volume-segmentation-analysis-biological-materials-using-survos-super

Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench

Segmentation is the process of isolating specific regions or objects within an imaged volume, so that further study can be undertaken on these areas of ...

Diamond Light Source

Aeration of the lung and the transition to air-breathing at birth is fundamental to mammalian life and initiates major changes in cardiopulmonary physiology. However, the dynamics of this process and the factors involved are largely unknown, because it has not been possible to observe or measure lung aeration on a breath-by-breath basis. We have used the high contrast and spatial resolution of phase contrast X-ray imaging to study lung aeration at birth in spontaneously breathing neonatal rabbits. As the liquid-filled fetal lungs provide little absorption or phase contrast, they are not visible and only become visible as they aerate, allowing a detailed examination of this process. Pups were imaged live from birth to determine the timing and spatial pattern of lung aeration, and relative levels of lung aeration were measured from the images using a power spectral analysis. We report the first detailed observations and measurements of lung aeration, demonstrating its dependence on inspiratory activity and body position; dependent regions aerated at much slower rates. The air/liquid interface moved toward the distal airways only during inspiration, with little proximal movement during expiration, indicating that trans-pulmonary pressures play an important role in airway liquid clearance at birth. Using these imaging techniques, the dynamics of lung aeration and the critical role it plays in regulating the physiological changes at birth can be fully explored.

Imaging lung aeration and lung liquid clearance at birth.

While there is currently a validated dance-specific exercise method of measuring aerobic fitness, no such test has been developed to measure high intensity capabilities in dance. The purpose of this study was to initiate an intermittent high intensity dance-specific fitness test. The test was designed to be able to observe changes in heart rate (HR), thereby allowing for a measurement of physical fitness at high intensities. Sixteen professional dancers (4 males and 12 females) volunteered to take part in this study. The fitness test protocol consists of movements that are representative of contemporary dance, and contains exercise and rest periods that mimic the intermittent nature of dance. The participants performed four trials. The physiological variables measured were HR (b.min(-1)) for each one minute bout of the four minute test for all trials, oxygen uptake (VO(2)) throughout the test, and end blood lactate (BLa mmol.L) for each trial. In addition, five of the participants undertook a maximal oxygen uptake treadmill test, and the scores obtained were compared with those from the dance test. Results show HR consistency across each one minute bout of the test and across each of the four trials of testing for all participants, indicating that the test is reliable. There was good reliability between bouts of each trial (typical error as % of CV = 1.5), intraclass "r" = 0.8, and good reliability between the four trials (typical error as % of CV = 2.1), intraclass "r" = 0.82. There were no significant differences between the maximal VO(2) and BLa scores established in the treadmill and dance tests, demonstrating validity. Thus, the results of this study indicate that the high intensity dance-specific test is a reliable and valid means of assessing and monitoring the cardiovascular fitness of dancers. The test allows dancers to be assessed within an environment that they are accustomed to (the studio), using a mode of exercise that is relevant (dance), and it is of adequate intensity to be representative of performance.

The development of a high intensity dance performance fitness test.

We present a time-resolved tomographic reconstruction of the velocity field associated with pulsatile blood flow through a rotationally-symmetric stenotic vessel model. The in-vitro sample was imaged using propagation-based phase contrast with monochromated X-rays from a synchrotron undulator source, and a fast shutter-synchronized detector with high-resolution used to acquire frames of the resulting dynamic speckle pattern. Having used phase retrieval to decode the phase contrast from the speckle patterns, the resulting projected-density maps were analysed using the statistical correlation methods of particle image velocimetry (PIV). This yields the probability density functions of blood-cell displacement within the vessel. The axial velocity-field component of the rotationally-symmetric flow was reconstructed using an inverse-Abel transform. A modified inverse-Abel transform was used to reconstruct the radial component. This vector tomographic phase-retrieval velocimetry was performed over the full pumping cycle, to completely characterize the velocity field of the pulsatile blood flow in both space and time.

Vector tomographic X-ray phase contrast velocimetry utilizing dynamic blood speckle.

