RecView

Outline

RecView is a program for microtomographic reconstruction and image processing. It's consisted of about 14,000 lines of originally-written source codes in C++, CUDA C, x86 and x64 machine languages. RecView is developed for processing tomographic data obtained at the BL20B2, BL20XU, and BL47XU beamlines of the synchrotron radiation facility SPring-8.

testPattern Three-dimensional structural analysis by SR microtomograph is performed by recording two-dimensional radiographs. Then the three-dimensional structure is determined by the convolution back-projection method. This reconstruction calculation is repeated for each tomographic slice, giving the three-dimensional structure. Therefore, the resolution in the tomographic slice should be affected by the reconstruction calculation. We examined the resolutions in the tomographic slice plane and perpendicular to it from modulation transfer functions. The through-plane resolution perpendicular to the tomographic slice corresponded to the spatial resolution of two-dimensional radiographs. In contrast, the in-plane resolution within the slice was approximately 1.5-times larger than the through-plane resolution. Although the two-dimensional radiographs were taken with the pixel width of half the x-ray optics resolution, the three-dimensional resolution analyses indicated that the zoom reconstruction should be performed to achieve the in-plane resolution comparable to the x-ray optics resolution. Micron 41(1), 90-95. preprint

Licence

RecView is available free of charge for all users.

References

R. Mizutani, A. Takeuchi, K. Uesugi and Y. Suzuki (2008). Evaluation of the improved three-dimensional resolution of a synchrotron radiation computed tomograph by using a micro-fabricated test pattern. J. Synchrotron Radiation 15(6), 648-654. DOI PubMed pdf
R. Mizutani, A. Takeuchi, R.Y. Osamura, S. Takekoshi, K. Uesugi and Y. Suzuki (2010). Submicrometer tomographic resolution examined using a micro-fabricated test object. Micron 41(1), 90-95. DOI PubMed preprint
R. Mizutani, K. Taguchi, A. Takeuchi, K. Uesugi and Y. Suzuki (2010). Estimation of presampling modulation transfer function in synchrotron radiation microtomography. Nuclear Instrum. Meth. A 621(1-3), 615-619. DOI preprint

Download

The RecView v3 released. Download...

The latest RecView release is v3.0.0, currently at here. This file contains several 'RecView' executables. Please use 'RecView' appropriate for your PC platform. If NVIDIA Tesla/GeForce/Quadro GPU processors are available on your PC, CUDA version can be used. The files 'cudart32_30_14.dll' and 'cufft32_30_14.dll' should be placed in the folder where the RecView CUDA executable was extracted. These DLLs are also available from the official NVIDIA site as a part of the CUDA toolkit. ATI stream processors Radeon/FireStream/FirePro are also supported in this release. The OpenCL library 'OpenCL.dll' provided as a part of the ATI Catalyst suite should be extracted to use the ATI processors.

