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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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3D image visualization and analysis for measuring single-cell gene expression of C. elegans.(a) Tri-view display of a confocal image of C. elegans (L1 stage). Green: DAPI staining (pseudo-colored); red: myo3:GFP labeled muscle cells. (b) Tri-view display of the 3D watershed segmented nuclei of (a). The co-localized image objects are indicated by crosses (white). (c) A spreadsheet display of 3D measured gene expression of various cells. All sub-figures are produced using VANO [39], a 3D annotation tool.
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pcbi-1002519-g003: 3D image visualization and analysis for measuring single-cell gene expression of C. elegans.(a) Tri-view display of a confocal image of C. elegans (L1 stage). Green: DAPI staining (pseudo-colored); red: myo3:GFP labeled muscle cells. (b) Tri-view display of the 3D watershed segmented nuclei of (a). The co-localized image objects are indicated by crosses (white). (c) A spreadsheet display of 3D measured gene expression of various cells. All sub-figures are produced using VANO [39], a 3D annotation tool.

Mentions: In many biological applications, different image analysis techniques need to be used as a whole pipeline. For instance, for profiling the gene expression at the single nucleus resolution of Caenorhabditis elegans[4], laser scanning microscopic images of this animal are first straightened (Figure 3a) [40], which can be categorized as a registration step. Then, C. elegans cells that are stained using DAPI are segmented (Figure 3b) using an adaptive 3D watershed algorithm. Cells are then recognized (Figure 3) based on their relative location patterns in the 3D standardized space. Once the cell identities are determined, quantifying the gene expression is as simple as computing the normalized intensity within the nucleus region. The segmentation and recognition steps can also be unified using a recent approach of atlas-to-image deforming model [38].


Visualization and analysis of 3D microscopic images.

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

3D image visualization and analysis for measuring single-cell gene expression of C. elegans.(a) Tri-view display of a confocal image of C. elegans (L1 stage). Green: DAPI staining (pseudo-colored); red: myo3:GFP labeled muscle cells. (b) Tri-view display of the 3D watershed segmented nuclei of (a). The co-localized image objects are indicated by crosses (white). (c) A spreadsheet display of 3D measured gene expression of various cells. All sub-figures are produced using VANO [39], a 3D annotation tool.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002519-g003: 3D image visualization and analysis for measuring single-cell gene expression of C. elegans.(a) Tri-view display of a confocal image of C. elegans (L1 stage). Green: DAPI staining (pseudo-colored); red: myo3:GFP labeled muscle cells. (b) Tri-view display of the 3D watershed segmented nuclei of (a). The co-localized image objects are indicated by crosses (white). (c) A spreadsheet display of 3D measured gene expression of various cells. All sub-figures are produced using VANO [39], a 3D annotation tool.
Mentions: In many biological applications, different image analysis techniques need to be used as a whole pipeline. For instance, for profiling the gene expression at the single nucleus resolution of Caenorhabditis elegans[4], laser scanning microscopic images of this animal are first straightened (Figure 3a) [40], which can be categorized as a registration step. Then, C. elegans cells that are stained using DAPI are segmented (Figure 3b) using an adaptive 3D watershed algorithm. Cells are then recognized (Figure 3) based on their relative location patterns in the 3D standardized space. Once the cell identities are determined, quantifying the gene expression is as simple as computing the normalized intensity within the nucleus region. The segmentation and recognition steps can also be unified using a recent approach of atlas-to-image deforming model [38].

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