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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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Comparison between the vessel measure based TF shift [27] and the proposed interactive exploration. (a) 1D TF preset visualization, (b) close-up visualization of the area A and B shifted by the vesselness measure, (c) the TF shift applied to the area, (d) interactive editing results by the proposed framework for tracing specific dendric structures with lower intensity and (e) the TF shift.
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Fig7: Comparison between the vessel measure based TF shift [27] and the proposed interactive exploration. (a) 1D TF preset visualization, (b) close-up visualization of the area A and B shifted by the vesselness measure, (c) the TF shift applied to the area, (d) interactive editing results by the proposed framework for tracing specific dendric structures with lower intensity and (e) the TF shift.

Mentions: Next, we apply this method to the area with dendric structures. The eye direction (νeye) during volume rendering is set as + z. Figure 7(a) shows volume rendering results obtained with 1D TFs, which fails to visualize thin dendric structures with lower intensities. Here, we focus on visual exploration of the local area A and B. Figure 7(b) is visualized using previous method, in which we modify the TFs of the area based on the vesselness measure used by Lathen et al. [27] for the feature. Linear structures of low intensity appear and run over the xy plane around the dendrites, but only some of the structures can be distinguished. Because all linear structures in the data are highlighted as shown in Figure 7(c), it is hard to present the endpoints of one linear structure in a form visible to the eye. By applying the proposed method to this dendritic region, we attempt to observe structures in detail. Equation (10) and λratio are used for the feature to highlight the linear structures. The expression used in this experiment is given:Figure 7


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)

Comparison between the vessel measure based TF shift [27] and the proposed interactive exploration. (a) 1D TF preset visualization, (b) close-up visualization of the area A and B shifted by the vesselness measure, (c) the TF shift applied to the area, (d) interactive editing results by the proposed framework for tracing specific dendric structures with lower intensity and (e) the TF shift.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Comparison between the vessel measure based TF shift [27] and the proposed interactive exploration. (a) 1D TF preset visualization, (b) close-up visualization of the area A and B shifted by the vesselness measure, (c) the TF shift applied to the area, (d) interactive editing results by the proposed framework for tracing specific dendric structures with lower intensity and (e) the TF shift.
Mentions: Next, we apply this method to the area with dendric structures. The eye direction (νeye) during volume rendering is set as + z. Figure 7(a) shows volume rendering results obtained with 1D TFs, which fails to visualize thin dendric structures with lower intensities. Here, we focus on visual exploration of the local area A and B. Figure 7(b) is visualized using previous method, in which we modify the TFs of the area based on the vesselness measure used by Lathen et al. [27] for the feature. Linear structures of low intensity appear and run over the xy plane around the dendrites, but only some of the structures can be distinguished. Because all linear structures in the data are highlighted as shown in Figure 7(c), it is hard to present the endpoints of one linear structure in a form visible to the eye. By applying the proposed method to this dendritic region, we attempt to observe structures in detail. Equation (10) and λratio are used for the feature to highlight the linear structures. The expression used in this experiment is given:Figure 7

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