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Comparison of super resolution reconstruction acquisition geometries for use in mouse phenotyping.

Manivannan N, Clymer BD, Bratasz A, Powell KA - Int J Biomed Imaging (2013)

Bottom Line: In this study, the effects of using three different low-resolution acquisition geometries (orthogonal, rotational, and shifted) on SRR images were evaluated and compared to a known standard.The results of the study indicate that super resolution reconstructed images based on orthogonally acquired low-resolution images resulted in reconstructed images with higher SNR and CNR in less acquisition time than those based on rotational and shifted acquisition geometries.However, interpolation artifacts were observed in SRR images based on orthogonal acquisition geometry, particularly when the slice thickness was greater than six times the inplane voxel size.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA.

ABSTRACT
3D isotropic imaging at high spatial resolution (30-100 microns) is important for comparing mouse phenotypes. 3D imaging at high spatial resolutions is limited by long acquisition times and is not possible in many in vivo settings. Super resolution reconstruction (SRR) is a postprocessing technique that has been proposed to improve spatial resolution in the slice-select direction using multiple 2D multislice acquisitions. Any 2D multislice acquisition can be used for SRR. In this study, the effects of using three different low-resolution acquisition geometries (orthogonal, rotational, and shifted) on SRR images were evaluated and compared to a known standard. Iterative back projection was used for the reconstruction of all three acquisition geometries. The results of the study indicate that super resolution reconstructed images based on orthogonally acquired low-resolution images resulted in reconstructed images with higher SNR and CNR in less acquisition time than those based on rotational and shifted acquisition geometries. However, interpolation artifacts were observed in SRR images based on orthogonal acquisition geometry, particularly when the slice thickness was greater than six times the inplane voxel size. Reconstructions based on rotational geometry appeared smoother than those based on orthogonal geometry, but they required two times longer to acquire than the orthogonal LR images.

No MeSH data available.


2D slice images (image plane represented is orthogonal to the long axis of the tube which is placed along Y-axis in Figure 2(a)) of resolution phantom where the long axis of the tubes is orthogonal to the acquisition plane, and LR image stacks were collected with a voxel AR of 1 : 1 : 5: (a) interpolated, (b) shifted, (c) rotational, (d) orthogonal, (e) inplane, and (f) line plot, and where the long axis of the tubes is oblique to the acquisition plane: (g) interpolated, (h) shifted, (i) rotational, (j) orthogonal, (k) inplane, and (l) line plot.
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fig5: 2D slice images (image plane represented is orthogonal to the long axis of the tube which is placed along Y-axis in Figure 2(a)) of resolution phantom where the long axis of the tubes is orthogonal to the acquisition plane, and LR image stacks were collected with a voxel AR of 1 : 1 : 5: (a) interpolated, (b) shifted, (c) rotational, (d) orthogonal, (e) inplane, and (f) line plot, and where the long axis of the tubes is oblique to the acquisition plane: (g) interpolated, (h) shifted, (i) rotational, (j) orthogonal, (k) inplane, and (l) line plot.

Mentions: Short-axis images of the resolution phantom (voxel AR = 1 : 1 : 5) where the long axis of the tubes were positioned along the Y-axis of Figure 2 are shown in Figures 5(a)–5(e). The lack of resolution in the slice-select direction is apparent in Figure 5(a), where the 2D images are acquired at a slice thickness greater than the distance between the tubes, and linear interpolation is used for reconstruction. Figures 5(b)–5(d) are the corresponding short axis images from the SRR images based on shifted, rotated, and orthogonal acquisition geometries, respectively. The five tubes are resolved in the SRR images based on all three acquisition geometries, however a significant blurring is observed in the slice-select direction for the SRR image based on parallel shifts (Figure 5(b)) and to a lesser extent for the SRR image based on rotational acquisition (Figure 5(c)). The SRR image based on orthogonal acquisition (Figure 5(d)) reproduced the five tubes with the least amount of blurring artifact and looked similar to that observed in the inplane short-axis image (Figure 5(e)), where the sampling rate is great enough to resolve the tubes in the image. The intensity line plot shown in Figure 5(f) illustrates a decrease in peak intensities in the SRR images relative to that observed for the inplane image, with the least amount of change observed in the SRR image based on the orthogonal acquisition geometry. Similar results were observed for the SRR HR images when the LR image stacks were collected with a voxel AR of 1 : 1 : 10 (Figure 6).


