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Visualization and analysis of 3D microscopic images.

Long F, Zhou J, Peng H - PLoS Comput. Biol. (2012)

Bottom Line: In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images.In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets.We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

View Article: PubMed Central - PubMed

Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America.

ABSTRACT
In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

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Vaa3D visualization of 4D and 5D microscopic images, as well as associated 3D surface objects, of different model animals.(a) The hierarchical (multi-scale) 3D visualization of a fluorescent confocal image of fruit fly (Drosophila melanogaster) brain using both global and local 3D viewers. In the global viewer, different brain compartments rendered using surface meshes (in different colors) are overlaid on top of the 3D volume of a fruit fly brain. When an image is very large, the global viewer can serve for navigation purpose. A user can quickly define any 3D local region of interest and display it in a local 3D viewer using full resolution. In this example, the brain voxels can be rendered in a different color from the global viewer, while the user can optionally display other surface objects, such as the single 3D-reconstructed neuron (yellow). (b) 5D visualization of a series of multi-color 3D image stacks of C. elegans (courtesy of Rex Kerr). Different 3D viewing angles can be adjusted in real-time in Vaa3D, with which the user can freely change the displayed time point (bottom).
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pcbi-1002519-g002: Vaa3D visualization of 4D and 5D microscopic images, as well as associated 3D surface objects, of different model animals.(a) The hierarchical (multi-scale) 3D visualization of a fluorescent confocal image of fruit fly (Drosophila melanogaster) brain using both global and local 3D viewers. In the global viewer, different brain compartments rendered using surface meshes (in different colors) are overlaid on top of the 3D volume of a fruit fly brain. When an image is very large, the global viewer can serve for navigation purpose. A user can quickly define any 3D local region of interest and display it in a local 3D viewer using full resolution. In this example, the brain voxels can be rendered in a different color from the global viewer, while the user can optionally display other surface objects, such as the single 3D-reconstructed neuron (yellow). (b) 5D visualization of a series of multi-color 3D image stacks of C. elegans (courtesy of Rex Kerr). Different 3D viewing angles can be adjusted in real-time in Vaa3D, with which the user can freely change the displayed time point (bottom).

Mentions: Live imaging experiments produce multi-time-point (MT) multi-color 3D image series (thus five-dimension [5D], see Table 1). In addition, when an image is large (e.g., 20 Gbytes/image), it is usually impractical and also unnecessary to load all image voxels in the computer memory and graphics card to visualize. Thus, there is a need to visualize an image dataset at multiple scales. The MT-MC-3D data sets, and multi-scale (MS) rendering (thus six-dimensional visualization [6D], see Table 1), impose significant challenges to current visualization hardware and software, due to the limited bandwidth between hard drives, computer memory, and graphics card. When the entire image series could be loaded in computer memory, Vaa3D could be used to produce real-time 5D or 6D rendering (Figure 2). Yet, in general they are unsolved problems for terabyte-sized image data sets.


Visualization and analysis of 3D microscopic images.

Long F, Zhou J, Peng H - PLoS Comput. Biol. (2012)

Vaa3D visualization of 4D and 5D microscopic images, as well as associated 3D surface objects, of different model animals.(a) The hierarchical (multi-scale) 3D visualization of a fluorescent confocal image of fruit fly (Drosophila melanogaster) brain using both global and local 3D viewers. In the global viewer, different brain compartments rendered using surface meshes (in different colors) are overlaid on top of the 3D volume of a fruit fly brain. When an image is very large, the global viewer can serve for navigation purpose. A user can quickly define any 3D local region of interest and display it in a local 3D viewer using full resolution. In this example, the brain voxels can be rendered in a different color from the global viewer, while the user can optionally display other surface objects, such as the single 3D-reconstructed neuron (yellow). (b) 5D visualization of a series of multi-color 3D image stacks of C. elegans (courtesy of Rex Kerr). Different 3D viewing angles can be adjusted in real-time in Vaa3D, with which the user can freely change the displayed time point (bottom).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375219&req=5

pcbi-1002519-g002: Vaa3D visualization of 4D and 5D microscopic images, as well as associated 3D surface objects, of different model animals.(a) The hierarchical (multi-scale) 3D visualization of a fluorescent confocal image of fruit fly (Drosophila melanogaster) brain using both global and local 3D viewers. In the global viewer, different brain compartments rendered using surface meshes (in different colors) are overlaid on top of the 3D volume of a fruit fly brain. When an image is very large, the global viewer can serve for navigation purpose. A user can quickly define any 3D local region of interest and display it in a local 3D viewer using full resolution. In this example, the brain voxels can be rendered in a different color from the global viewer, while the user can optionally display other surface objects, such as the single 3D-reconstructed neuron (yellow). (b) 5D visualization of a series of multi-color 3D image stacks of C. elegans (courtesy of Rex Kerr). Different 3D viewing angles can be adjusted in real-time in Vaa3D, with which the user can freely change the displayed time point (bottom).
Mentions: Live imaging experiments produce multi-time-point (MT) multi-color 3D image series (thus five-dimension [5D], see Table 1). In addition, when an image is large (e.g., 20 Gbytes/image), it is usually impractical and also unnecessary to load all image voxels in the computer memory and graphics card to visualize. Thus, there is a need to visualize an image dataset at multiple scales. The MT-MC-3D data sets, and multi-scale (MS) rendering (thus six-dimensional visualization [6D], see Table 1), impose significant challenges to current visualization hardware and software, due to the limited bandwidth between hard drives, computer memory, and graphics card. When the entire image series could be loaded in computer memory, Vaa3D could be used to produce real-time 5D or 6D rendering (Figure 2). Yet, in general they are unsolved problems for terabyte-sized image data sets.

Bottom Line: In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images.In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets.We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

View Article: PubMed Central - PubMed

Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America.

ABSTRACT
In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

Show MeSH