3D Visualization of Maize Stem by MRI Technology

2001 ◽  
Vol 7 (S2) ◽  
pp. 100-101
Author(s):  
P. C. Cheng ◽  
J. H. Chen ◽  
S. C. Hwang ◽  
C. K. Sun ◽  
D. B. Walden ◽  
...  
Keyword(s):  
Soft Tissues ◽  
Sweet Corn ◽  
3D Visualization ◽  
Spin Echo ◽  
Three Dimensional ◽  
Slice Thickness ◽  
Volumetric Imaging ◽  
Dimensional Reconstruction ◽  
Inner Diameter ◽  
Imaging Artifact

Recent development in confocal and multi-photon microscopy allows 3D imaging of plant tissue in high resolution. However, other than physical sectioning, macroscopical study of plant organs in 3D remains a difficult task. Among various available technologies for macroscopical imaging (e.g., Xray macro-tomography, optical coherent tomography and MRI), MRI is an ideal choice for its contrasting modality in volumetric imaging of soft tissues. A 3T Biospect MRI system (Brucker, Germany)(FIG 1) equipped with a 6cm inner diameter micro-quadrature coil (FIG 2) for RF transmission and reception of MRI signals was used in this study. Spin echo based RARE sequence was used to obtain T2 weighted images with TR/TE = 3160.5/58.5ms and field-of-view of 1.67cm × 1.67cm (256 × 256 pixels) at a slice thickness of 0.8mm. This corresponds to a voxel size of 65 × 65 × 800μm. Data was obtained within 1/2 hour with number-of-excitations (nex) set at 16. Figure 4 (a-x) shows a series of MRI sections through a stem node (the node below the main ear insertion) from field-grown maize (Zea mays, van Odyssey sweet corn). The stem was fixed in 1:3 EtOH/acetic acid, washed thoroughly in water prior to imaging. Air bubbles trapped in the tissue were removed by vacuuming, to avoid imaging artifact due to low magnetic susceptibility of air. Figure 5 (a-g) shows reconstructed longitudinal sections. Three-dimensional reconstruction (FIG. 3) was performed by using Vaytek VoxBlast™ and AutoQuant’s AutoVisulize 3D™ software. in combination with image segmentation and tracing tools, the MRI technology will greatly enhance our capability in the understanding of vascular architecture and its development in plants.

scholarly journals 3D visualization of macromolecule synthesis

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Timothy J Duerr ◽  
Ester Comellas ◽  
Eun Kyung Jeon ◽  
Johanna E Farkas ◽  
Marylou Joetzjer ◽  
...  
Keyword(s):  
3D Visualization ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Light Sheet ◽  
Macromolecular Synthesis ◽  
Volumetric Imaging ◽  
Processing Pipeline ◽  
Powerful Means

Measuring nascent macromolecular synthesis in vivo is key to understanding how cells and tissues progress through development and respond to external cues. Here we perform in vivo injection of alkyne- or azide-modified analogs of thymidine, uridine, methionine, and glucosamine to label nascent synthesis of DNA, RNA, protein, and glycosylation. Three-dimensional volumetric imaging of nascent macromolecule synthesis was performed in axolotl salamander tissue using whole-mount click chemistry-based fluorescent staining followed by light sheet fluorescent microscopy. We also developed an image processing pipeline for segmentation and classification of morphological regions of interest and individual cells, and we apply this pipeline to the regenerating humerus. We demonstrate our approach is sensitive to biological perturbations by measuring changes in DNA synthesis after limb denervation. This method provides a powerful means to quantitatively interrogate macromolecule synthesis in heterogenous tissues at the organ, cellular, and molecular levels of organization.

scholarly journals A 3D Visualization Method for Bladder Filling Examination Based on EIT

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Wei He ◽  
Peng Ran ◽  
Zheng Xu ◽  
Bing Li ◽  
Song-nong Li
Keyword(s):  
3D Visualization ◽  
Three Dimensional ◽  
Electrode Array ◽  
Human Bladder ◽  
Impedance Tomography ◽  
Regularization Algorithm ◽  
3D Images ◽  
Dimensional Reconstruction ◽  
2D Imaging ◽  
Medical Examinations

As the researches of electric impedance tomography (EIT) applications in medical examinations deepen, we attempt to produce the visualization of 3D images of human bladder. In this paper, a planar electrode array system will be introduced as the measuring platform and a series of feasible methods are proposed to evaluate the simulated volume of bladder to avoid overfilling. The combined regularization algorithm enhances the spatial resolution and presents distinguishable sketch of disturbances from the background, which provides us with reliable data from inverse problem to carry on to the three-dimensional reconstruction. By detecting the edge elements and tracking down the lost information, we extract quantitative morphological features of the object from the noises and background. Preliminary measurements were conducted and the results showed that the proposed algorithm overcomes the defects of holes, protrusions, and debris in reconstruction. In addition, the targets' location in space and roughly volume could be calculated according to the grid of finite element of the model, and this feature was never achievable for the previous 2D imaging.

