Sources of Noise in Three-Dimensional Microscopical Data Sets

1994 ◽  
pp. 47-94 ◽  
Author(s):  
James B. Pawley
Keyword(s):  
Three Dimensional ◽  
Data Sets

Computer-aided methods for 3-D visualization of serial sections and thick biological specimens

1992 ◽  
Vol 50 (2) ◽  
pp. 1060-1061
Author(s):  
Mark Ellisman ◽  
Maryann Martone ◽  
Gabriel Soto ◽  
Eleizer Masliah ◽  
David Hessler ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Three Dimensional ◽  
Neuritic Plaque ◽  
Dimensional Structure ◽  
Data Sets ◽  
Molecular Physiology ◽  
Research Activities ◽  
Computer Aided ◽  
Dimensional Reconstruction

Structurally-oriented biologists examine cells, tissues, organelles and macromolecules in order to gain insight into cellular and molecular physiology by relating structure to function. The understanding of these structures can be greatly enhanced by the use of techniques for the visualization and quantitative analysis of three-dimensional structure. Three projects from current research activities will be presented in order to illustrate both the present capabilities of computer aided techniques as well as their limitations and future possibilities.The first project concerns the three-dimensional reconstruction of the neuritic plaques found in the brains of patients with Alzheimer's disease. We have developed a software package “Synu” for investigation of 3D data sets which has been used in conjunction with laser confocal light microscopy to study the structure of the neuritic plaque. Tissue sections of autopsy samples from patients with Alzheimer's disease were double-labeled for tau, a cytoskeletal marker for abnormal neurites, and synaptophysin, a marker of presynaptic terminals.

scholarly journals Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonas Albers ◽  
Angelika Svetlove ◽  
Justus Alves ◽  
Alexander Kraupner ◽  
Francesca di Lillo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
High Specificity ◽  
Histopathological Analysis ◽  
Specific Information ◽  
Data Sets ◽  
Virtual Histology ◽  
Novel Approach ◽  
Cell Tissue ◽  
Immuno Histochemistry ◽  
3D Information

AbstractAlthough X-ray based 3D virtual histology is an emerging tool for the analysis of biological tissue, it falls short in terms of specificity when compared to conventional histology. Thus, the aim was to establish a novel approach that combines 3D information provided by microCT with high specificity that only (immuno-)histochemistry can offer. For this purpose, we developed a software frontend, which utilises an elastic transformation technique to accurately co-register various histological and immunohistochemical stainings with free propagation phase contrast synchrotron radiation microCT. We demonstrate that the precision of the overlay of both imaging modalities is significantly improved by performing our elastic registration workflow, as evidenced by calculation of the displacement index. To illustrate the need for an elastic co-registration approach we examined specimens from a mouse model of breast cancer with injected metal-based nanoparticles. Using the elastic transformation pipeline, we were able to co-localise the nanoparticles to specifically stained cells or tissue structures into their three-dimensional anatomical context. Additionally, we performed a semi-automated tissue structure and cell classification. This workflow provides new insights on histopathological analysis by combining CT specific three-dimensional information with cell/tissue specific information provided by classical histology.

scholarly journals Validation of Scolioscan Air-Portable Radiation-Free Three-Dimensional Ultrasound Imaging Assessment System for Scoliosis

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2858
Author(s):  
Kelly Ka-Lee Lai ◽  
Timothy Tin-Yan Lee ◽  
Michael Ka-Shing Lee ◽  
Joseph Chi-Ho Hui ◽  
Yong-Ping Zheng
Keyword(s):  
Ultrasound Imaging ◽  
Imaging System ◽  
Outcome Measurement ◽  
Three Dimensional ◽  
3D Ultrasound ◽  
Mean Difference ◽  
Assessment System ◽  
Absolute Difference ◽  
Data Sets ◽  
Low Profile

To diagnose scoliosis, the standing radiograph with Cobb’s method is the gold standard for clinical practice. Recently, three-dimensional (3D) ultrasound imaging, which is radiation-free and inexpensive, has been demonstrated to be reliable for the assessment of scoliosis and validated by several groups. A portable 3D ultrasound system for scoliosis assessment is very much demanded, as it can further extend its potential applications for scoliosis screening, diagnosis, monitoring, treatment outcome measurement, and progress prediction. The aim of this study was to investigate the reliability of a newly developed portable 3D ultrasound imaging system, Scolioscan Air, for scoliosis assessment using coronal images it generated. The system was comprised of a handheld probe and tablet PC linking with a USB cable, and the probe further included a palm-sized ultrasound module together with a low-profile optical spatial sensor. A plastic phantom with three different angle structures built-in was used to evaluate the accuracy of measurement by positioning in 10 different orientations. Then, 19 volunteers with scoliosis (13F and 6M; Age: 13.6 ± 3.2 years) with different severity of scoliosis were assessed. Each subject underwent scanning by a commercially available 3D ultrasound imaging system, Scolioscan, and the portable 3D ultrasound imaging system, with the same posture on the same date. The spinal process angles (SPA) were measured in the coronal images formed by both systems and compared with each other. The angle phantom measurement showed the measured angles well agreed with the designed values, 59.7 ± 2.9 vs. 60 degrees, 40.8 ± 1.9 vs. 40 degrees, and 20.9 ± 2.1 vs. 20 degrees. For the subject tests, results demonstrated that there was a very good agreement between the angles obtained by the two systems, with a strong correlation (R2 = 0.78) for the 29 curves measured. The absolute difference between the two data sets was 2.9 ± 1.8 degrees. In addition, there was a small mean difference of 1.2 degrees, and the differences were symmetrically distributed around the mean difference according to the Bland–Altman test. Scolioscan Air was sufficiently comparable to Scolioscan in scoliosis assessment, overcoming the space limitation of Scolioscan and thus providing wider applications. Further studies involving a larger number of subjects are worthwhile to demonstrate its potential clinical values for the management of scoliosis.

