Microsc. Microanal. 7, 13–23, 2001 DOI: 10.1007/s100050010053
Microscopy AND
Microanalysis
© MICROSCOPY SOCIETY OF AMERICA 2001
Fast Algorithm for Xray Conebeam Microtomography
Ang Shih, ^{1} Ge Wang, ^{2} and PingChin Cheng ^{1} *
^{1} Advanced Microscopy and Imaging Laboratory, Department of Electrical Engineering, State University of New York at Buffalo, 315 Bonner Hall, Buffalo, NY 14260 ^{2} Department of Radiology, University of Iowa, Iowa City, IA 52242
Abstract: Conebeam Xray microtomography attracts increasing attention due to its applications in biomedi cal sciences, material engineering, and industrial nondestructive evaluation. Rapid volumetric image recon struction is highly desirable in all these areas for prompt visualization and analysis of complex structures of interest. In this article, we reformulate a generalized Feldkamp conebeam image reconstruction algorithm, utilize curved voxels and mapping tables, improve the reconstruction efficiency by an order of magnitude relative to a direct implementation of the standard algorithm, and demonstrate the feasibility with numerical simulation and experiments using a prototype conebeam Xray microtomographic system. Our fast algorithm reconstructs a 256voxel cube from 100 projections within 2 min on an Intel Pentium II 233 MHz personal computer, produces satisfactory image quality, and can be further accelerated using special hardware and/or parallel processing techniques.
Key words: Xray computed tomography, conebeam, microtomography, image reconstruction, realtime, nondestructive evaluation
INTRODUCTION
Due to its penetration ability and contrast mechanism, conebeam Xray microtomography is a powerful tool in studies on 3D microstructures of opaque specimens in bio logical, medical, material, and industrial applications (Russ, 1988; Kinney et al., 1989; Cheng et al., 1991; Pan et al., 1997; Wang et al., 1999). With an Xray point source and a 2D detector array, Xrays intersecting a spherical specimen form a cone, giving rise to the nomenclature conebeam. Compared to parallelbeam or fanbeam approaches, the conebeam geometry is beneficial for faster data collection,
Received January 11, 1999; accepted June 13, 2000. *Corresponding author
higher image resolution, better radiation utilization and easier hardware implementation (Cheng et al., 1991; Wang et al., 1999). Despite impressive progress in exact conebeam recon struction, approximate conebeam algorithms remain im portant, which allow incomplete scanning loci and partial detection coverage. The Feldkamp conebeam image recon struction algorithm is the most popular approximate cone beam algorithm, but it is limited by circular scanning, spherical specimen reconstruction, and longitudinal image blurring (Feldkamp et al., 1984; Kak et al., 1988). We de veloped a prototype conebeam Xray microtomographic system (Cheng et al., 1991), and generalized the Feldkamp algorithm to allow flexible scanning loci including helical/ helicallike scanning patterns, and reconstruct spherical,
14 Ang Shih et al.
rodshaped, and planar specimens (Wang et al., 1992, 1993,
1999).
A major problem with the conebeam image recon
struction has been lack of fast algorithms for realtime or near realtime performance. The computational complexity
of the standard Feldkamptype reconstruction requires ex
pensive computing resources and/or leads to lengthy com putational time, which preclude many important applica tions, such as online inspection of industrial products, massive screening of certain objects, and dynamic studies of timevarying specimens/processes. Substantial efforts have been made to shorten the re construction time by algorithmic improvement. A STRETCH algorithm approximates bilinearly interpolated projection data with nearest neighbors that are efficiently computed with a sufficiently small step (Peters, 1981). An incremental reconstruction algorithm utilizes beam geom
etrybased pixels, instead of Cartesian grid points (He et al., 1993). The beamoriented pixels are also useful in emission computed tomography (CT) (Gullberg et al., 1996).
In this article, we report a fast reconstruction algorithm
for generalized Feldkamp image backprojection using a table mapping strategy on a personal computer. In the next section, both a prototype conebeam Xray microtomo graphic system and the generalized Feldkamp algorithm are described, then the generalized Feldkamp algorithm is re formulated using curved voxels and mapping tables, and the computational complexity analyzed. In the third section, a speed performance review of our new algorithm is numeri cally and experimentally demonstrated using a personal computer. In the last section, several relevant issues and further research topics are discussed.
