scholarly journals Simultaneous imaging of hard and soft biological tissues in a low-field dental MRI scanner

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
José M. Algarín ◽  
Elena Díaz-Caballero ◽  
José Borreguero ◽  
Fernando Galve ◽  
Daniel Grau-Ruiz ◽  
...  
Keyword(s):  
Spatial Information ◽  
Ex Vivo ◽  
Signal To Noise Ratio ◽  
Spin Echo ◽  
Pulse Sequences ◽  
Three Dimensional ◽  
Biological Tissues ◽  
Human Teeth ◽  
Low Field ◽  
The Impact

AbstractMagnetic Resonance Imaging (MRI) of hard biological tissues is challenging due to the fleeting lifetime and low strength of their response to resonant stimuli, especially at low magnetic fields. Consequently, the impact of MRI on some medical applications, such as dentistry, continues to be limited. Here, we present three-dimensional reconstructions of ex-vivo human teeth, as well as a rabbit head and part of a cow femur, all obtained at a field strength of 260 mT. These images are the first featuring soft and hard tissues simultaneously at sub-Tesla fields, and they have been acquired in a home-made, special-purpose, pre-medical MRI scanner designed with the goal of demonstrating dental imaging at low field settings. We encode spatial information with two pulse sequences: Pointwise-Encoding Time reduction with Radial Acquisition and a new sequence we have called Double Radial Non-Stop Spin Echo, which we find to perform better than the former. For image reconstruction we employ Algebraic Reconstruction Techniques (ART) as well as standard Fourier methods. An analysis of the resulting images shows that ART reconstructions exhibit a higher signal-to-noise ratio with a more homogeneous noise distribution.

scholarly journals Quantitative Radiomics: Impact of Pulse Sequence Parameter Selection on MRI-Based Textural Features of the Brain

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
John Ford ◽  
Nesrin Dogan ◽  
Lori Young ◽  
Fei Yang
Keyword(s):  
Pulse Sequence ◽  
Spin Echo ◽  
Pulse Sequences ◽  
Parameter Selection ◽  
Inversion Recovery ◽  
Textural Features ◽  
Imaging Data ◽  
Gradient Echo ◽  
The Impact ◽  
The Brain

Objectives. Radiomic features extracted from diverse MRI modalities have been investigated regarding their predictive and/or prognostic value in a variety of cancers. With the aid of a 3D realistic digital MRI phantom of the brain, the aim of this study was to examine the impact of pulse sequence parameter selection on MRI-based textural parameters of the brain. Methods. MR images of the employed digital phantom were realized with SimuBloch, a simulation package made for fast generation of image sequences based on the Bloch equations. Pulse sequences being investigated consisted of spin echo (SE), gradient echo (GRE), spoiled gradient echo (SP-GRE), inversion recovery spin echo (IR-SE), and inversion recovery gradient echo (IR-GRE). Twenty-nine radiomic textural features related, respectively, to gray-level intensity histograms (GLIH), cooccurrence matrices (GLCOM), zone size matrices (GLZSM), and neighborhood difference matrices (GLNDM) were evaluated for the obtained MR realizations, and differences were identified. Results. It was found that radiomic features vary considerably among images generated by the five different T1-weighted pulse sequences, and the deviations from those measured on the T1 map vary among features, from a few percent to over 100%. Radiomic features extracted from T1-weighted spin-echo images with TR varying from 360 ms to 620 ms and TE = 3.4 ms showed coefficients of variation (CV) up to 45%, while up to 70%, for T2-weighted spin-echo images with TE varying over the range 60–120 ms and TR = 6400 ms. Conclusion. Variability of radiologic textural appearance on MR realizations with respect to the choice of pulse sequence and imaging parameters is feature-dependent and can be substantial. It calls for caution in employing MRI-derived radiomic features especially when pooling imaging data from multiple institutions with intention of correlating with clinical endpoints.

