scholarly journals Regularization of DT-MRI Using 3D Median Filtering Methods

2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
Soondong Kwon ◽  
Dongyoun Kim ◽  
Bongsoo Han ◽  
Kiwoon Kwon
Keyword(s):  
Diffusion Tensor ◽  
Three Dimensional ◽  
Synthetic Data ◽  
Regularization Methods ◽  
Median Filtering ◽  
Two Dimensional ◽  
Median Filters ◽  
Highly Sensitive ◽  
The Central Nervous System ◽  
Processing Techniques

DT-MRI (diffusion tensor magnetic resonance imaging) tractography is a method to determine the architecture of axonal fibers in the central nervous system by computing the direction of the principal eigenvectors obtained from tensor matrix, which is different from the conventional isotropic MRI. Tractography based on DT-MRI is known to need many computations and is highly sensitive to noise. Hence, adequate regularization methods, such as image processing techniques, are in demand. Among many regularization methods we are interested in the median filtering method. In this paper, we extended two-dimensional median filters already developed to three-dimensional median filters. We compared four median filtering methods which are two-dimensional simple median method (SM2D), two-dimensional successive Fermat method (SF2D), three-dimensional simple median method (SM3D), and three-dimensional successive Fermat method (SF3D). Three kinds of synthetic data with different altitude angles from axial slices and one kind of human data from MR scanner are considered for numerical implementation by the four filtering methods.

scholarly journals Automated Quantification of Pneumothorax in CT

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Synho Do ◽  
Kristen Salvaggio ◽  
Supriya Gupta ◽  
Mannudeep Kalra ◽  
Nabeel U. Ali ◽  
...  
Keyword(s):  
Processing Time ◽  
Three Dimensional ◽  
Average Error ◽  
Two Dimensional ◽  
Algorithm Performance ◽  
Automated Method ◽  
Automated Quantification ◽  
Overall Performance ◽  
Processing Techniques ◽  
Aided Diagnosis

An automated, computer-aided diagnosis (CAD) algorithm for the quantification of pneumothoraces from Multidetector Computed Tomography (MDCT) images has been developed. Algorithm performance was evaluated through comparison to manual segmentation by expert radiologists. A combination of two-dimensional and three-dimensional processing techniques was incorporated to reduce required processing time by two-thirds (as compared to similar techniques). Volumetric measurements on relative pneumothorax size were obtained and the overall performance of the automated method shows an average error of just below 1%.

3D Photonic Crystals Fabricated by Micromanipulation Technique

2002 ◽  
Vol 722 ◽  
Author(s):  
Kanna Aoki ◽  
Hideki T. Miyazaki ◽  
Hideki Hirayama ◽  
Kyoji Inoshita ◽  
Toshihiko Baba ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Photonic Band Gap ◽  
Three Dimensional ◽  
Wavelength Region ◽  
Two Dimensional ◽  
Positioning Error ◽  
Proper Position ◽  
Number Of Layers ◽  
Processing Techniques ◽  
Photonic Band

AbstractThree-dimensional (3D) photonic crystals with one to four layers of woodpile structures have been fabricated by stacking two-dimensional (2D) photonic plates by micromanipulation. First, air-bridge photonic plates were fabricated as unit structures using conventional IC processing techniques. Then, the 2D photonic plates were stacked using a micromanipulation system. To obtain lattices with precise periodicity, microspheres were inserted into the round openings which were prepared in the frame of the plates. Since neighboring plates have pore openings at the same position, plates were laminated at the proper position automatically. Consequently, positioning error was kept within 50 nm. Optical characteristics of the crystals were evaluated by their reflectance and transmittance at wavenumber between 700 and 7000 cm-1. The formed photonic crystals were expected to have a photonic band gap at around 3030 cm-1. As the number of layers was increased, the reflectance at around 3030 cm-1 increased to 60 %, and the transmittance at the same wavelength region decreased to 30 %.