Release notes

v3.0.0 is released (27 May 2010). Back projection routines running on Tesla/GeForce/Quadro processors were updated to support CUDA 3.0 computing environment. The OpenCL 1.0 routines for ATI Radeon/FireStream/FirePro processors were also implemented. Peformances are:
- Tau(448 cores, 607 MHz) = 0.0813 nsec (23.4 sec/4500projection,8000x8000tomogram) by using GeForce GTX470 with 1.28 GB GDDR5 memory,
- Tau(112 cores, 500 MHz) = 0.243 nsec (1.75 sec/1800projection,2000x2000tomogram) by using Quadro FX 3700 with 512 MB GDDR3 memory,
- Tau(80 cores, 650 MHz) = 2.86 nsec (20.6 sec/1800projection,2000x2000tomogram) by using Radeon HD 5450 with 512 MB DDR2 memory,
- Tau(4 threads, 3.16 GHz) = 0.825 nsec (5.94 sec/1800projection,2000x2000tomogram) by using Xeon (x86),
- Tau(4 threads, 3.16 GHz) = 0.808 nsec (5.82 sec/1800projection,2000x2000tomogram) by using Xeon (x64).
Tau is a time constant required for one pixel projection. For example, one tomogram of 2000 x 2000 pixels from 1800 projection frames can be reconstructed in tau x 2000 x 2000 x 1800 sec. Drift correction options were also released in this revision.
v2.0.10 is released (2 Sep 2009). Tilted reconstruction was released. Angular interpolation was implemented for compatibility with the ct_cbp reconstruction suite. Trimming of marginal region can be performed in the 8-bit TIFF conversion process.
v2.0.6 is released (13 Mar 2009). Bug fix release revising memory allocation procedures in the CUDA reconstruction routine.
v2.0.5 is released (9 Feb 2009). Back projection routines running on Tesla/GeForce/Quadro processors supporting CUDA programming environment were implemented. The x86 and x64 assembler routines were also revised. Peformances are:
- Tau(112 cores, 500 MHz) = 0.314 nsec (2.28 sec/2000x2000tomogram) by using a Quadro FX 3700,
- Tau(3.16 GHz) = 0.633 nsec (4.56 sec/tomogram) by using Core2Duo (x86, #thread = 2), or tau = 1.336 nsec (x86, single thread),
- Tau(3.16 GHz) = 0.802 nsec (5.77 sec/tomogram) by using Xeon (x86, #thread = 4), or tau = 1.724 nsec (x86, single thread),
- Tau(3.16 GHz) = 0.768 nsec (5.53 sec/tomogram) by using Xeon (x64, #thread = 4), or tau = 1.651 nsec (x64, single thread).
Tau is a time constant required for one pixel projection. For example, one tomogram of 2000 x 2000 pixels from 1800 projection frames can be reconstructed in tau x 2000 x 2000 x 1800 sec.
v2.0.0 is released (21 Jan 2009). x64 platform is now supported. The x64 version can generate larger tomograms upto 10⁶ x 10⁶ pixels. Performance: tau(3.16 GHz) = 0.789 nsec by using Xeon (x64, #thread = 4). Performace of x86 version: tau(3.16 GHz) = 0.849 nsec by using Core2Duo (x86, #thread = 2), or tau = 1.395 nsec (x86, single thread).
v1.0.7 is released (23 Aug 2008). Interpolated tomographic reconstruction was implemented. Performance: tau(3.16 GHz) = 1.209 nsec by using Core2Duo (x86, #thread = 2).
v1.0.4 is released (1 Apr 2008). Multi-threaded reconstruction routine was implemented. This function is partially written in x86 machine language, allowing the faster execution of the reconstruction calculation.
v1.0.0 is released (6 Mar 2008).

How to use

One can find a concise help from the 'Help'-'About' menu. I believe this program is self-explanational, but following tips would help understanding.

Installation
Download the RecView compressed file. Extract the executable and corresponding DLL files in any folder you like.

Execution
Double click the 'RecView' executable.

Open radiograph
From the menu bar, select 'File'-'Open...' and choose an ITEX file. Click the 'OK' button.

Computing environment
GPU or CPU computing environment can be selected in 'Tomography'-'Property' dialog.

Reconstruction
Open 'Tomography'-'Reconstruction...' dialog. Enter appropriate parameters for your reconstruction calculation. 'Get center' determines the position of the rotation axis. After examining a tomogram by 'Show image', 'Batch' executes the reconstruction calculation.

Trimming or reformatting images
'Tomography'-'Histogram=>8bitTIF...' menu provides several tools for generating 8-bit TIFF images.

Frequently asked questions

System requirements.

RecView can be executed on Windows XP/Vista/7 PC with x86/x64 CPU and local storage drive.

Is there any manuals available?

A brief How-to-use 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)

What kind of data can be processed?

RecView is developed for the reconstruction of tomographic data obtained at SPring-8. However, any kind of data can be processed. Please contact if you wish to use this program with data obtained by your tomograph.

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/