MATERIALS AND METHODS
Conebeam Microtomographic System
A conebeam Xray microtomographic system has been
constructed at the Advanced Microscopy and Imaging Laboratory (AMIL), State University of New York at Buffalo (SUNY/Buffalo). The system consists of an Xray source, a 3D translation and rotation stage, an Xray scintillation phosphor screen (built at SUNY/Buffalo), a high resolution (1288 × 1004) slowscan cooled chargecoupled device (CCD) camera (Photometric C200, Tucson, AZ; Kodak KAF 1400, Rochester, NY), and a personal computer (Mi croexpert, Cheektowaga, NY). The Xray source can be ei
ther a dental Xray source (Aztech 65, Boulder, CO) or a microfocused electron optical column, depending on the image resolution requirement. Figures 1 and 2 are a pho tograph and a diagram of this conebeam imaging system, respectively.
Generalized Feldkamp Algorithm
The generalized Feldkamp conebeam image reconstruction algorithm is expressed as follows:
g _{} x,y,z _{} =
2
2
0
1
D
^{2}
s 2 ^{}
−
_{} D −
R
_{} p, ,
D
h _{} q − p _{} D _{2} + p _{2} + _{2} dpd ,
(1)
where g (x,y,z) is a 3D image, D the distance between the source and the zaxis, the source rotation angle relative to the z axis, R(p, , ) conebeam projection data,
=
q
=
Dz
D − s
Dt
D − s
t = x cos − ysin
s = −xsin − ycos
_{} _{,}
(2)
(3)
as illustrated in Figure 3. The generalized Feldkamp reconstruction can be di vided into the following three steps:
1. Obtain weighted projection data
D
R p, , = D _{2} + p _{2} + _{2} R _{} p, , ,
2. Filter the weighted data
Q _{} q, , = R q, , _{*} h _{} q _{} ,
(4)
(5)
3. Weight and backproject the filtered data
g _{} x,y,z _{} = _{} _{0}
2
2
^{D} − s _{2} Q _{} q, , d . _{} D
2
(6)
Conebeam Xray Microtomography
15
Figure 1. Diagram of the Xray conebeam microtomographic system of the Advanced Microscopy and Imaging Laboratory (AMIL), State University of New York at Buffalo (SUNY/Buffalo). CCD, chargecoupled device.
Our first conebeam image reconstruction software was di rectly based on a discrete version of the above formulas to test the feasibility and provide the gold standard.
Fast Reconstruction Techniques
The Feldkamptype conebeam reconstruction is cast in the filtered backprojection framework. Specifically, the Feld kamptype reconstruction consists of two processes: (1) fil tration, and (2) backprojection. In the filtration process, horizontal projection profiles are rampfiltered in the Fou rier domain after zero padding. In the backprojection pro cess, an image volume is reconstructed by backprojecting filtered data along Xray paths with appropriate weights. Let us consider reconstruction of an N voxel cube from M projections. Roughly speaking, a standard Feldkamptype algorithm requires MN ^{2} weighting operations, 2MN ^{2} + 10MN ^{2} log _{2} 2N filtration operations, and 17MN ^{3} backpro jection operations. Typically, more than 80% of the total reconstruction time is devoted to backprojection. There fore, the backprojection is the computational bottleneck of
filtered backprojectionbased reconstruction and, in this subsection, we will focus on acceleration of backprojection for Feldkamptype reconstruction. The table mapping can be very effective for reduction of computational time. The limiting factor is available ran dom memory space. Typically, a current personal computer has a random memory space of 128 megabytes to 1 gi gabytes. As a representative problem, we consider recon struction of a 256voxel cube from 100 conebeam projec tions. Clearly, a direct table mapping in terms of x, y, and z indexes would require a random memory space of 4 gi gabytes in this case (i.e., 256 ^{3} for every reconstruct voxel, times 100 for different directions, and times 3 for separate tables of xaxis index, yaxis index, and coefficients). How ever, this requirement may be significantly reduced if we reformulate the generalized Feldkamp algorithm in the dis crete domain as follows:
M
g _{} x,y,z _{} = _{} W _{} s _{} Q _{} A _{} t,s _{} ,A _{} z,s _{} , _{1} _{} ,
l=1
(7)
16 Ang Shih et al.
Figure 2. Photograph of the Xray conebeam microtomographic system of AMIL, SUNY/Buffalo. Xray source (A); specimen holder (B); scintillator (C); relay lens (D); slowscan cooled CCD (E); xaxis translation stage (F); zaxis translation stage (H); tilt and yow stage (I).