TWO‐DIMENSIONAL AND THREE‐DIMENSIONAL MIGRATION OF MODEL‐EXPERIMENT REFLECTION PROFILES

Geophysics ◽  
1974 ◽  
Vol 39 (3) ◽  
pp. 265-277 ◽  
Author(s):  
William S. French
Keyword(s):  
Model Experiment ◽  
Three Dimensional ◽  
Structural Models ◽  
Computer Processing ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Migration Process ◽  
Subsurface Structures ◽  
Reflection Data ◽  
Processing Techniques

A reflection profile represents an unfocused picture of the subsurface. In areas of rapid structural change, this unfocused picture may not reveal directly the true geometry of subsurface structures. Computer processing techniques, collectively called migration, have been used by many companies to focus 2-D reflection data. A description of the migration process can be given which allows immediate generalization to three‐dimensions with arbitrary source and receiver positions. Reflection profiles digitally recorded in the laboratory over known acoustically semitransparent structural models establish the effectiveness of migration. Processed reflection data over 3-D models demonstrate that 3-D migration eliminates many of the lateral correlation ambiguities caused by “sideswipes” and “blind structures.” Structure maps developed from the results of 3-D migration of reflection data give a true and precise picture of 3-D models. When the same data are processed using 2-D migration, the mapped structures are distorted. In structurally complex areas it is desirable to collect 3-D reflection data. Single profiles cannot, and conventional grids may not, reveal adequate cross‐dip information.

High Resolution Microscopy of Multi-Layered Biological Crystals

1982 ◽  
Vol 40 ◽  
pp. 80-83
Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Low Dose ◽  
Three Dimensional ◽  
Data Interpretation ◽  
Two Dimensional ◽  
Biological Objects ◽  
Density Maps ◽  
Density Map ◽  
Complex Crystal ◽  
High Resolution Microscopy

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.

Instrumentation For Quantitative Microscopy

1977 ◽  
Vol 35 ◽  
pp. 206-209
Author(s):  
B. Ralph ◽  
A.R. Jones
Keyword(s):  
Volume Fraction ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Automatic Data ◽  
Phase Volume Fraction ◽  
Statistical Confidence ◽  
Resultant Data ◽  
Automatic Data Collection ◽  
Third Dimension ◽  
Evolution Of Microstructure

In all fields of microscopy there is an increasing interest in the quantification of microstructure. This interest may stem from a desire to establish quality control parameters or may have a more fundamental requirement involving the derivation of parameters which partially or completely define the three dimensional nature of the microstructure. This latter categorey of study may arise from an interest in the evolution of microstructure or from a desire to generate detailed property/microstructure relationships. In the more fundamental studies some convolution of two-dimensional data into the third dimension (stereological analysis) will be necessary.In some cases the two-dimensional data may be acquired relatively easily without recourse to automatic data collection and further, it may prove possible to perform the data reduction and analysis relatively easily. In such cases the only recourse to machines may well be in establishing the statistical confidence of the resultant data. Such relatively straightforward studies tend to result from acquiring data on the whole assemblage of features making up the microstructure. In this field data mode, when parameters such as phase volume fraction, mean size etc. are sought, the main case for resorting to automation is in order to perform repetitive analyses since each analysis is relatively easily performed.

A linearity test for thick specimens imaged by HVEM over a 180° angular range

1991 ◽  
Vol 49 ◽  
pp. 552-553
Author(s):  
Yu Liu
Keyword(s):  
Phase Contrast ◽  
Three Dimensional ◽  
Angular Range ◽  
Two Dimensional ◽  
Back Projection ◽  
Line Integral ◽  
Exponential Law ◽  
Transmission Electron ◽  
Absorption Law ◽  
Linearity Test

The image obtained in a transmission electron microscope is the two-dimensional projection of a three-dimensional (3D) object. The 3D reconstruction of the object can be calculated from a series of projections by back-projection, but this algorithm assumes that the image is linearly related to a line integral of the object function. However, there are two kinds of contrast in electron microscopy, scattering and phase contrast, of which only the latter is linear with the optical density (OD) in the micrograph. Therefore the OD can be used as a measure of the projection only for thin specimens where phase contrast dominates the image. For thick specimens, where scattering contrast predominates, an exponential absorption law holds, and a logarithm of OD must be used. However, for large thicknesses, the simple exponential law might break down due to multiple and inelastic scattering.