Rapid Lumbar Spine MR Myelography: Imaging Findings Using a Single-Shot Technique

1997 ◽  
Vol 10 (2) ◽  
pp. 181-187 ◽  
Author(s):  
P. Demaerel ◽  
P. Van Hover ◽  
A. Broeders ◽  
B. Kiefer ◽  
A.L. Baert
Keyword(s):  
Spin Echo ◽  
Pulse Sequences ◽  
Three Dimensional ◽  
Projection Algorithm ◽  
Fast Spin Echo ◽  
Single Shot ◽  
Rapid Acquisition ◽  
Spin Echo Sequence ◽  
Echo Pulse ◽  
Mr Myelography

MR myelography has been performed by several authors. Most authors have used techniques based on three-dimensional gradient-echo pulse sequences or fast spin-echo pulse sequences. The examination time varied between 5 and 13 minutes and postprocessing with a maximum-intensity projection algorithm was necessary for three-dimensional visualization. The rapid acquisition with relaxation enhancement (RARE) was initially described by Hennig et Al. In this technical note we present our experience with a single-shot turbo spin-echo sequence, derived from RARE, of approximately 2 seconds to obtain one view. MR myelography can replace conventional myelography in all different types of pathology. In addition MR myelography provides additional information compared to MR imaging in a minority of the cases. Taking into account the ultra-rapid acquisition and the absence of postprocessing procedures, we recommended this technique in the appropriate clinical setting. The MR myelogram increases the level of conficence of the neuroradiologist.

A unique three-dimensional model for evaluating the impact of therapy on multiple myeloma

Blood ◽  
2008 ◽  
Vol 112 (7) ◽  
pp. 2935-2945 ◽  
Author(s):  
Julia Kirshner ◽  
Kyle J. Thulien ◽  
Lorri D. Martin ◽  
Carina Debes Marun ◽  
Tony Reiman ◽  
...  
Keyword(s):  
Stem Cells ◽  
Multiple Myeloma ◽  
Plasma Cells ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Preclinical Model ◽  
Drug Resistant ◽  
Three Dimensional Model ◽  
The Impact

AbstractAlthough the in vitro expansion of the multiple myeloma (MM) clone has been unsuccessful, in a novel three-dimensional (3-D) culture model of reconstructed bone marrow (BM, n = 48) and mobilized blood autografts (n = 14) presented here, the entire MM clone proliferates and undergoes up to 17-fold expansion of malignant cells harboring the clonotypic IgH VDJ and characteristic chromosomal rearrangements. In this system, MM clone expands in a reconstructed microenvironment that is ideally suited for testing specificity of anti-MM therapeutics. In the 3-D model, melphalan and bortezomib had distinct targets, with melphalan targeting the hematopoietic, but not stromal com-partment. Bortezomib targeted only CD138+CD56+ MM plasma cells. The localization of nonproliferating cells to the reconstructed endosteum, in contact with N-cadherin–positive stroma, suggested the presence of MM-cancer stem cells. These drug-resistant CD20+ cells were enriched more than 10-fold by melphalan treatment, exhibited self-renewal, and generated clonotypic B and plasma cell progeny in colony forming unit assays. This is the first molecularly verified demonstration of proliferation in vitro by ex vivo MM cells. The 3-D culture provides a novel biologically relevant preclinical model for evaluating therapeutic vulnerabilities of all compartments of the MM clone, including presumptive drug-resistant MM stem cells.

scholarly journals Deep Learning For Denoising Hi-C Chromosomal Contact Data

2019 ◽  
Author(s):  
Max Highsmith ◽  
Oluwatosin Oluwadare ◽  
Jianlin Cheng
Keyword(s):  
Deep Learning ◽  
Signal To Noise Ratio ◽  
Pearson Correlation ◽  
3D Structure ◽  
Three Dimensional ◽  
Yeast Genome ◽  
Chromosome Conformation ◽  
Contact Matrix ◽  
The Impact

