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

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

Abstract Although 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 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.

Ambiguity assessment of small-angle scattering curves from monodisperse systems

2015 ◽  
Vol 71 (5) ◽  
pp. 1051-1058 ◽  
Author(s):  
Maxim V. Petoukhov ◽  
Dmitri I. Svergun
Keyword(s):  
A Priori ◽  
Three Dimensional ◽  
Shape Reconstruction ◽  
Scattering Data ◽  
Biological Macromolecules ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
Model Calculations ◽  
Novel Approach

A novel approach is presented for ana prioriassessment of the ambiguity associated with spherically averaged single-particle scattering. The approach is of broad interest to the structural biology community, allowing the rapid and model-independent assessment of the inherent non-uniqueness of three-dimensional shape reconstruction from scattering experiments on solutions of biological macromolecules. One-dimensional scattering curves recorded from monodisperse systems are nowadays routinely utilized to generate low-resolution particle shapes, but the potential ambiguity of such reconstructions remains a major issue. At present, the (non)uniqueness can only be assessed bya posterioricomparison and averaging of repetitive Monte Carlo-based shape-determination runs. The newa prioriambiguity measure is based on the number of distinct shape categories compatible with a given data set. For this purpose, a comprehensive library of over 14 000 shape topologies has been generated containing up to seven beads closely packed on a hexagonal grid. The computed scattering curves rescaled to keep only the shape topology rather than the overall size information provide a `scattering map' of this set of shapes. For a given scattering data set, one rapidly obtains the number of neighbours in the map and the associated shape topologies such that in addition to providing a quantitative ambiguity measure the algorithm may also serve as an alternative shape-analysis tool. The approach has been validated in model calculations on geometrical bodies and its usefulness is further demonstrated on a number of experimental X-ray scattering data sets from proteins in solution. A quantitative ambiguity score (a-score) is introduced to provide immediate and convenient guidance to the user on the uniqueness of theab initioshape reconstruction from the given data set.

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.

Analyzing the Impact of X-Ray Tomography on the Reliability of Integrated Circuits

2015 ◽  
Author(s):  
Halit Dogan ◽  
Md Mahbub Alam ◽  
Navid Asadizanjani ◽  
Sina Shahbazmohamadi ◽  
Domenic Forte ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Integrated Circuit ◽  
3D Imaging ◽  
Three Dimensional ◽  
Serial Sectioning ◽  
Promising Technique ◽  
Flash Memories ◽  
X Ray ◽  
3D Information ◽  
The Impact

Abstract X-ray tomography is a promising technique that can provide micron level, internal structure, and three dimensional (3D) information of an integrated circuit (IC) component without the need for serial sectioning or decapsulation. This is especially useful for counterfeit IC detection as demonstrated by recent work. Although the components remain physically intact during tomography, the effect of radiation on the electrical functionality is not yet fully investigated. In this paper we analyze the impact of X-ray tomography on the reliability of ICs with different fabrication technologies. We perform a 3D imaging using an advanced X-ray machine on Intel flash memories, Macronix flash memories, Xilinx Spartan 3 and Spartan 6 FPGAs. Electrical functionalities are then tested in a systematic procedure after each round of tomography to estimate the impact of X-ray on Flash erase time, read margin, and program operation, and the frequencies of ring oscillators in the FPGAs. A major finding is that erase times for flash memories of older technology are significantly degraded when exposed to tomography, eventually resulting in failure. However, the flash and Xilinx FPGAs of newer technologies seem less sensitive to tomography, as only minor degradations are observed. Further, we did not identify permanent failures for any chips in the time needed to perform tomography for counterfeit detection (approximately 2 hours).