scholarly journals Three-dimensional deformation time series of glacier motion from multiple-aperture DInSAR observation

2019 ◽  
Vol 93 (12) ◽  
pp. 2651-2660 ◽  
Author(s):  
Sergey Samsonov
Keyword(s):  
Time Series ◽  
Surface Deformation ◽  
Ground Deformation ◽  
Three Dimensional ◽  
Data Sets ◽  
Ice Flow ◽  
The North ◽  
Glacier Ice ◽  
Deformation Component ◽  
3D Deformation

AbstractThe previously presented Multidimensional Small Baseline Subset (MSBAS-2D) technique computes two-dimensional (2D), east and vertical, ground deformation time series from two or more ascending and descending Differential Interferometric Synthetic Aperture Radar (DInSAR) data sets by assuming that the contribution of the north deformation component is negligible. DInSAR data sets can be acquired with different temporal and spatial resolutions, viewing geometries and wavelengths. The MSBAS-2D technique has previously been used for mapping deformation due to mining, urban development, carbon sequestration, permafrost aggradation and pingo growth, and volcanic activities. In the case of glacier ice flow, the north deformation component is often too large to be negligible. Historically, the surface-parallel flow (SPF) constraint was used to compute the static three-dimensional (3D) velocity field at various glaciers. A novel MSBAS-3D technique has been developed for computing 3D deformation time series where the SPF constraint is utilized. This technique is used for mapping 3D deformation at the Barnes Ice Cap, Baffin Island, Nunavut, Canada, during January–March 2015, and the MSBAS-2D and MSBAS-3D solutions are compared. The MSBAS-3D technique can be used for studying glacier ice flow at other glaciers and other surface deformation processes with large north deformation component, such as landslides. The software implementation of MSBAS-3D technique can be downloaded from http://insar.ca/.

Human aorta: preliminary results with virtual endoscopy based on three-dimensional MR imaging data sets.

Radiology ◽  
1996 ◽  
Vol 199 (1) ◽  
pp. 37-40 ◽  
Author(s):  
C P Davis ◽  
M E Ladd ◽  
B J Romanowski ◽  
S Wildermuth ◽  
J F Knoplioch ◽  
...  
Keyword(s):  
Mr Imaging ◽  
Three Dimensional ◽  
Virtual Endoscopy ◽  
Human Aorta ◽  
Data Sets ◽  
Imaging Data ◽  
Preliminary Results

scholarly journals Nervous Activity of the Brain in Five Dimensions

Biophysica ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 38-47
Author(s):  
Arturo Tozzi ◽  
James F. Peters ◽  
Norbert Jausovec ◽  
Arjuna P. H. Don ◽  
Sheela Ramanna ◽  
...  
Keyword(s):  
Fourier Analysis ◽  
Nervous Activity ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Data Sets ◽  
Spatial And Temporal Patterns ◽  
Five Dimensions ◽  
Four Dimensions ◽  
Scale Free ◽  
The Brain

The nervous activity of the brain takes place in higher-dimensional functional spaces. It has been proposed that the brain might be equipped with phase spaces characterized by four spatial dimensions plus time, instead of the classical three plus time. This suggests that global visualization methods for exploiting four-dimensional maps of three-dimensional experimental data sets might be used in neuroscience. We asked whether it is feasible to describe the four-dimensional trajectories (plus time) of two-dimensional (plus time) electroencephalographic traces (EEG). We made use of quaternion orthographic projections to map to the surface of four-dimensional hyperspheres EEG signal patches treated with Fourier analysis. Once achieved the proper quaternion maps, we show that this multi-dimensional procedure brings undoubted benefits. The treatment of EEG traces with Fourier analysis allows the investigation the scale-free activity of the brain in terms of trajectories on hyperspheres and quaternionic networks. Repetitive spatial and temporal patterns undetectable in three dimensions (plus time) are easily enlightened in four dimensions (plus time). Further, a quaternionic approach makes it feasible to identify spatially far apart and temporally distant periodic trajectories with the same features, such as, e.g., the same oscillatory frequency or amplitude. This leads to an incisive operational assessment of global or broken symmetries, domains of attraction inside three-dimensional projections and matching descriptions between the apparently random paths hidden in the very structure of nervous fractal signals.