AbstractMotivationThe three-dimensional (3D) organization of an organism’s genome and chromosomes plays a significant role in many biological processes. Currently, methods exist for modeling chromosomal 3D structure using contact matrices generated via chromosome conformation capture (3C) techniques such as Hi-C. However, the effectiveness of these methods is inherently bottlenecked by the quality of the Hi-C data, which may be corrupted by experimental noise. Consequently, it is valuable to develop methods for eliminating the impact of noise on the quality of reconstructed structures.ResultsWe develop unsupervised and semi-supervised deep learning algorithms (i.e. deep convolutional autoencoders) to denoise Hi-C contact matrix data and improve the quality of chromosome structure predictions. When applied to noisy synthetic contact matrices of the yeast genome, our network demonstrates consistent improvement across metrics for contact matrix similarity including: Pearson Correlation, Spearman Correlation and Signal-to-Noise Ratio. Positive improvement across these metrics is seen consistently across a wide space of parameters to both gaussian and poisson noise [email protected] and [email protected]

Biological applications of microscopic magnetic resonance imaging

1993 ◽  
Vol 51 ◽  
pp. 90-91
Author(s):  
Russell E. Jacobs ◽  
S. Earl Fraser
Keyword(s):  
Magnetic Resonance ◽  
Spatial Resolution ◽  
Biological Samples ◽  
Spatial Information ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Water Concentration ◽  
Clinical Tool ◽  
Mr Image ◽  
Magnetic Field Gradients

The ability of MRI to provide three dimensional images of thick opaque samples in a noninvasive manner has made it an extremely important clinical tool. In addition, the large number of types of contrast mechanisms in a MR experiment offer the clinician and research scientist the possibility of adapting the image contrast to fit the problem of interest. While typical resolutions employed clinically are on the order of a millimeter, the notion of using MRI at microscopic resolutions arose early in the development of this technique. Spatial information is encoded in both the frequency and phase of the nuclear magnetic resonance signal by selective application of magnetic field gradients. Spatial resolution in biological samples is typically limited by a number of physical effects as well as signal-to-noise ratio (S/N) considerations. Estimate of the theoretical limits of resolution in the MR image arising from these phenomena range from 2 to 0.5μm. The practical spatial resolution is currently determined by the S/N which is often limited by the amount of time available to actually acquire the image (i.e. the temporal resolution). For example, a reasonable S/N clinical MR image can be obtained in about 5 minutes with a voxel (volume element) size of (1mm). We are interested in voxels down to ∼1μm on a side. Because most of the proton MR signal arises from water in biological samples and water concentration is roughly constant, the S/N change in the image will be proportional to the volume change: a factor of 10−9. Of course, this is true only if all experimental parameters are the same.

scholarly journals The Effect of Mechanical Overloading on Surface Roughness of the Coronary Arteries

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Hanna E. Burton ◽  
Daniel M. Espino
Keyword(s):  
Surface Roughness ◽  
Coronary Arteries ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Longitudinal Direction ◽  
Biological Tissues ◽  
Chemical Processing ◽  
Physiological Loading ◽  
Before And After ◽  
Tissue Specimens

Background. Surface roughness can be used to identify disease within biological tissues. Quantifying surface roughness in the coronary arteries aids in developing treatments for coronary heart disease. This study investigates the effect of extreme physiological loading on surface roughness, for example, due to a rupture of an artery.Methods. The porcine left anterior descending (LAD) coronary arteries were dissected ex vivo.Mechanical overloading was applied to the arteries in the longitudinal direction to simulate extreme physiological loading. Surface roughness was calculated from three-dimensional reconstructed images. Surface roughness was measured before and after damage and after chemical processing to dehydrate tissue specimens.Results. Control specimens confirmed that dehydration alone results in an increase of surface roughness in the circumferential direction only. No variation was noted between the hydrated healthy and damaged specimens, in both the longitudinal (0.91±0.26and1.05±0.25 μm) and circumferential (1.46±0.38and1.47±0.39 μm) directions. After dehydration, an increase in surface roughness was noted for damaged specimens in both the longitudinal (1.28±0.33 μm) and circumferential (1.95±0.56 μm) directions.Conclusions. Mechanical overloading applied in the longitudinal direction did not significantly affect surface roughness. However, when combined with chemical processing, a significant increase in surface roughness was noted in both the circumferential and longitudinal directions. Mechanical overloading causes damage to the internal constituents of the arteries, which is significantly noticeable after dehydration of tissue.