Proteomics: Opportunities and Challenges

2011 ◽  
Vol 3 (4) ◽  
pp. 1165-1172 ◽  
Author(s):  
Parag A Pathade ◽  
Vinod A Bairagi ◽  
Yogesh S. Ahire ◽  
Neela M Bhatia
Keyword(s):  
Biomedical Research ◽  
Therapy Monitoring ◽  
Dynamic State ◽  
Data Sets ◽  
Protein Markers ◽  
Drug Target Discovery ◽  
Proteomic Data ◽  
Cell Tissue ◽  
A Cell ◽  
Analytical Tools

‘‘Proteomics’’, is the emerging technology leading to high-throughput identification and understanding of proteins. Proteomics is the protein equivalent of genomics and has captured the imagination of biomolecular scientists, worldwide. Because proteome reveals more accurately the dynamic state of a cell, tissue, or organism, much is expected from proteomics to indicate better disease markers for diagnosis and therapy monitoring. Proteomics is expected to play a major role in biomedical research, and it will have a significant impact on the development of diagnostics and therapeutics for cancer, heart ailments and infectious diseases, in future. Proteomics research leads to the identification of new protein markers for diagnostic purposes and novel molecular targets for drug discovery.  Though the potential is great, many challenges and issues remain to be solved, such as gene expression, peptides, generation of low abundant proteins, analytical tools, drug target discovery and cost. A systematic and efficient analysis of vast genomic and proteomic data sets is a major challenge for researchers, today. Nevertheless, proteomics is the groundwork for constructing and extracting useful comprehension to biomedical research. This review article covers some opportunities and challenges offered by proteomics.   

Cardiovascular Imaging for Guiding Interventional Therapy in Structural Heart Diseases

2020 ◽  
Vol 16 (2) ◽  
pp. 111-122
Author(s):  
Nora Rat ◽  
Iolanda Muntean ◽  
Diana Opincariu ◽  
Liliana Gozar ◽  
Rodica Togănel ◽  
...  
Keyword(s):  
Heart Diseases ◽  
Interventional Procedure ◽  
Imaging Techniques ◽  
Ductus Arteriosus ◽  
Three Dimensional ◽  
High Specificity ◽  
Interventional Therapy ◽  
Structural Defects ◽  
Imaging Method ◽  
Three Dimensional Echocardiography

Development of interventional methods has revolutionized the treatment of structural cardiac diseases. Given the complexity of structural interventions and the anatomical variability of various structural defects, novel imaging techniques have been implemented in the current clinical practice for guiding the interventional procedure and for selection of the device to be used. Three– dimensional echocardiography is the most used imaging method that has improved the threedimensional assessment of cardiac structures, and it has considerably reduced the cost of complications derived from malalignment of interventional devices. Assessment of cardiac structures with the use of angiography holds the advantage of providing images in real time, but it does not allow an anatomical description. Transesophageal Echocardiography (TEE) and intracardiac ultrasonography play major roles in guiding Atrial Septal Defect (ASD) or Patent Foramen Ovale (PFO) closure and device follow-up, while TEE is the procedure of choice to assess the flow in the Left Atrial Appendage (LAA) and the embolic risk associated with a decreased flow. On the other hand, contrast CT and MRI have high specificity for providing a detailed description of structure, but cannot assess the flow through the shunt or the valvular mobility. This review aims to present the role of modern imaging techniques in pre-procedural assessment and intraprocedural guiding of structural percutaneous interventions performed to close an ASD, a PFO, an LAA or a patent ductus arteriosus.

scholarly journals Integrated magnetotelluric and seismic investigation of Cenozoic graben structure near Obrzycko, Poland

2021 ◽  
Author(s):  
Adam Cygal ◽  
Michał Stefaniuk ◽  
Anna Kret
Keyword(s):  
Seismic Data ◽  
Geophysical Methods ◽  
Geological Structure ◽  
Data Sets ◽  
Low Velocity ◽  
Shallow Subsurface ◽  
Geophysical Model ◽  
Novel Approach ◽  
Loose Deposits ◽  
Static Corrections