Diagnosis of COVID-19 using 3D CT scans and vaccination for COVID-19

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Gangadhar Ch ◽  
S. Jana ◽  
Sankararao Majji ◽  
Prathyusha Kuncha ◽  
Fantin Irudaya Raj E. ◽  
...  
Keyword(s):  
Virus Isolate ◽  
Research Work ◽  
Three Dimensional ◽  
Ct Scans ◽  
Data Sets ◽  
Content Type ◽  
Infected People ◽  
3D Data ◽  
Ct Classification ◽  
First Time

Purpose For the first time in a decade, a new form of pneumonia virus, coronavirus, COVID-19, appeared in Wuhan, China. To date, it has affected millions of people, killed thousands and resulted in thousands of deaths around the world. To stop the spread of this virus, isolate the infected people. Computed tomography (CT) imaging is very accurate in revealing the details of the lungs and allows oncologists to detect COVID. However, the analysis of CT scans, which can include hundreds of images, may cause delays in hospitals. The use of artificial intelligence (AI) in radiology could help to COVID-19-positive cancer in this manner is the main purpose of the work. Design/methodology/approach CT scans are a medical imaging procedure that gives a three-dimensional (3D) representation of the lungs for clinical purposes. The volumetric 3D data sets can be regarded as axial, coronal and transverse data sets. By using AI, we can diagnose the virus presence. Findings The paper discusses the use of an AI for COVID-19, and CT classification issue and vaccination details of COVID-19 have been detailed in this paper. Originality/value Originality of the work is, all the data can be collected genuinely and did research work doneown methodology.

Measuring stress-induced martensite microstructures using far-field high-energy diffraction microscopy

2018 ◽  
Vol 74 (5) ◽  
pp. 425-446 ◽  
Author(s):  
Ashley Nicole Bucsek ◽  
Darren Dale ◽  
Jun Young Peter Ko ◽  
Yuriy Chumlyakov ◽  
Aaron Paul Stebner
Keyword(s):  
Phase Transformation ◽  
Three Dimensional ◽  
Infinite Plate ◽  
Direct Analysis ◽  
High Energy ◽  
Data Sets ◽  
Far Field ◽  
X Ray Diffraction ◽  
Parent Austenite ◽  
Diffraction Microscopy

Modern X-ray diffraction techniques are now allowing researchers to collect long-desired experimental verification data sets that are in situ, three-dimensional, on the same length scales as critical microstructures, and using bulk samples. These techniques need to be adapted for advanced material systems that undergo combinations of phase transformation, twinning and plasticity. One particular challenge addressed in this article is direct analysis of martensite phases in far-field high-energy diffraction microscopy experiments. Specifically, an algorithmic forward model approach is presented to analyze phase transformation and twinning data sets of shape memory alloys. In the present implementation of the algorithm, the crystallographic theory of martensite (CTM) is used to predict possible martensite microstructures (i.e. martensite orientations, twin mode, habit plane, twin plane and twin phase fractions) that could form from the parent austenite structure. This approach is successfully demonstrated on three single- and near-single-crystal NiTi samples where the fundamental assumptions of the CTM are not upheld. That is, the samples have elastically strained lattices, inclusions, precipitates, subgrains, R-phase transformation and/or are not an infinite plate. The results indicate that the CTM still provides structural solutions that match the experiments. However, the widely accepted maximum work criterion for predicting which solution of the CTM should be preferred by the material does not work in these cases. Hence, a more accurate model that can simulate these additional structural complexities can be used within the algorithm in the future to improve its performance for non-ideal materials.

scholarly journals Simultaneous Robot–World and Hand–Eye Calibration without a Calibration Object

Sensors ◽  
2018 ◽  
Vol 18 (11) ◽  
pp. 3949 ◽  
Author(s):  
Wei Li ◽  
Mingli Dong ◽  
Naiguang Lu ◽  
Xiaoping Lou ◽  
Peng Sun
Keyword(s):  
Three Dimensional ◽  
Real Data ◽  
Medical Robotics ◽  
Calibration Method ◽  
Bundle Adjustment ◽  
Data Sets ◽  
Rigid Transformation ◽  
Validation Experiment ◽  
Dimensional Reconstruction ◽  
Sparse Bundle Adjustment

An extended robot–world and hand–eye calibration method is proposed in this paper to evaluate the transformation relationship between the camera and robot device. This approach could be performed for mobile or medical robotics applications, where precise, expensive, or unsterile calibration objects, or enough movement space, cannot be made available at the work site. Firstly, a mathematical model is established to formulate the robot-gripper-to-camera rigid transformation and robot-base-to-world rigid transformation using the Kronecker product. Subsequently, a sparse bundle adjustment is introduced for the optimization of robot–world and hand–eye calibration, as well as reconstruction results. Finally, a validation experiment including two kinds of real data sets is designed to demonstrate the effectiveness and accuracy of the proposed approach. The translation relative error of rigid transformation is less than 8/10,000 by a Denso robot in a movement range of 1.3 m × 1.3 m × 1.2 m. The distance measurement mean error after three-dimensional reconstruction is 0.13 mm.

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