The purpose of this study was to investigate a selection of psychological variables (help-seeking behaviors, mental imagery, self-esteem) in relation to injury among UK dancers. We recruited 216 participants from eight dance styles and six levels of involvement. It was found that 83.5% of the participants had experienced at least one injury in the past year. The most common response to injury was to inform someone, and most continued to dance when injured, albeit carefully. Physical therapy was the most common treatment sought when an injury occurred (38.1%), and dancers seemed to follow recommendations offered. Injured and non-injured dancers did not differ in their imagery frequencies (facilitative, debilitative, or injury-related) and scored similarly (and relatively high) in self-esteem. Neither facilitative nor debilitative imagery was correlated with self-esteem, but dancers who engaged in more facilitative imagery in general also reported doing so when injured. Altogether, it appears that injury is not related to dancers' self-esteem or imagery, at least not when injuries are mild or moderate. Even so, such conclusions should be made with caution, given that most dancers do sustain at least one injury each year.

Injury, imagery, and self-esteem in dance healthy minds in injured bodies?

Rats display little to no haversian remodeling of cortical bone. This fact, combined with the endochondral formation of cortical bone, means that rat femoral cortical bone contains highly mineralized cartilage islands in a central band of mid-femoral cross sections. We demonstrate that these islands have a significantly higher degree of mineralization than the surrounding bone, using quantitative backscattered electron imaging. The cartilaginous nature of the islands was verified by immunostaining for collagen type II. Toluidine blue staining of longitudinal sections and three-dimensional synchrotron radiation X-ray tomographic microscopy confirmed that the islands are elongated along the femoral long axis. Nanoindentation revealed significantly higher values of both reduced modulus and hardness in the islands compared to the surrounding bone, reflecting a higher degree of mineralization. The calcified cartilage islands were distributed in a central zone of the bone, from the growth plates through the mid-femoral bone. The presence of these cartilage islands and their possible effect on mechanical properties could be an additional reason why haversian remodeling is observed in higher-order species.

Calcified cartilage islands in rat cortical bone.

Newly developed high-speed, synchrotron-based X-ray computed microtomography enabled us to directly image pore-scale displacement events in porous rock in real time. Common approaches to modeling macroscopic fluid behavior are phenomenological, have many shortcomings, and lack consistent links to elementary pore-scale displacement processes, such as Haines jumps and snap-off. Unlike the common singular pore jump paradigm based on observations of restricted artificial capillaries, we found that Haines jumps typically cascade through 10-20 geometrically defined pores per event, accounting for 64% of the energy dissipation. Real-time imaging provided a more detailed fundamental understanding of the elementary processes in porous media, such as hysteresis, snap-off, and nonwetting phase entrapment, and it opens the way for a rigorous process for upscaling based on thermodynamic models.

Real-time 3D imaging of Haines jumps in porous media flow.

Phase contrast x-ray imaging (PCXI) is a promising imaging modality, capable of sensitively differentiating soft tissue structures at high spatial resolution. However, high sensitivity often comes at the cost of a long exposure time or multiple exposures per image, limiting the imaging speed and possibly increasing the radiation dose. Here, we demonstrate a PCXI method that uses a single short exposure to sensitively capture sample phase information, permitting high speed x-ray movies and live animal imaging. The method illuminates a checkerboard phase grid to produce a fine grid-like intensity reference pattern at the detector, then spatially maps sample-induced distortions of this pattern to recover differential phase images of the sample. The use of a phase grid is an improvement on our previous absorption grid work in two ways. There is minimal loss in x-ray flux, permitting faster imaging, and, a very fine pattern is produced for homogenous high spatial resolution. We describe how this pattern permits retrieval of five images from a single exposure; the sample phase gradient images in the horizontal and vertical directions, a projected phase depth image, an edge-enhanced image, and a type of scattering image. Finally, we describe how the reconstruction technique can achieve subpixel distortion retrieval and study the behavior of the technique in regard to analysis technique, Talbot distance, and exposure time.

A sensitive x-ray phase contrast technique for rapid imaging using a single phase grid analyzer.

Floods can completely submerge terrestrial plants but some wetland species can sustain O2 and CO2 exchange with the environment via gas films forming on superhydrophobic leaf surfaces. We used high resolution synchrotron X-ray phase contrast micro-tomography in a novel approach to visualise gas films on submerged leaves of common cordgrass (Spartina anglica). 3D tomograms enabled a hitherto unmatched level of detail regarding the micro-topography of leaf gas films. Gas films formed only on the superhydrophobic adaxial leaf side (water droplet contact angle, Φ=162°) but not on the abaxial side (Φ=135°). The adaxial side of the leaves of common cordgrass is plicate with a longitudinal system of parallel grooves and ridges and the vast majority of the gas film volume was found in large ∼180μm deep elongated triangular volumes in the grooves and these volumes were connected to each neighbouring groove via a fine network of gas tubules (∼1.7μm diameter) across the ridges. In addition to the gas film retained on the leaf exterior, the X-ray phase contrast micro-tomography also successfully distinguished gas spaces internally in the leaf tissues, and the tissue porosity (gas volume per unit tissue volume) ranged from 6.3% to 20.3% in tip and base leaf segments, respectively. We conclude that X-ray phase contrast micro-tomography is a powerful tool to obtain quantitative data of exterior gas features on biological samples because of the significant difference in electron density between air, biological tissues and water.

