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Interactive visual exploration of overlapping similar structures for three-dimensional microscope images.

Nakao M, Takemoto S, Sugiura T, Sawada K, Kawakami R, Nemoto T, Matsuda T - BMC Bioinformatics (2014)

Bottom Line: However, because the emissions from fluorescent materials and the optical properties based on point spread functions affect the imaging results, the intensity value can differ locally, even in the same structure.Further, images obtained from brain tissues contain a variety of neural structures such as dendrites and axons with complex crossings and overlapping linear structures.A direct editing interface is also provided to specify both the target region and structures with characteristic features, where all manual operations can be performed on the rendered image.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto, Japan. megumi@i.kyoto-u.ac.jp.

ABSTRACT

Background: Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the transfer functions. However, because the emissions from fluorescent materials and the optical properties based on point spread functions affect the imaging results, the intensity value can differ locally, even in the same structure. Further, images obtained from brain tissues contain a variety of neural structures such as dendrites and axons with complex crossings and overlapping linear structures. In these cases, the transfer functions previously used fail to optimize image generation, making it difficult to explore the connectivity of these tissues.

Results: This paper proposes an interactive visual exploration method by which the transfer functions are modified locally and interactively based on multidimensional features in the images. A direct editing interface is also provided to specify both the target region and structures with characteristic features, where all manual operations can be performed on the rendered image. This method is demonstrated using two-photon microscope images acquired from living mice, and is shown to be an effective method for interactive visual exploration of overlapping similar structures.

Conclusions: An interactive visualization method was introduced for local improvement of visualization by volume rendering in two-photon microscope images containing regions in which linear nerve structures crisscross in a complex manner. The proposed method is characterized by the localized multidimensional transfer function and interface where the parameters can be determined by the user to suit their particular visualization requirements.

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Related in: MedlinePlus

Three-dimensional TF shift distribution globally computed based on (a) the orientation of the structures, (b) vertically overlapping structures and (c) locally selected by the user.
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Fig6: Three-dimensional TF shift distribution globally computed based on (a) the orientation of the structures, (b) vertically overlapping structures and (c) locally selected by the user.

Mentions: We now qualitatively examine the process of visualization by the proposed method by first discussing the validity of the calculated dF. The value of the feature at x0 is e′3(x0) = (−0.847, 0.527, 0.0650). The results of the visualization of all voxels having the dissimilarity of the feature with dF ≤ 0.5 are shown in Figure 6(a). The structures visualized in (a) are those in which the angle with e′3(x0) is within 60°. Figure 6(b) displays the vector e′3⊥(x0), which is perpendicular to e′3(x0) in the xy plane, showing the visualization results of all voxels with dF ≤ 0.5, and structures in which the angle with e′3⊥(x0) is within 60° are visualized. By calculating dF with the feature 60°, we find that each linear structure in a different direction can be separated. With the proposed method, the visualized area is limited by visualizing structures only within Ω after separating the visualization target structures from other structures by using dF. Figure 6(c) shows the shift Δ of the TF when the proposed method is tested with α = 10 and β = 6. Structures around the computer mouse cursor are visualized during the operation. Users can use the visualized structures as a guide and can interactively specify these structures targeted for visualization. We see that only TFs of the target structures can be modified by using dF within the visualized region Ω. Furthermore, the average frames per second for visualization is 53, confirming that the proposed method is interactive in practice.Figure 6


Interactive visual exploration of overlapping similar structures for three-dimensional microscope images.

Nakao M, Takemoto S, Sugiura T, Sawada K, Kawakami R, Nemoto T, Matsuda T - BMC Bioinformatics (2014)

Three-dimensional TF shift distribution globally computed based on (a) the orientation of the structures, (b) vertically overlapping structures and (c) locally selected by the user.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4279998&req=5

Fig6: Three-dimensional TF shift distribution globally computed based on (a) the orientation of the structures, (b) vertically overlapping structures and (c) locally selected by the user.
Mentions: We now qualitatively examine the process of visualization by the proposed method by first discussing the validity of the calculated dF. The value of the feature at x0 is e′3(x0) = (−0.847, 0.527, 0.0650). The results of the visualization of all voxels having the dissimilarity of the feature with dF ≤ 0.5 are shown in Figure 6(a). The structures visualized in (a) are those in which the angle with e′3(x0) is within 60°. Figure 6(b) displays the vector e′3⊥(x0), which is perpendicular to e′3(x0) in the xy plane, showing the visualization results of all voxels with dF ≤ 0.5, and structures in which the angle with e′3⊥(x0) is within 60° are visualized. By calculating dF with the feature 60°, we find that each linear structure in a different direction can be separated. With the proposed method, the visualized area is limited by visualizing structures only within Ω after separating the visualization target structures from other structures by using dF. Figure 6(c) shows the shift Δ of the TF when the proposed method is tested with α = 10 and β = 6. Structures around the computer mouse cursor are visualized during the operation. Users can use the visualized structures as a guide and can interactively specify these structures targeted for visualization. We see that only TFs of the target structures can be modified by using dF within the visualized region Ω. Furthermore, the average frames per second for visualization is 53, confirming that the proposed method is interactive in practice.Figure 6

Bottom Line: However, because the emissions from fluorescent materials and the optical properties based on point spread functions affect the imaging results, the intensity value can differ locally, even in the same structure.Further, images obtained from brain tissues contain a variety of neural structures such as dendrites and axons with complex crossings and overlapping linear structures.A direct editing interface is also provided to specify both the target region and structures with characteristic features, where all manual operations can be performed on the rendered image.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo, Kyoto, Japan. megumi@i.kyoto-u.ac.jp.

ABSTRACT

Background: Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the transfer functions. However, because the emissions from fluorescent materials and the optical properties based on point spread functions affect the imaging results, the intensity value can differ locally, even in the same structure. Further, images obtained from brain tissues contain a variety of neural structures such as dendrites and axons with complex crossings and overlapping linear structures. In these cases, the transfer functions previously used fail to optimize image generation, making it difficult to explore the connectivity of these tissues.

Results: This paper proposes an interactive visual exploration method by which the transfer functions are modified locally and interactively based on multidimensional features in the images. A direct editing interface is also provided to specify both the target region and structures with characteristic features, where all manual operations can be performed on the rendered image. This method is demonstrated using two-photon microscope images acquired from living mice, and is shown to be an effective method for interactive visual exploration of overlapping similar structures.

Conclusions: An interactive visualization method was introduced for local improvement of visualization by volume rendering in two-photon microscope images containing regions in which linear nerve structures crisscross in a complex manner. The proposed method is characterized by the localized multidimensional transfer function and interface where the parameters can be determined by the user to suit their particular visualization requirements.

Show MeSH
Related in: MedlinePlus