Comparison of super resolution reconstruction acquisition geometries for use in mouse phenotyping.

Manivannan N, Clymer BD, Bratasz A, Powell KA - Int J Biomed Imaging (2013)

2D slice images (image plane represented is orthogonal to the long axis of the tube which is placed along Y-axis in Figure 2(a)) of resolution phantom where the long axis of the tubes is orthogonal to the acquisition plane, and LR image stacks were collected with a voxel AR of 1 : 1 : 5: (a) interpolated, (b) shifted, (c) rotational, (d) orthogonal, (e) inplane, and (f) line plot, and where the long axis of the tubes is oblique to the acquisition plane: (g) interpolated, (h) shifted, (i) rotational, (j) orthogonal, (k) inplane, and (l) line plot.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3794539&req=5

fig5: 2D slice images (image plane represented is orthogonal to the long axis of the tube which is placed along Y-axis in Figure 2(a)) of resolution phantom where the long axis of the tubes is orthogonal to the acquisition plane, and LR image stacks were collected with a voxel AR of 1 : 1 : 5: (a) interpolated, (b) shifted, (c) rotational, (d) orthogonal, (e) inplane, and (f) line plot, and where the long axis of the tubes is oblique to the acquisition plane: (g) interpolated, (h) shifted, (i) rotational, (j) orthogonal, (k) inplane, and (l) line plot.
Mentions: Short-axis images of the resolution phantom (voxel AR = 1 : 1 : 5) where the long axis of the tubes were positioned along the Y-axis of Figure 2 are shown in Figures 5(a)–5(e). The lack of resolution in the slice-select direction is apparent in Figure 5(a), where the 2D images are acquired at a slice thickness greater than the distance between the tubes, and linear interpolation is used for reconstruction. Figures 5(b)–5(d) are the corresponding short axis images from the SRR images based on shifted, rotated, and orthogonal acquisition geometries, respectively. The five tubes are resolved in the SRR images based on all three acquisition geometries, however a significant blurring is observed in the slice-select direction for the SRR image based on parallel shifts (Figure 5(b)) and to a lesser extent for the SRR image based on rotational acquisition (Figure 5(c)). The SRR image based on orthogonal acquisition (Figure 5(d)) reproduced the five tubes with the least amount of blurring artifact and looked similar to that observed in the inplane short-axis image (Figure 5(e)), where the sampling rate is great enough to resolve the tubes in the image. The intensity line plot shown in Figure 5(f) illustrates a decrease in peak intensities in the SRR images relative to that observed for the inplane image, with the least amount of change observed in the SRR image based on the orthogonal acquisition geometry. Similar results were observed for the SRR HR images when the LR image stacks were collected with a voxel AR of 1 : 1 : 10 (Figure 6).

Bottom Line: In this study, the effects of using three different low-resolution acquisition geometries (orthogonal, rotational, and shifted) on SRR images were evaluated and compared to a known standard.The results of the study indicate that super resolution reconstructed images based on orthogonally acquired low-resolution images resulted in reconstructed images with higher SNR and CNR in less acquisition time than those based on rotational and shifted acquisition geometries.However, interpolation artifacts were observed in SRR images based on orthogonal acquisition geometry, particularly when the slice thickness was greater than six times the inplane voxel size.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA.

ABSTRACT
3D isotropic imaging at high spatial resolution (30-100 microns) is important for comparing mouse phenotypes. 3D imaging at high spatial resolutions is limited by long acquisition times and is not possible in many in vivo settings. Super resolution reconstruction (SRR) is a postprocessing technique that has been proposed to improve spatial resolution in the slice-select direction using multiple 2D multislice acquisitions. Any 2D multislice acquisition can be used for SRR. In this study, the effects of using three different low-resolution acquisition geometries (orthogonal, rotational, and shifted) on SRR images were evaluated and compared to a known standard. Iterative back projection was used for the reconstruction of all three acquisition geometries. The results of the study indicate that super resolution reconstructed images based on orthogonally acquired low-resolution images resulted in reconstructed images with higher SNR and CNR in less acquisition time than those based on rotational and shifted acquisition geometries. However, interpolation artifacts were observed in SRR images based on orthogonal acquisition geometry, particularly when the slice thickness was greater than six times the inplane voxel size. Reconstructions based on rotational geometry appeared smoother than those based on orthogonal geometry, but they required two times longer to acquire than the orthogonal LR images.

No MeSH data available.