Outline
MCTrace is a program for microtomographic model building and refinement
with a graphical user interface. It consists of over 50,000 lines of custom source code
in C++.
Licence
The limited version of MCTrace is available free of charge to anyone. The licence agreement is included in the online distribution. Users who wish to use all of the functions including automatic model building should contact the copyright holder to arrange for a full license agreement.Download
The latest MCTrace release is v2.2.1, currently available from here. This file contains the 'MCTrace' executable, parameter files and licence agreement. Further updates will be released since this program is still under development.
Release notes
The latest release is v2.2.1
- v2.2.1 (relesed 6 Dec 2010). Graphics are accelerated with DirectX libraries. Functions for microtomographic analysis were thoroughly updated.
- v2.0.2 (released 9 Jun 2009). Functions for tomographic analysis were implemented.
- v1.0.2 (released 9 Jan 2007). Cut, copy and paste functions were debugged. Refinement dialog was updated. Users now can specify regions to be refined.
- v1.0.1 (released 12 Dec 2006). Cut, copy and paste functions were implemented. Exponential subroutine was replaced with a custom one. This makes the structure factor calculation over three times faster than before.
- v1.0.0 is released (12 Nov 2006).
How to use
I believe that this program is self-explanatory, but the following tips should be helpful.
Installation
Download the MCTrace distribution file. Double click the downloaded file. A standard dialog warns that downloaded files cannot be trusted. If you trust me, follow the instructions to install MCTrace. Executable and parameter files will be saved in the 'Program files' folder by default. Shortcuts to MCTrace are created in the 'Start' menu and on your desktop.
Execution
Double click the 'MCTrace' or its shortcut.
Open model
From the menu bar, select 'File'-'Open' and choose a coordinate file. Click the 'OK' button. You can focus on any particular part of the model by selecting 'View'-'Focus'. Useful popup menus can be accessed via the right mouse button. If you have no model coordinate, 'File'-'New' generates a new model.
Modify model
First, double click the model to be replaced, modified, deleted, or otherwise manipulated. Select 'Edit'-'Delete' to delete part of the model, 'Move' to rotate or translate, or 'Torsion' to edit torsion angles.
Three-dimensional density map
After you have opened a working model, select 'Tomography'-'Load slices' to load TIFF slices. Open the map dialog from the 'Tomography'-'Coeff map' menu, select 'Keep current map', and enter appropriate parameters for map display. 'Apply' invokes map update.
Refinement
Open the 'Tomography'-'Refine' dialog. Enter appropriate parameters for dynamics and/or minimization calculation. 'Start' executes refinement. Models under refinement are dynamically displayed and can be manipulated.
Statistical analysis
The 'Analyze' menu provides several analysis tools.
Download the MCTrace distribution file. Double click the downloaded file. A standard dialog warns that downloaded files cannot be trusted. If you trust me, follow the instructions to install MCTrace. Executable and parameter files will be saved in the 'Program files' folder by default. Shortcuts to MCTrace are created in the 'Start' menu and on your desktop.
Execution
Double click the 'MCTrace' or its shortcut.
Open model
From the menu bar, select 'File'-'Open' and choose a coordinate file. Click the 'OK' button. You can focus on any particular part of the model by selecting 'View'-'Focus'. Useful popup menus can be accessed via the right mouse button. If you have no model coordinate, 'File'-'New' generates a new model.
Modify model
First, double click the model to be replaced, modified, deleted, or otherwise manipulated. Select 'Edit'-'Delete' to delete part of the model, 'Move' to rotate or translate, or 'Torsion' to edit torsion angles.
Three-dimensional density map
After you have opened a working model, select 'Tomography'-'Load slices' to load TIFF slices. Open the map dialog from the 'Tomography'-'Coeff map' menu, select 'Keep current map', and enter appropriate parameters for map display. 'Apply' invokes map update.
Refinement
Open the 'Tomography'-'Refine' dialog. Enter appropriate parameters for dynamics and/or minimization calculation. 'Start' executes refinement. Models under refinement are dynamically displayed and can be manipulated.
Statistical analysis
The 'Analyze' menu provides several analysis tools.
Frequently asked questions
- System requirements.
- Are any manuals available?
- How can I execute the program?
MCTrace runs on most of Windows notebook computers and desktop PCs.
A brief how-to-use guide has been published as the appendix of the following paper:
R. Mizutani, A. Takeuchi, K. Uesugi, S. Takekoshi, R.Y. Osamura and Y. Suzuki (2009). Three-dimensional microstructural analysis of human brain tissue by using synchrotron radiation microtomographs. In Handbook on White Matter, eds. Westland, T.B. & Calton, R.N., New York, Nova Science Publishers, pp. 247-277. pdf (9.5 MB)
R. Mizutani, A. Takeuchi, K. Uesugi, S. Takekoshi, R.Y. Osamura and Y. Suzuki (2009). Three-dimensional microstructural analysis of human brain tissue by using synchrotron radiation microtomographs. In Handbook on White Matter, eds. Westland, T.B. & Calton, R.N., New York, Nova Science Publishers, pp. 247-277. pdf (9.5 MB)
Download the MCTrace distribution file. Double click the distribution file and follow the instructions.
Contact / bug report
Ryuta Mizutani, Dr.
Department of Applied Biochemistry
School of Engineering, Tokai University
Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
E-mail ryuta(at)tokai-u.jp
HP http://www.el.u-tokai.ac.jp/ryuta/
Department of Applied Biochemistry
School of Engineering, Tokai University
Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
E-mail ryuta(at)tokai-u.jp
HP http://www.el.u-tokai.ac.jp/ryuta/