}-Microprobe in Rats. J. Nucl. Med., September 1, 2004; 45(9): 1577 - 1582. | ||
| + | # Christian BT, Narayanan T, Shi B, Morris ED, Mantil J, Mukherjee J. Measuring the In Vivo Binding Parameters of [18 F]-Fallypride in Monkeys Using a PET Multiple-Injection Protocol. Journal of Cerebral Blood Flow & Metabolism. 2004;24:309-322. | ||
| + | |||
{{DISPLAYTITLE:About COMKAT}} | {{DISPLAYTITLE:About COMKAT}} | ||
Latest revision as of 14:46, 28 February 2013
COMKAT, which stands for 'COmpartment Model Kinetic Analysis Tool', is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user.
What makes COMKAT unique?
Integration between biomedical imaging and compartment modeling
Although there have been various software packages for processing biomedical imaging, few of them provide the functionalities of compartment modeling. In COMKAT, the COMKAT Image Tool can be used to load images, fuse images and draw volume or region of interest (VOI or ROI). For PET images, time-activity curves can be generated and passed to the COMKAT GUI for modeling analysis. With the enhanced integration for both imaging and modeling, COMKAT is convenient to use for research and data analysis.
Fast model solving with compiled solver
Based on the SUNDIALS package [1] developed by Lawrence Livermore National Laboratory, COMKAT provides a compiled (mex) version of cvodes solver that is much faster than the Matlab built-in solver.
Easy and intuitive model implementation
Compartment models can be easily created, configured and solved in COMKAT using either GUI or command line functions. Parameter estimation and sensitivity is also simple and intuitive using COMKAT.
Extensive analysis tools
We provide many tools in COMKAT, including input function estimation, graphical method analysis, simulation and more!
Friendly user interface
COMKAT provides various command line functions for modeling and imaging needs. Based on those, we also developed graphical user interfaces (GUIs) for modeling, imaging and lots of analysis functionalities. Even for people who are not familiar with Matlab programming COMKAT is friendly and intuitive.
Complete online support
COMKAT website provides complete documentation of manuals, tutorials and examples. The wiki-based website also provides an environment for inputs around the world.
Open source and free non-commercial use
Almost all the functions in COMKAT provide source code. Using COMKAT for non-commercial research use is free.
Latest version
The latest version of COMKAT is COMKAT R3, released on January, 2008.
Latest features
The latest added functions of COMKAT include:
- Input function estimation
We have developed a method to estimate the input function from images. It's now a GUI included in COMKAT.
- Revised COMKAT Image tool
The new COMKAT image tool is more powerful! You can now easily translate and rotate images. Automatic image fusion is within clicks away by mutual information algorithms.
- Fast DICOM reading and more image formats supported
Our own DICOM reading function written as a mex file speeds up reading DICOM images by a factor of 10 compared to the Matlab built-in functions. We also support NIFTI images now.
- Graphical methods
New command line functions for graphical methods of modeling analysis
COMKAT developers
Dr. Raymond Muzic, PhD is the main COMKAT developer. He is an associate professor of Radiology in Case Western Reserve University. Go to People:mainpage to find out more about the people involved in developing COMKAT.
Inside COMKAT
COMKAT serves as a bridge between biomedical imaging and modeling analysis. It can be divided into the following components:
- Command line functions
The command line functions of COMKAT provides functionalities to both imaging and modeling analysis. You can write a Matlab script to construct a compartment model with as simple as several lines. Models can be solved or used to estimate parameters. These functions are the basis of COMKAT because all the GUIs call underlying functions.
- COMKAT GUI
This GUI is designed for compartment modeling. Input and output can be loaded from various file formats. You may also set the output directly from images with COMKAT Image Tool. You can use the COMKAT GUI to fit experimental data and simply to simulate model output.
- COMKAT Image Tool
This GUI is designed for image display, fusion and region of interest. We support various image formats.
- COMKAT Input function GUI
To load input functions from files or functions, a user can use the input function GUI.
COMKAT GUI 
|
COMKAT Image Tool 
|
System requirement
Available version
COMKAT was originally designed to run as a Matlab toolbox. It is recommended that the users use COMKAT under Matlab.
Operating system
COMKAT has been tested on Windows XP, MacOS 10.4 and Linux.
Matlab
We recommend using COMKAT under Matlab R14 or newer.
License
COMKAT is free for non-commercial use. Please contact us [2] if you are considering using it in commercial purposes.