Visualisation by high resolution synchrotron X-ray phase contrast micro-tomography of gas films on submerged superhydrophobic leaves.

Data-constrained modeling is a method that enables three-dimensional distribution of mineral phases and porosity in a sample to be modeled based on micro-computed tomography scans acquired at different X-ray energies. Here we describe an alternative method for measuring porosity, synchrotron K-edge subtraction using xenon gas as a contrast agent. Results from both methods applied to the same Darai limestone sample are compared. Reasonable agreement between the two methods and with other porosity measurements is obtained. The possibility of a combination of data-constrained modeling and K-edge subtraction methods for more accurate sample characterization is discussed.

Characterization of Darai Limestone Composition and Porosity Using Data-Constrained Modeling and Comparison with Xenon K-Edge Subtraction Imaging.

X-ray phase contrast enables weakly-attenuating structures to be imaged, with bright synchrotron sources adding the ability to capture time sequences and analyse sample dynamics. Here, we describe the translation of dynamical differential phase contrast imaging from the synchrotron to a compact x-ray source, in order to achieve this kind of time sequence imaging in the laboratory. We formulate broadly-applicable set-up guidelines for the single-grid, single-exposure imaging technique using a divergent source, exploring the experimental factors that restrict set-up size, imaging sensitivity and sample size. Experimental images are presented using the single-grid phase contrast technique with a steel attenuation grid and a liquid-metal-jet x-ray source, enabling exposure times as short as 0.5 s for dynamic imaging. Differential phase contrast images were retrieved from phantoms, incorporating noise filtering to improve the low-count images encountered when imaging dynamics using short exposures.

Requirements for dynamical differential phase contrast x-ray imaging with a laboratory source.

Small angle x-ray scattering has been proven to be a valuable method for accessing structural information below the spatial resolution limit implied by direct imaging. Here, we theoretically derive the relation that links the subpixel differential phase signal provided by the sample to the moments of scattering distributions accessible by refraction sensitive x-ray imaging techniques. As an important special case we explain the scatter or dark-field contrast in terms of the sample's phase signal. Further, we establish that, for binary phase objects, the nth moment scales with the difference of the refractive index decrement to the power of n. Finally, we experimentally demonstrate the utility of the moments by quantitatively determining the particle sizes of a range of powders with a laboratory-based setup.

Article	Year
Imaging lung aeration and lung liquid clearance at birth. FASEB journal : official publication of the Federation of American Societies for Experimental Biology\| PubMed ID: 17536040	2007
The development of a high intensity dance performance fitness test. Journal of dance medicine & science : official publication of the International Association for Dance Medicine & Science\| PubMed ID: 19416609	2009
Vector tomographic X-ray phase contrast velocimetry utilizing dynamic blood speckle. Optics express\| PubMed ID: 20174067	2010
Injury, imagery, and self-esteem in dance healthy minds in injured bodies? Journal of dance medicine & science : official publication of the International Association for Dance Medicine & Science\| PubMed ID: 21703096	2011
Calcified cartilage islands in rat cortical bone. Calcified tissue international\| PubMed ID: 23274728	2013
Real-time 3D imaging of Haines jumps in porous media flow. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23431151	2013
A sensitive x-ray phase contrast technique for rapid imaging using a single phase grid analyzer. Optics letters\| PubMed ID: 24322085	2013
Visualisation by high resolution synchrotron X-ray phase contrast micro-tomography of gas films on submerged superhydrophobic leaves. Journal of structural biology\| PubMed ID: 25175398	2014
Characterization of Darai Limestone Composition and Porosity Using Data-Constrained Modeling and Comparison with Xenon K-Edge Subtraction Imaging. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada\| PubMed ID: 26021343	2015
Requirements for dynamical differential phase contrast x-ray imaging with a laboratory source. Physics in medicine and biology\| PubMed ID: 27893458	2016
Interpretation and Utility of the Moments of Small-Angle X-Ray Scattering Distributions. Physical review letters\| PubMed ID: 28707948	2017

Sarah Irvine

Biography

JoVE Journal Publications

Other Publications