Reconstruction and exploration of three-dimensional confocal microscopy data in an immersive virtual environment

Ai, Zhuming; Xue, Chen; Rasmussen, Mary Lou; Folberg, Robert

doi:10.1016/j.compmedimag.2005.01.003

Cited by 7 publications

(5 citation statements)

References 11 publications

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“…1). 7,25 The currently available alternative to volumetric-assisted construction requires the insertion of fiduciary markers into tissue that may distort the tissue. Second, if one reconstructs tissue without considering the information contained within the thickness of each serial section, then information (resolution) is lost: the thicker the section used for reconstruction purposes, the more the information lost.…”

Section: Discussionmentioning

confidence: 99%

“…In our previous work 7, 25 and in this study, we selected a manual method to align volumetric confocal data with the confocal stacks using the ImmersaDesk visualization environment. It is now possible to port much of the functionality of the ImmersaDesk to individual computer workstations (unpublished data).…”

Section: Discussionmentioning

confidence: 99%

“…We use automated image reconstruction (AIR) software to apply a 2D nonlinear warping algorithm to match the bottom image of the z-series from layer 1 with the top image from the z-series of layer 2, resulting in a 2D nth-order polynomial transformation that is expanded to 3D (n+1)th order as described in detail elsewhere. 25 With the known boundary conditions and some reasonable assumptions, all the coefficients in the (n+1)th-order polynomial can be determined, and with this nonlinear transformation, the z-series from adjacent serial sections can be warped to connect to each other smoothly. The size of each reconstructed volume was restrained to less than …”

Section: Three-dimensional Reconstructionsmentioning

confidence: 99%

See 2 more Smart Citations

Comparing Vasculogenic Mimicry With Endothelial Cell-lined Vessels: Techniques for 3D Reconstruction and Quantitative Analysis of Tissue Components from Archival Paraffin Blocks

Lin

Lee

et al. 2007

Applied Immunohistochemistry &Amp; Molecular Morphology

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We previously described techniques to generate 3-dimensional reconstructions of the tumor microcirculation using immunofluorescence histochemistry and laser scanning confocal microscopy on serial sections from archival formalin-fixed, paraffin-embedded tissues. By aligning sequential z-stacks in an immersive visualization environment (ImmersaDesk), the need to insert fiduciary markers into tissue was eliminated. In this study, we developed methods to stitch overlapping confocal z-series together to extend the surface area of interest well beyond that captured by the confocal microscope objective and developed methods to quantify the distribution of markers of interest in 3 dimensions. These techniques were applied to the problem of comparing the surface area of nonendothelial cell-lined, laminin-rich looping vasculogenic mimicry (VM) patterns that are known to transmit fluid, with the surface area of endothelial cell-lined vessels in metastatic uveal melanoma to the liver in 3 dimensions. After labeling sections with antibodies to CD34 and laminin, the surface area of VM patterns to vessels was calculated by segmenting out structures that labeled with laminin but not with CD34 from those structures labeling with CD34, or CD34 and laminin. In metastatic uveal melanoma tissues featuring colocalization of high microvascular density [66.4 microvessels adjusted for 0.313 mm2 area (range 56.7 to 72.7)] and VM patterning, the surface area of VM patterns was 11.6-fold greater (range 10.8 to 14.1) than the surface provided by CD34-positive vessels. These methods may be extended to visualize and quantify molecular markers in 3 dimensions in a variety of pathologic entities from archival paraffin-embedded tissues.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Three-dimensional Reconstructionsmentioning

confidence: 99%

See 1 more Smart Citation

Comparing Vasculogenic Mimicry With Endothelial Cell-lined Vessels: Techniques for 3D Reconstruction and Quantitative Analysis of Tissue Components from Archival Paraffin Blocks

Lin

Lee

et al. 2007

Applied Immunohistochemistry &Amp; Molecular Morphology

Self Cite

View full text Add to dashboard Cite

show abstract

“…On the other hand, immersive visualization systems, where a user walks into the data volume/model, may enable one to analyze the data like playing a video game. A few systems, such as NCMIR's ATLAS in silico system that utilizes CalIT2’s 100-million-pixel autosterographic display (West, 2007 ), the ImmersaDesk TM system (Ai et al , 2005 ), etc., support such immersive visualization, which requires virtual reality methods.…”

Section: Critical Techniquesmentioning

confidence: 99%

Bioimage informatics: a new area of engineering biology

2008

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In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called ‘bioimage informatics’. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.Contact: pengh@janelia.hhmi.orgSupplementary information: Supplementary data are available at Bioinformatics online.

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“…A more common approach is performing a manual registration (Capek et al, 2009) between volumes or using sophisticated viewing software that allows for the stitching of volumes interactively (Ai et al, 2005). The volume transformation used to align serial sections is generally a 2D transform, which can be a simple global affine transformation (Lee and Bajcsy, 2008), a polynomial warping (Ai et al, 2005), or a more elaborate spline solution, as done for the elastic registration in Capek et al (2009). However, with thick section volume reconstruction, one must address carefully the issues of tissue unevenness, specimen orientation, and out-of-plane distortions.…”

Section: Introductionmentioning

confidence: 99%

Three-Dimensional Reconstruction of Serial Mouse Brain Sections: Solution for Flattening High-Resolution Large-Scale Mosaics

Berlanga¹,

Phan²,

Bushong³

et al. 2011

Front. Neuroanat.

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Recent advances in high-throughput technology facilitate massive data collection and sharing, enabling neuroscientists to explore the brain across a large range of spatial scales. One such form of high-throughput data collection is the construction of large-scale mosaic volumes using light microscopy (Chow et al., 2006; Price et al., 2006). With this technology, researchers can collect and analyze high-resolution digitized volumes of whole brain sections down to 0.2 μm. However, until recently, scientists lacked the tools to easily handle these large high-resolution datasets. Furthermore, artifacts resulting from specimen preparation limited volume reconstruction using this technique to only a single tissue section. In this paper, we carefully describe the steps we used to digitally reconstruct a series of consecutive mouse brain sections labeled with three stains, a stain for blood vessels (DiI), a nuclear stain (TO-PRO-3), and a myelin stain (FluoroMyelin). These stains label important neuroanatomical landmarks that are used for stacking the serial sections during reconstruction. In addition, we show that the use of two software applications, ir-Tweak and Mogrifier, in conjunction with a volume flattening procedure enable scientists to adeptly work with digitized volumes despite tears and thickness variations within tissue sections. These applications make processing large-scale brain mosaics more efficient. When used in combination with new database resources, these brain maps should allow researchers to extend the lifetime of their specimens indefinitely by preserving them in digital form, making them available for future analyses as our knowledge in the field of neuroscience continues to expand.

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Reconstruction and exploration of three-dimensional confocal microscopy data in an immersive virtual environment

Cited by 7 publications

References 11 publications

Comparing Vasculogenic Mimicry With Endothelial Cell-lined Vessels: Techniques for 3D Reconstruction and Quantitative Analysis of Tissue Components from Archival Paraffin Blocks

Comparing Vasculogenic Mimicry With Endothelial Cell-lined Vessels: Techniques for 3D Reconstruction and Quantitative Analysis of Tissue Components from Archival Paraffin Blocks

Bioimage informatics: a new area of engineering biology

Three-Dimensional Reconstruction of Serial Mouse Brain Sections: Solution for Flattening High-Resolution Large-Scale Mosaics

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