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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.

Show MeSH
Apical dendric region represented using (a) TF preset visualization, (b) MIP-based DVR, (c) surface reconstruction by neuron tracing, (d) TF shift applied to the low contrast area locally and interactively and (e) the improved DVR result, which clarifies the connectivity of neural structures.
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Fig8: Apical dendric region represented using (a) TF preset visualization, (b) MIP-based DVR, (c) surface reconstruction by neuron tracing, (d) TF shift applied to the low contrast area locally and interactively and (e) the improved DVR result, which clarifies the connectivity of neural structures.

Mentions: Finally, a visualization experiment targeting the apical dendritic region is performed. We applied our data to the Vaa3D visualization software employing virtual finger (VF) techniques [7,8] and compared the visualization results. We tried the visualization functions and the tracing tool in the Vaa3D software, and finally decided to focus on the two functions of MIP (maximum intensity projection) based direct volume rendering (DVR) and Vaa3D-Neuron2 auto-tracing for comparison with our local TF shift techniques. Our visualization targets are the dendric structures possessing a lower intensity located under the blood vessels. Although there are linear dendric structures that cross the blood vessels in FigureĀ 8(a), their connectivity and distribution are not clear with the 1D preset TF.Figure 8


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)

Apical dendric region represented using (a) TF preset visualization, (b) MIP-based DVR, (c) surface reconstruction by neuron tracing, (d) TF shift applied to the low contrast area locally and interactively and (e) the improved DVR result, which clarifies the connectivity of neural structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig8: Apical dendric region represented using (a) TF preset visualization, (b) MIP-based DVR, (c) surface reconstruction by neuron tracing, (d) TF shift applied to the low contrast area locally and interactively and (e) the improved DVR result, which clarifies the connectivity of neural structures.
Mentions: Finally, a visualization experiment targeting the apical dendritic region is performed. We applied our data to the Vaa3D visualization software employing virtual finger (VF) techniques [7,8] and compared the visualization results. We tried the visualization functions and the tracing tool in the Vaa3D software, and finally decided to focus on the two functions of MIP (maximum intensity projection) based direct volume rendering (DVR) and Vaa3D-Neuron2 auto-tracing for comparison with our local TF shift techniques. Our visualization targets are the dendric structures possessing a lower intensity located under the blood vessels. Although there are linear dendric structures that cross the blood vessels in FigureĀ 8(a), their connectivity and distribution are not clear with the 1D preset TF.Figure 8

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