Development of a Tridimensional Visualization and Model Reconstruction System Based on Computed Tomographic Data

2011 ◽  
Author(s):  
Hugo I. Medelli´n Castillo ◽  
Manuel A. Ochoa Alfaro
Keyword(s):  
Soft Tissues ◽  
3D Visualization ◽  
Three Dimensional ◽  
Volume Visualization ◽  
3D Models ◽  
Research Area ◽  
Implant Design ◽  
Ray Casting ◽  
Model Reconstruction ◽  
Surgical Guides

Medical image processing constitutes an important research area of the biomedical engineering since it provides accurate human body information for 3D visualization and analysis, diagnostic, surgical treatment planning, surgical training, prosthesis and implant design, wafer and surgical guides design. Computed tomography (CT) and magnetic resonance imaging (MRI) have had a great impact in the medicine since they can represent complex three dimensional (3D) anomalities or deformities. In this paper, the development of a system for tridimensional visualization and model reconstruction based on CT data is presented. The aim is to provide a system capable to assist the design process of prosthesis, implants and surgical guides by reconstructing anatomical 3D models which can be exported to any CAD program or computer aided surgery (CAS) system. A complete description of the proposed system is presented. The new system is able to visualize and reconstruct bone and/or soft tissues. Three types of renders are used: one for 3D visualization based on three planes, other for 3D surface reconstruction based on the well known marching cubes algorithm, and the other for 3D volume visualization based on the ray-casting algorithm. The functionality and performance of the system are evaluated by means of four case studies. The results have proved the capability of the system to visualize and reconstruct anatomical 3D models from medical images.

Three-dimensional reconstruction of gene expression patterns during cardiac development

2003 ◽  
Vol 13 (3) ◽  
pp. 187-195 ◽  
Author(s):  
Alexandre T. Soufan ◽  
Jan M. Ruijter ◽  
Maurice J. B. van den Hoff ◽  
Piet A. J. de Boer ◽  
Jaco Hagoort ◽  
...  
Keyword(s):  
Gene Expression ◽  
3D Reconstruction ◽  
Cardiac Development ◽  
3D Visualization ◽  
Expression Patterns ◽  
Genetic Regulation ◽  
Three Dimensional ◽  
Specific Staining ◽  
Dimensional Reconstruction

The study of the genetic regulation of embryonic development requires the three-dimensional (3D) mapping of gene expression at the microscopic level. Despite the recent burst in the number of methods focusing on 3D reconstruction of embryonic specimens, an adequate and accessible 3D reconstruction protocol for the visualization of patterns of gene expression is lacking. In this communication we describe a protocol that was developed for the 3D visualization of patterns of gene expression determined by in situ hybridization (ISH) on serial sections. The method still requires tissue sectioning, due to penetration limits of the specific staining agents into whole embryo preparations. With regard to expenditure of resources, i.e., hardware, software, and time, the protocol is relatively undemanding. Because the variation between specimens requires the visualization of multiple specimens per stage, it was decided to “do more, less well.” The current protocol, therefore, results in reconstructions of sufficient, but not the highest, quality. The use of the protocol is demonstrated on a series of serially sectioned mouse hearts, ranging from embryonic day 8.5 to 14.5. The myocardium of the hearts was identified by ISH using a mixture of specific mRNA probes and reconstructed.

scholarly journals 3D Visualization of Macromolecule Synthesis

2020 ◽  
Author(s):  
Timothy J. Duerr ◽  
Ester Comellas ◽  
Eun Kyung Jeon ◽  
Johanna E. Farkas ◽  
Marylou Joetzjer ◽  
...  
Keyword(s):  
3D Visualization ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Light Sheet ◽  
Macromolecular Synthesis ◽  
Volumetric Imaging ◽  
Processing Pipeline ◽  
Powerful Means

AbstractMeasuring nascent macromolecular synthesis in vivo is key to understanding how cells and tissues progress through development and respond to external cues. Here, we perform in vivo injection of alkyne- or azide-modified analogs of thymidine, uridine, methionine, and glucosamine to label nascent synthesis of DNA, RNA, protein, and glycosylation. Three-dimensional volumetric imaging of nascent macromolecule synthesis was performed in axolotl salamander tissue using whole mount click chemistry-based fluorescent staining followed by light sheet fluorescent microscopy. We also developed an image processing pipeline for segmentation and classification of morphological regions of interest and individual cells, and we apply this pipeline to the regenerating humerus. We demonstrate our approach is sensitive to biological perturbations by measuring changes in DNA synthesis after limb denervation. This method provides a powerful means to quantitatively interrogate macromolecule synthesis in heterogenous tissues at the organ, cellular, and molecular levels of organization.

scholarly journals Estimation of Forensic Sex Based on Three-Dimensional Reconstruction of Skull in Korean: Non-metric Study

2021 ◽  
Vol 45 (3) ◽  
pp. 79-86
Author(s):  
Yun Taek Shim ◽  
Ye Hwon Jeong ◽  
Yi-Suk Kim ◽  
Nahyun Aum ◽  
Seung Gyu Choi ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Sex Determination ◽  
Three Dimensional ◽  
Estimation Method ◽  
Ct Images ◽  
Slice Thickness ◽  
Sex Estimation ◽  
3D Image ◽  
3D Images ◽  
Dimensional Reconstruction

This study performed the forensic anthropological sex estimation of Koreans in a non-metric way by reconstructing three-dimensional (3D) computed tomography (CT) images of skulls. The skull CT images used in this study were 100 (51 males, 49 females), and all CT images were taken with a slice thickness of 0.75 mm and then reconstructed into 3D images using the MIMICS 23.0 program. Using the reconstructed 3D image, measurements were repeated twice. The sex determination was male if the 4 point to 5 point was relatively more in five landmarks, and female if the points of 1 to 2 were relatively more. Results of the study show that, 88 of the 100 cases matched the actual sex. Among the 12 discrepant cases, ten cases were mismatched with the actual sex even though the estimation and repeated estimation readout of sexestimating were the same. Two cases, were “unknown,” showing different sexes in the first and repeated estimations. In conclusion, this study indicated that a forensic anthropological analysis from 3D images provided accurate point information on the landmarks of skulls, showing as high an accuracy as the sex estimation method using real bones. The ten cases of sex mismatch, except the two “Unknown” cases, are considered to be errors that did not consider differences in population groups. In further studies, further establishing a nonmetric, specifically Korean methods to increase the accuracy and reliability of sex estimation is need.

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