AbstractThis article presents the results of an integrated interpretation of measurements made using Audio-Magnetotellurics and Seismic Reflection geophysical methods. The obtained results were used to build an integrated geophysical model of shallow subsurface cover consisting of Cenozoic deposits, which then formed the basis for a detailed lithological and tectonic interpretation of deeper Mesozoic sediments. Such shallow covers, consisting mainly of glacial Pleistocene deposits, are typical for central and northern Poland. This investigation concentrated on delineating the accurate geometry of Obrzycko Cenozoic graben structure filled with loose deposits, as it was of great importance to the acquisition, processing and interpretation of seismic data that was to reveal the tectonic structure of the Cretaceous and Jurassic sediments which underly the study area. Previously, some problems with estimation of seismic static corrections over similar grabens filled with more recent, low-velocity deposits were encountered. Therefore, a novel approach to estimating the exact thickness of such shallow cover consisting of low-velocity deposits was applied in the presented investigation. The study shows that some alternative geophysical data sets (such as magnetotellurics) can be used to significantly improve the imaging of geological structure in areas where seismic data are very distorted or too noisy to be used alone

scholarly journals Artificial Tumor Microenvironments in Neuroblastoma

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1629
Author(s):  
Colin H. Quinn ◽  
Andee M. Beierle ◽  
Elizabeth A. Beierle
Keyword(s):  
Extracellular Matrix ◽  
Three Dimensional ◽  
Therapeutic Interventions ◽  
3D Bioprinting ◽  
Culture Studies ◽  
In Vivo Models ◽  
Novel Treatments ◽  
Tumor Microenvironments ◽  
Novel Approach

In the quest to advance neuroblastoma therapeutics, there is a need to have a deeper understanding of the tumor microenvironment (TME). From extracellular matrix proteins to tumor associated macrophages, the TME is a robust and diverse network functioning in symbiosis with the solid tumor. Herein, we review the major components of the TME including the extracellular matrix, cytokines, immune cells, and vasculature that support a more aggressive neuroblastoma phenotype and encumber current therapeutic interventions. Contemporary treatments for neuroblastoma are the result of traditional two-dimensional culture studies and in vivo models that have been translated to clinical trials. These pre-clinical studies are costly, time consuming, and neglect the study of cofounding factors such as the contributions of the TME. Three-dimensional (3D) bioprinting has become a novel approach to studying adult cancers and is just now incorporating portions of the TME and advancing to study pediatric solid. We review the methods of 3D bioprinting, how researchers have included TME pieces into the prints, and highlight present studies using neuroblastoma. Ultimately, incorporating the elements of the TME that affect neuroblastoma responses to therapy will improve the development of innovative and novel treatments. The use of 3D bioprinting to achieve this aim will prove useful in developing optimal therapies for children with neuroblastoma.

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 3D monitoring of the surface slippage effect on micro-particle sedimentation by digital holographic microscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Majid Panahi ◽  
Ramin Jamali ◽  
Vahideh Farzam Rad ◽  
Mojtaba Khorasani ◽  
Ahamd Darudi ◽  
...  
Keyword(s):  
Slip Length ◽  
Particle Interaction ◽  
Three Dimensional ◽  
Digital Holographic Microscopy ◽  
Particle Sedimentation ◽  
Micro Particles ◽  
Slippage Effect ◽  
Holographic Microscopy ◽  
3D Information ◽  
Experimental Findings

AbstractIn several phenomena in biology and industry, it is required to understand the comprehensive behavior of sedimenting micro-particles in fluids. Here, we use the numerical refocusing feature of digital holographic microscopy (DHM) to investigate the slippage effect on micro-particle sedimentation near a flat wall. DHM provides quantitative phase contrast and three-dimensional (3D) imaging in arbitrary time scales, which suggests it as an elegant approach to investigate various phenomena, including dynamic behavior of colloids. 3D information is obtained by post-processing of the recorded digital holograms. Through analysis of 3D trajectories and velocities of multiple sedimenting micro-particles, we show that proximity to flat walls of higher slip lengths causes faster sedimentation. The effect depends on the ratio of the particle size to (1) the slip length and (2) its distance to the wall. We corroborate our experimental findings by a theoretical model which considers both the proximity and the particle interaction to a wall of different hydrophobicity in the hydrodynamic forces.

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