Figure 3. Generalized Feldkamp conebeam reconstruction system and variables.
where x,y and z are defined only at finitely many prespeci fied locations (a regular 3D Cartesian grid), t and s depend on x and y,
and
W _{} s _{} =
D ^{2}
2 _{} D − s _{} ^{2} _{,}
(8)
A _{} u,s _{} =
Du
D − s
^{(}^{9}^{)}
are 1D and 2D, respectively.
To accumulate the terms W(s)Q[A(t,s),A(z,s), _{l} ] effi ciently, we introduce curved voxels that are discretely in dexed by (r, , z), as shown in Figure 4. With curved voxels, backprojection components W(s)Q[A(t,s),A(z,s), _{l} ] for
Figure 4. Curved voxels in a cylindrical coordinate system.
each source angle _{l} can be easily accumulated after an appropriate translation in . Also, backprojection based on curved voxels naturally avoids computation for voxels out side the reliable reconstruction cylinder, in which voxels are seen from all the Xray source positions. To rapidly compute (t,s) from (r, ), two tables are de signed for conversion from polar coordinates (r, ) to Car tesian coordinates (t,s), which are denoted as T(r, ) and S(r, ), independent of z. As shown in Figure 5, intervals in t and s should be made small so that quantization errors are insignificant, but these intervals should not be too small to result in manage able sizes of memory space for W(s) and A(u,s), T(r, ) and S(r, ). For every curved voxel (r, ,z) and each source angle _{l} , (t,s) are well approximated from T(r, ) and S(r, ), W(s), A(t,s), and A(z,s) subsequently retrieved, and W(s)Q [A(t,s),A(z,s), _{l} ] computed. After backprojection over the curved voxels is done, the reconstructed image volume in dexed by (r, ,z) should be transformed into the conven tional format indexed by (x,y,z) for direct use with image visualization and analysis software. Hence, two more tables, R(x,y) and (x,y), are needed to find values of voxels at (x,y,z) from values at cylindrical coordinates (r, ,z). A refinement should be made to correct the drawback of the curved voxels in Figure 4, in which voxels along inner rings are substantially smaller than those along outer rings.
Conebeam Xray Microtomography
17
Figure 5. Small intervals in t and s for reduction of quantization errors in the mapping process.
Figure 6. Arrangement of curved voxels of similar sizes.
With loss of generality, let us assume an Nvoxel cubic volume and the unit size of cubic voxels. Suppose there are K centered rings participating a transaxial slice, as shown in Figure 6 while K = 4, the thickness of each ring = N/2K, the perimeter of the ith ring P _{i} = 2 (i − 1/2), i = 1, , K, and we would distribute V _{i} = ceil(P _{i} / ) voxels along the ith ring to produce a roughly squared pixel. To loop through curved voxels rapidly, we stored V _{i} as a function of the ring index i in table V(i). A tradeoff must be made in selection of K. The larger K, the higher recon struction accuracy will be achieved, but the larger memory space and the longer computational time will be involved. Practically, we may just set K to N/2. In this case, only /4 voxels will be processed as compared to the Cartesian sys tembased reconstruction. Figure 7 shows a flowchart for the table mapping reconstruction algorithm.
Computational Complexity
We use a Pentium II 233MHz computer under Windows NT 4.0 and Microsoft Visual C++ 4.2. Table 1 lists the central processing unit (CPU) time in seconds for each of
18 Ang Shih et al.
Figure 7. Flowchart for conebeam reconstruction using curved voxels and mapping tables.
basic data operations, including addition, multiplication, division, sine, cosine, tangent, and indexing of a 1D array. The operations time was recorded with the instruction ex ecution time (set up in a 2 ^{2}^{4} loops) subtract the empty loop
execution time. Table 2 compares time consumed by the standard Feldkamptype reconstruction and our accelerated implementation for a 256voxel cube from 100 conebeam projections keyed to each of basic operations. Clearly, our
Central Processing Unit (CPU) Time (in seconds) for
Basic Data Processing Operations, Each of Which Was Executed
Table 1.