scholarly journals Cellular maps of gastrointestinal organs: getting the most from tissue clearing

2020 ◽  
Vol 319 (1) ◽  
pp. G1-G10
Author(s):  
Cambrian Y. Liu ◽  
D. Brent Polk
Keyword(s):  
Large Scale ◽  
Alimentary Tract ◽  
Three Dimensional ◽  
Short Review ◽  
Biological Tissues ◽  
Tissue Clearing ◽  
Relative Paucity ◽  
Whole Mount ◽  
Chemical Concepts ◽  
The Impact

The development of modern methods to induce optical transparency (“clearing”) in biological tissues has enabled the three-dimensional (3D) reconstruction of intact organs at cellular resolution. New capabilities in visualization of rare cellular events, long-range interactions, and irregular structures will facilitate novel studies in the alimentary tract and gastrointestinal systems. The tubular geometry of the alimentary tract facilitates large-scale cellular reconstruction of cleared tissue without specialized microscopy setups. However, with the rapid pace of development of clearing agents and current relative paucity of research groups in the gastrointestinal field using these techniques, it can be daunting to incorporate tissue clearing into experimental workflows. Here, we give some advice and describe our own experience bringing tissue clearing and whole mount reconstruction into our laboratory’s investigations. We present a brief overview of the chemical concepts that underpin tissue clearing, what sorts of questions whole mount imaging can answer, how to choose a clearing agent, an example of how to clear and image alimentary tissue, and what to do after obtaining the image. This short review will encourage other gastrointestinal researchers to consider how utilizing tissue clearing and creating 3D “maps” of tissue might deepen the impact of their studies.

scholarly journals Pressure-Enabled Drug Delivery Approach in the Pancreas with Retrograde Venous Infusion of Lipiodol with Ex Vivo Analysis

2020 ◽  
Vol 44 (1) ◽  
pp. 141-149
Author(s):  
Aravind Arepally ◽  
James Chomas ◽  
Steven C. Katz ◽  
David Jaroch ◽  
K. Pallav Kolli ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Ex Vivo ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Organ Damage ◽  
Pancreatic Tissue ◽  
Histological Evaluation ◽  
Ethiodized Oil ◽  
Venous Infusion ◽  
Infusion System

Abstract Purpose To determine the safety and feasibility of pancreatic retrograde venous infusion (PRVI) utilizing a microvalvular infusion system (MVI) to deliver ethiodized oil (lipiodol) by means of the Pressure-Enabled Drug Delivery (PEDD) approach. Methods Utilizing transhepatic access, mapping of the pancreatic body and head venous anatomy was performed in 10 swine. PEDD was performed by cannulation of veins in the head (n = 4) and body (n = 10) of the pancreas with a MVI (Surefire® Infusion System (SIS), Surefire Medical, Inc (DBA TriSalus™ Life Sciences)) followed by infusion with lipiodol. Sets of animals were killed either immediately (n = 8) or at 4 days post-PRVI (n = 2). All pancreata were harvested and studied with micro-CT and histology. We also performed three-dimensional volumetric/multiplanar imaging to assess the vascular distribution of lipiodol within the glands. Results A total of 14 pancreatic veins were successfully infused with an average of 1.7 (0.5–2.0) mL of lipiodol. No notable change in serum chemistries was seen at 4 days. The signal-to-noise ratio (SNR) of lipiodol deposition was statistically increased both within the organ in target relative to non-target pancreatic tissue and compared to extra pancreatic tissue (p < 0.05). Histological evaluation demonstrated no evidence of pancreatic edema or ischemia. Conclusions PEDD using the RVI approach for targeted pancreatic infusions is technically feasible and did not result in organ damage in this pilot animal study.

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