Terms of Usage for registering for a user on COMKAT website:
1. I have registered (free for noncommercial use) as a user at comkat.case.edu and agree to use COMKAT for non-commercial research. I will not share my copy of COMKAT with others who have not registered as COMKAT users. Note: Commercial use requires written permission of Ray Muzic (muzic@case.edu)
2. Via citation, I will properly acknowledge use of make a crepe COMKAT in grant applications, proposals, manuscripts, etc....
3. I will inform Ray Muzic (muzic@case.edu) of citations to COMKAT in my publications so that he can use this information to seek support for COMKAT.
4. If I modify COMKAT for my own use, I will clearly identify in publications, grant applications, etc...., that I have used a customized version of COMKAT. (I will consider sharing my modifications with Ray Muzic. If they are of general interest, and all parties agree, modifications might be made available to others (with proper acknowledgement for efforts).
5. I have read and understand the Disclaimer which essentially states: COMKAT IS NOT INTENDED FOR CLINICAL / DIAGNOSTIC USE. USER ASSUMES ALL RISK.
Publication
Reference
To cite COMKAT , please refer to the following: Muzic RF, Jr., Cornelius S. COMKAT: compartment model kinetic analysis tool. J Nucl Med. Apr 2001;42(4):636-645. [3]
Papers using COMKAT from our group
- Muzic RF, Jr., Nelson AD, Saidel GM, Miraldi F. Optimal Experiment Design for PET Quantification of Receptor Concentration. IEEE Trans.Med.Imag. 1996;15:2-12.
- Muzic, RF, Jr., Saidel GM, Zhu N*, Nelson, AD, Zheng, L, and Berridge MS. Iterative Optimal Design of PET Experiments for Estimating b-Adrenergic Receptor Concentration. Med. & Biol. Engr. & Comput.. 2000;38(6):593-602.
- Muzic, RF, Jr., Saidel GM. Distributed Vs. Compartment Models for PET Receptor Studies, IEEE Trans.Med.Imag., 2003; 21(1):11-21.
- Salinas CA, Pagel MD, Muzic Jr RF. Measurement of arterial input functions in rats. Paper presented at: 2004 Society for Molecular Imaging Annual Meeting, 2004; St. Louis.
- Muzic RF, Jr., Christian BT. Evaluation of objective functions for estimation of kinetic parameters. Med Phys. Feb 2006;33(2):342-353.
- Salinas C, Muzic Jr RF, Berridge M, Ernsberger P. PET Imaging of Myocardial [beta]-Adrenergic Receptors with Fluorocarazolol: Lack of Interference by Endogenous Catecholamines. Journal of Cardiovascular Pharmacology. 2005;46(2):222-231.
- CA Salinas, RF Muzic Jr, GM Saidel. Validity of model approximations for receptor-ligand kinetics in nuclear medicine. Medical Physics, 2007.
- Salem N, MacLennan GT, Kuang Y, et al. Quantitative Evaluation of 2-Deoxy-2 [F-18] fluoro-d-glucose-Positron Emission Tomography Imaging on the Woodchuck Model of Hepatocellular Carcinoma with Histological Correlation. Molecular Imaging and Biology. 2007;9(3):135-143.
Papers using COMKAT outside our group
Find papers citing COMKAT through Google scholar: [4]
Selected citation
- Morris ED, Christian BT, Yoder KK, Muzic RF Jr. Estimation of Local Receptor Density, B'(max), and Other Parameters via Multiple-Injection Positron Emission Tomography Experiments Methods Enzymol. 2004;385:184-213.
- K. K. Yoder, C. Wang, and E. D. Morris. Change in Binding Potential as a Quantitative Index of Neurotransmitter Release Is Highly Sensitive to Relative Timing and Kinetics of the Tracer and the Endogenous Ligand. J. Nucl. Med., May 1, 2004; 45(5): 903 - 911.
- F. Pain, P. Laniece, R. Mastrippolito, P. Gervais, P. Hantraye, and L. Besret. Arterial Input Function Measurement Without Blood Sampling Using a {beta}-Microprobe in Rats. J. Nucl. Med., September 1, 2004; 45(9): 1577 - 1582.
- Christian BT, Narayanan T, Shi B, Morris ED, Mantil J, Mukherjee J. Measuring the In Vivo Binding Parameters of [18 F]-Fallypride in Monkeys Using a PET Multiple-Injection Protocol. Journal of Cerebral Blood Flow & Metabolism. 2004;24:309-322.