2 ^{2}^{4} Times in a Loop
+×/ 
Sin 
Cos 
Index 

Short 

integer 
0.778 
1.798 
2.937 
NA 
NA 
1.313 
Float 
2.564 
2.314 
7.272 
37.067 
42.203 
0.904 
Double 
3.447 
4.713 
4.480 
NA 
NA 
1.059 
NA, not available.
fast reconstruction schemes improve the computational ef ficiency by more than 22 times.
RESULTS
Our earlier standard software for generalized Feldkamp re construction was used as the reference, and modified to implement the fast reconstruction techniques described above. The programs were coded in Microsoft Visual C++ 4.2, and tested on an Intel Pentium II 233 CPU installed on a Gigabyte 686LX2 motherboard with 128 megabyte SDRAM under NT 4.0. Nearest neighbor interpolation was applied whenever interpolation was needed. Both nu merical simulation and physical experiments were per formed to refine reconstruction parameters and verify pro grams. A point Xray source, point detectors, and circular scanning were assumed. The sourcetoorigin distance was set to 6 cm. The image volume to be reconstructed was assumed to be a 256voxel cube. The detector plane was 2.2 by 2.2 cm with 256 by 256 detectors, and for the ease of computation it was scaled to pass through the zaxis of the reconstruction coordinate system. Specifically, the detector plane was so placed that its center is at the origin of the x–y–z system, its horizontal axis p stays in the x–y plane, and its vertical axis was superimposed upon the zaxis. A 3D version of Shepp and Logan’s (1974) head phantom was used as the testing object. One hundred conebeam projec tions with a 3.6° angular interval were used for the recon struction. Conebeam projection data were synthesized based on analytically derived formulas. This phantom was reconstructed using both our direct implementation of the generalized Feldkamp algorithm and the table mappingbased software to evaluate effects of re construction parameters on image quality. As mentioned in
Conebeam Xray Microtomography
19
the proceeding section, oversampling in t and s would reduce the reconstruction error without compromising the reconstruction speed, but this gain is at cost of enlarged mapping tables. The standard deviation of reconstruction errors against the oversampling size were plotted in Figure 8, which helped determine the lengths of t and s intervals for design of related tables. We also monitored the change in edge sharpness as a function of table sizes, but would not include those curves for sake of brevity. In this study, we used 512 intervals of the same length for both t and s. Compared to the ideal values of the phantom, the stan dard deviation of reconstruction errors with the direct implementation and the tablemapping improvement was 0.03 and 0.05, respectively. The original image and two reconstructed counterparts of a representative slice at z = −0.25 are shown in Figure 9. The intensity profiles of origi nal and reconstructed values for the line at (y,z) = (0.2, −0.25) were plotted in Figure 10. An analysis on a 100 by 100 homogeneous region in the slice at z = 0 indicated that the image noise standard deviation with the direct imple mentation and the tablemapping improvement are 0.0125 and 0.0122, respectively. Visual inspection with different settings of brightness and contrast of display suggested that our fast algorithm produced comparable image quality rela tive to our earlier standard software. As a real example, Figure 11 includes two rendered views of a small electrolytic capacitor, which was scanned with our prototype microtomographic system described in the preceding section, and reconstructed using our table mappingbased software. The specimentosource distance was 8.13 cm. The specimentodetector distance was 3.81 cm. Hundred conebeam projections were taken. Each pro jection was exposed and integrated for 0.5 sec. The recon struction time was 2 min, much shorter than 20 min taken by our earlier software that directly implemented the gen eralized Feldkamp formula. In comparison to the incre mental algorithm (He et al., 1993), our version of incre mental backprojection implementation has a reconstruc tion time of 5 min.
DISCUSSION AND CONCLUSIONS
The system setup we described in this article was for testing the feasibility of our tablemappingbased generalized Feld kamp reconstruction. The next step is to use a micro focused Xray source and a higher density CCD detector array to obtain microtomographic image volumes in near realtime. We are actively working along this direction.
20
Ang Shih et al.
Table 2.
Implementation for a 256Voxel Cube from 100 Conebeam Projections, Keyed to Each of Basic Operations
Relative Time Consumed by the Direct Implementation of the Generalized Feldkamp Reconstruction and the Accelerated
Basic operation 
Direct implementation 
Mapping implementation 

Operation 
Relative time per instruction 
Instruction no. 
Relative time 
Instruction no. 
