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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.


Cutaway section from 3D volume rendering of the in vivo mouse abdomen based on orthogonal SRR (a) with AR equal to 1 : 1 : 10 and single interpolated view (b). The solid arrow points to the wall of the stomach, dashed arrow to the kidney, and dotted arrow to the liver vasculature. Biological structures can be observed clearly in any oblique cutting plane of the SRR image as opposed to single 2D multislice image with linear interpolation.
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fig9: Cutaway section from 3D volume rendering of the in vivo mouse abdomen based on orthogonal SRR (a) with AR equal to 1 : 1 : 10 and single interpolated view (b). The solid arrow points to the wall of the stomach, dashed arrow to the kidney, and dotted arrow to the liver vasculature. Biological structures can be observed clearly in any oblique cutting plane of the SRR image as opposed to single 2D multislice image with linear interpolation.

Mentions: A 3D volume rendering of the SRR image of the live mouse is presented in Figure 9. Biological structures, such as the wall of the stomach, kidneys, and liver vasculature are clearly observed in all three image planes of the SRR image. A 3D volume rendering based on the sagitally acquired LR image with linear interpolation illustrates the loss of image quality in planes other than the primary HR acquisition plane. The streaking artifacts normally observed in the 2D slice view of the SRR images obtained from orthogonal acquisition are not observed in the volume rendered images. The total time to acquire all three LR image stacks used for the in vivo SRR was 45 minutes due to the respiratory and cardiac gating. A full 3D isotropic scan of this mouse would have taken more than 4 hrs with gating and would not be possible for live animal applications.


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)

Cutaway section from 3D volume rendering of the in vivo mouse abdomen based on orthogonal SRR (a) with AR equal to 1 : 1 : 10 and single interpolated view (b). The solid arrow points to the wall of the stomach, dashed arrow to the kidney, and dotted arrow to the liver vasculature. Biological structures can be observed clearly in any oblique cutting plane of the SRR image as opposed to single 2D multislice image with linear interpolation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig9: Cutaway section from 3D volume rendering of the in vivo mouse abdomen based on orthogonal SRR (a) with AR equal to 1 : 1 : 10 and single interpolated view (b). The solid arrow points to the wall of the stomach, dashed arrow to the kidney, and dotted arrow to the liver vasculature. Biological structures can be observed clearly in any oblique cutting plane of the SRR image as opposed to single 2D multislice image with linear interpolation.
Mentions: A 3D volume rendering of the SRR image of the live mouse is presented in Figure 9. Biological structures, such as the wall of the stomach, kidneys, and liver vasculature are clearly observed in all three image planes of the SRR image. A 3D volume rendering based on the sagitally acquired LR image with linear interpolation illustrates the loss of image quality in planes other than the primary HR acquisition plane. The streaking artifacts normally observed in the 2D slice view of the SRR images obtained from orthogonal acquisition are not observed in the volume rendered images. The total time to acquire all three LR image stacks used for the in vivo SRR was 45 minutes due to the respiratory and cardiac gating. A full 3D isotropic scan of this mouse would have taken more than 4 hrs with gating and would not be possible for live animal applications.

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.