An Image Reconstruction System Applied to High Voltage Microscopy

1975 ◽  
Vol 33 ◽  
pp. 292-293
Author(s):  
D. E. Johnson
Keyword(s):  
High Voltage ◽  
Prior Information ◽  
Block Diagram ◽  
Three Dimensional ◽  
Real Space ◽  
Two Dimensional ◽  
Efficient Manner ◽  
Fourier Methods ◽  
Tilt Series ◽  
Methods Of Reconstruction

Increased specimen penetration; the principle advantage of high voltage microscopy, is accompanied by an increased need to utilize information on three dimensional specimen structure available in the form of two dimensional projections (i.e. micrographs). We are engaged in a program to develop methods which allow the maximum use of information contained in a through tilt series of micrographs to determine three dimensional speciman structure.In general, we are dealing with structures lacking in symmetry and with projections available from only a limited span of angles (±60°). For these reasons, we must make maximum use of any prior information available about the specimen. To do this in the most efficient manner, we have concentrated on iterative, real space methods rather than Fourier methods of reconstruction. The particular iterative algorithm we have developed is given in detail in ref. 3. A block diagram of the complete reconstruction system is shown in fig. 1.

Specific Labeling of Protein Domains with Antibody Fragments

1981 ◽  
Vol 39 ◽  
pp. 416-417
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler
Keyword(s):  
Image Processing ◽  
Specific Protein ◽  
Antibody Fragments ◽  
Supramolecular Organization ◽  
Two Dimensional ◽  
Ordered Structures ◽  
Virus Capsids ◽  
Processing Techniques

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.

Computer Assisted Image Reconstruction of Oligomer Structure

1976 ◽  
Vol 34 ◽  
pp. 472-473
Author(s):  
A.M. Jones ◽  
A. Max Fiskin
Keyword(s):  
Three Dimensional ◽  
Depth Of Field ◽  
Computer Assisted ◽  
Projection Data ◽  
Two Dimensional ◽  
Single Particles ◽  
Dimensional Reconstruction ◽  
Computer Assisted Image ◽  
The Fourier Transform ◽  
Space Approach

If the tilt of a specimen can be varied either by the strategy of observing identical particles orientated randomly or by use of a eucentric goniometer stage, three dimensional reconstruction procedures are available (l). If the specimens, such as small protein aggregates, lack periodicity, direct space methods compete favorably in ease of implementation with reconstruction by the Fourier (transform) space approach (2). Regardless of method, reconstruction is possible because useful specimen thicknesses are always much less than the depth of field in an electron microscope. Thus electron images record the amount of stain in columns of the object normal to the recording plates. For single particles, practical considerations dictate that the specimen be tilted precisely about a single axis. In so doing a reconstructed image is achieved serially from two-dimensional sections which in turn are generated by a series of back-to-front lines of projection data.

Polymorphic phase transition of a membrane protein - analysis of continuous diffuse electron diffraction intensity

1986 ◽  
Vol 44 ◽  
pp. 166-167
Author(s):  
Douglas L. Dorset ◽  
Andrew K. Massalski
Keyword(s):  
Molecular Sieve ◽  
Three Dimensional ◽  
Pore Geometry ◽  
Two Dimensional ◽  
Diffraction Intensity ◽  
Polymorphic Phase Transition ◽  
E Coli ◽  
Crystallographic Study ◽  
Hexagonal Form ◽  
Polymorphic Forms

Matrix porin, the ompF gene product of E. coli, has been the object of a electron crystallographic study of its pore geometry in an attempt to understand its function as a membrane molecular sieve. Three polymorphic forms have been found for two-dimensional crystals reconstituted in phospholipid, two hexagonal forms with different lipid content and an orthorhombic form coexisting with and similar to the hexagonal form found after lipid loss. In projection these have been shown to retain the same three-fold pore triplet geometry and analyses of three-dimensional data reveal that the small hexagonal and orthorhombic polymorphs have similar structure as well as unit cell spacings.

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