Relative time 
+ × / Sin Cos Index Total relative time 
2.564 
4 
10.256 
1 
2.564 
2.314 
9 
20.826 
1 
2.314 

7.272 
3 
21.816 
0 
0 

37.067 
2 
74.134 
0 
0 

42.203 
2 
84.406 
0 
0 

0.904 
1 
0.904 
5 
4.520 

209.778 
9.398 
Figure 8. Plots of the standard deviation of reconstruction errors against the oversampling size.
Figure 9. Comparison of reconstructed image quality for slice z = −0.25. a: The image reconstructed using our direct implementation of the generalized Feldkamp reconstruction; b: the counterpart using our tablemapping algorithm.
Conebeam Xray Microtomography
_{2}_{1}
Figure 10. Examination of a representative profile at y = 0.2, z = −0.25. a: The original profile and the reconstructed profile using our direct implementation of the generalized Feldkamp reconstruction; b: the counterparts using our tablemapping algorithm. Examination of a representative profile at y = −0.6, z = −0.25. c: The original profile and the reconstructed profile using our direct implementation of the generalized Feldkamp reconstruction; d: the counterparts using our tablemapping algorithm.
Further refinements of our tablemapping and curved voxel techniques are possible. For example, utilization of mapping tables can effectively shorten the backprojection process. However, a paradox is that large mapping tables are not practical in many cases, while small mapping tables will not yield satisfactory image quality. A balance must be ap plicationdependent. The general relationships between im age quality indexes and table design parameters may be analytically quantified (Kriete, 1994). Although our emphasis was put on backprojection, similar fast processing techniques can be applied to improve the speed of data preprocessing and filtration. Some rela tively timeconsuming parts could be even implemented in
assembly language for minimum computational overhead. Also, all the software work could surely be done by specially designed hardware. Furthermore, Feldkamptype recon struction is highly parallel in its computational structure. With rapid development of computing technologies, real time conebeam tomography should be a reality in near future. Our fast reconstruction techniques may be adapted for iterative conebeam reconstruction as well (Wang et al., 1996, 1999). Currently available noniterative conebeam al gorithms require that projections should not be truncated along at least one direction. Therefore, satisfactory cone beam reconstruction with these algorithms is impossible in
22 Ang Shih et al.
Figure 11. a,b: Two rendered views of a small electrolytic capacitor, which was scanned with our prototype microtomographic system and reconstructed using our tablemapping algorithm.
cases where objects contain Xray opaque components and/ or are larger than the conebeam aperture defined by effec tive detection area and Xray source position. Recently, it was demonstrated that both EM and ARTtype algorithms are effective for metal artifact reduction and local region reconstruction. These iterative algorithms share a fully par allel reprojection and backprojection format, and can be efficiently implemented using the techniques we developed in this article. The fast tablemapping reconstruction algorithm has simplified the backprojection process to noncalculation in tensive steps. Therefore, the reconstruction procedure would not require highspeed floating point calculation anymore; in fact, in our experiment, even though our work station has three times the GFLOP performance. Our gen eralized personal computer outperforms our 10 times ex pensive workstation. Furthermore, the noncalculation in tensive algorithm is a parallel process and pipeline architecture friendly algorithm for load distribution imple mentation. On the other hand, the tablemapping algo rithm has less advantage on an highperformance worksta tion, due to the algorithm not depending on fast processors. In conclusion, we have significantly accelerated the generalized Feldkamp algorithm using curved voxels and mapping tables, and improved the reconstruction efficiency by an order of magnitude relative to a direct implementa tion, in comparison with an incremental implementation of the standard algorithm which is, to our best knowledge, the fastest method (He et al., 1993). The tablemapping algo rithm improved the reconstruction efficient more than a factor of two. The tablemapping algorithm accelerates the generalized computer to provide a lowcost solution for computer tomography reconstruction. Using our tech
niques, a 256voxel cube from 100 projections of 256 by 256 detectors can be reconstructed within 2 min on an Intel Pentium II 233MHz personal computer. With our method, computationally intensive backprojection has been turned into simple mapping, which allows even faster hard ware implementation. With everimproving computing re sources, we believe that realtime or near realtime cone beam tomography will play a substantial role in various applications.
ACKNOWLEDGMENTS
The authors thank Mr. W. Schulze for excellent machining work, Mr. C. Shen for technical assistance, and Dr. Carl Crawford for helpful discussion. This project was supported in part by the Academic Development Fund of the State University of New York.
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