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Episcopic 3D Imaging Methods: Tools for Researching Gene Function.

Weninger WJ, Geyer SH - Curr. Genomics (2008)

Bottom Line: The most advanced are capable of generating high-resolution volume data (voxel sizes from 0.5x0.5x1 microm upwards) of small to large embryos of model organisms and tissue samples.Beside anatomy and tissue architecture, gene expression and gene product patterns can be three dimensionally analyzed in their precise anatomical and histological context with the aid of whole mount in situ hybridization or whole mount immunohistochemical staining techniques.Such applications, however, are not yet routine and currently only preliminary results are available.

View Article: PubMed Central - PubMed

Affiliation: IMG, Centre for Anatomy and Cell Biology, Medical University of Vienna, Waehringer Str. 13, A-1090 Vienna, Austria.

ABSTRACT
This work aims at describing episcopic 3D imaging methods and at discussing how these methods can contribute to researching the genetic mechanisms driving embryogenesis and tissue remodelling, and the genesis of pathologies. Several episcopic 3D imaging methods exist. The most advanced are capable of generating high-resolution volume data (voxel sizes from 0.5x0.5x1 microm upwards) of small to large embryos of model organisms and tissue samples. Beside anatomy and tissue architecture, gene expression and gene product patterns can be three dimensionally analyzed in their precise anatomical and histological context with the aid of whole mount in situ hybridization or whole mount immunohistochemical staining techniques. Episcopic 3D imaging techniques were and are employed for analyzing the precise morphological phenotype of experimentally malformed, randomly produced, or genetically engineered embryos of biomedical model organisms. It has been shown that episcopic 3D imaging also fits for describing the spatial distribution of genes and gene products during embryogenesis, and that it can be used for analyzing tissue samples of adult model animals and humans. The latter offers the possibility to use episcopic 3D imaging techniques for researching the causality and treatment of pathologies or for staging cancer. Such applications, however, are not yet routine and currently only preliminary results are available. We conclude that, although episcopic 3D imaging is in its very beginnings, it represents an upcoming methodology, which in short terms will become an indispensable tool for researching the genetic regulation of embryo development as well as the genesis of malformations and diseases.

No MeSH data available.


Related in: MedlinePlus

From pixel to voxel. a. Schematic drawing of three subsequent two-dimensional (2D) images. Each image consists of 10 x 13 pixels. b. Volume data created from images of 1 µm thick sections. The voxels are cubic, because the distance between the images is the same as the length of the x and y coordinate of the pixels of the 2D images. c. Volume data created from images of 7 µm thick sections. While the 2D resolution (resolution of the 2D images) is relatively high, the 3D resolution (resolution of the volume data set) is low.
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Figure 3: From pixel to voxel. a. Schematic drawing of three subsequent two-dimensional (2D) images. Each image consists of 10 x 13 pixels. b. Volume data created from images of 1 µm thick sections. The voxels are cubic, because the distance between the images is the same as the length of the x and y coordinate of the pixels of the 2D images. c. Volume data created from images of 7 µm thick sections. While the 2D resolution (resolution of the 2D images) is relatively high, the 3D resolution (resolution of the volume data set) is low.

Mentions: After data generation, the stack of aligned episcopic images is converted into a volume data set. The dimension of one voxel is defined by the resolution of the captured block face image (its Pixel size) and the thickness of the slice of embedding medium removed (Fig. 3). Virtual volume or surface rendered 3D models can be created and visualized with state of the art 3D visualization software packages (e.g., Amira (Visage Imaging), Volocity (Improvision), SURFdriver (www.surfdriver.com), Osirix (www.osirix-viewer.com)).


Episcopic 3D Imaging Methods: Tools for Researching Gene Function.

Weninger WJ, Geyer SH - Curr. Genomics (2008)

From pixel to voxel. a. Schematic drawing of three subsequent two-dimensional (2D) images. Each image consists of 10 x 13 pixels. b. Volume data created from images of 1 µm thick sections. The voxels are cubic, because the distance between the images is the same as the length of the x and y coordinate of the pixels of the 2D images. c. Volume data created from images of 7 µm thick sections. While the 2D resolution (resolution of the 2D images) is relatively high, the 3D resolution (resolution of the volume data set) is low.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2682936&req=5

Figure 3: From pixel to voxel. a. Schematic drawing of three subsequent two-dimensional (2D) images. Each image consists of 10 x 13 pixels. b. Volume data created from images of 1 µm thick sections. The voxels are cubic, because the distance between the images is the same as the length of the x and y coordinate of the pixels of the 2D images. c. Volume data created from images of 7 µm thick sections. While the 2D resolution (resolution of the 2D images) is relatively high, the 3D resolution (resolution of the volume data set) is low.
Mentions: After data generation, the stack of aligned episcopic images is converted into a volume data set. The dimension of one voxel is defined by the resolution of the captured block face image (its Pixel size) and the thickness of the slice of embedding medium removed (Fig. 3). Virtual volume or surface rendered 3D models can be created and visualized with state of the art 3D visualization software packages (e.g., Amira (Visage Imaging), Volocity (Improvision), SURFdriver (www.surfdriver.com), Osirix (www.osirix-viewer.com)).

Bottom Line: The most advanced are capable of generating high-resolution volume data (voxel sizes from 0.5x0.5x1 microm upwards) of small to large embryos of model organisms and tissue samples.Beside anatomy and tissue architecture, gene expression and gene product patterns can be three dimensionally analyzed in their precise anatomical and histological context with the aid of whole mount in situ hybridization or whole mount immunohistochemical staining techniques.Such applications, however, are not yet routine and currently only preliminary results are available.

View Article: PubMed Central - PubMed

Affiliation: IMG, Centre for Anatomy and Cell Biology, Medical University of Vienna, Waehringer Str. 13, A-1090 Vienna, Austria.

ABSTRACT
This work aims at describing episcopic 3D imaging methods and at discussing how these methods can contribute to researching the genetic mechanisms driving embryogenesis and tissue remodelling, and the genesis of pathologies. Several episcopic 3D imaging methods exist. The most advanced are capable of generating high-resolution volume data (voxel sizes from 0.5x0.5x1 microm upwards) of small to large embryos of model organisms and tissue samples. Beside anatomy and tissue architecture, gene expression and gene product patterns can be three dimensionally analyzed in their precise anatomical and histological context with the aid of whole mount in situ hybridization or whole mount immunohistochemical staining techniques. Episcopic 3D imaging techniques were and are employed for analyzing the precise morphological phenotype of experimentally malformed, randomly produced, or genetically engineered embryos of biomedical model organisms. It has been shown that episcopic 3D imaging also fits for describing the spatial distribution of genes and gene products during embryogenesis, and that it can be used for analyzing tissue samples of adult model animals and humans. The latter offers the possibility to use episcopic 3D imaging techniques for researching the causality and treatment of pathologies or for staging cancer. Such applications, however, are not yet routine and currently only preliminary results are available. We conclude that, although episcopic 3D imaging is in its very beginnings, it represents an upcoming methodology, which in short terms will become an indispensable tool for researching the genetic regulation of embryo development as well as the genesis of malformations and diseases.

No MeSH data available.


Related in: MedlinePlus