Mike Marsh
VSG, Applications Engineering, Department Member
Research Interests:
Research Interests:
Research Interests:
Segmenting bone from background is required to quantify bone architecture in computed tomography (CT) image data. A deep learning approach using convolutional neural networks (CNN) is a promising alternative method for automatic... more
Segmenting bone from background is required to quantify bone architecture in computed tomography (CT) image data. A deep learning approach using convolutional neural networks (CNN) is a promising alternative method for automatic segmentation. The study objectives were to evaluate the performance of CNNs in automatic segmentation of human vertebral body (micro-CT) and femoral neck (nano-CT) data and to investigate the performance of CNNs to segment data across scanners.Scans of human L1 vertebral bodies (microCT [North Star Imaging], n=28, 53μm3) and femoral necks (nano-CT [GE], n=28, 27μm3) were used for evaluation. Six slices were selected for each scan and then manually segmented to create ground truth masks (Dragonfly 4.0, ORS). Two-dimensional U-Net CNNs were trained in Dragonfly 4.0 with images of the [FN] femoral necks only, [VB] vertebral bodies only, and [F+V] combined CT data. Global (i.e., Otsu and Yen) and local (i.e., Otsu r = 100) thresholding methods were applied to ea...
Research Interests:
Research Interests:
Research Interests:
AbstractPartially saturated compacted-sand specimens were characterized by using three-dimensional (3D) image registration of dual-modal (neutron and X-ray) tomography data. Neutron and X-ray imaging provide complementary information for... more
AbstractPartially saturated compacted-sand specimens were characterized by using three-dimensional (3D) image registration of dual-modal (neutron and X-ray) tomography data. Neutron and X-ray imaging provide complementary information for precisely identifying the three phases (silica sand, air, and water) of a compacted sand specimen that is partially saturated. Neutron tomography provides high contrast of the water phase, whereas X-ray tomography provides high contrast of the silica sand phase due to different fundamental interaction mechanisms of neutron and X-ray with matters. X-ray interacts with the electron cloud surrounding the nucleus, whereas neutron radiation interacts with the nucleus of an atom. In this paper, a computational technique was developed to unify digital images of dual-modal data obtained at different image resolution and specimen orientations based on the maximization of the normalized mutual information to combine the information from the water phase inferred from a neutron image...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
The complexity of unconventional reservoirs is manifested both in compositional variance of the matrix and the vast heterogeneity of the pore geometry. These complications confound proper understanding of transport properties and,... more
The complexity of unconventional reservoirs is manifested both in compositional variance of the matrix and the vast heterogeneity of the pore geometry. These complications confound proper understanding of transport properties and, consequently, recoverability for all stages in the production life cycle. Imaging techniques have emerged as a technical solution to aid how we decipher these complexities at the appropriate scales. In this study, we use the Woodford Shale as a representative of a commercially viable unconventional reservoir, and we apply multi-scale imaging analytics to a core sample. Our observations across four different length scales from imaging results of micro-x-ray microscopy (micro-XRM), nano-x-ray microscopy (nano-XRM), and focused ion-beam scanning electron microscopy (FIB-SEM) demonstrate both heterogeneity and anisotropy at every scale. We describe our multi-scale imaging workflow, which proved necessary to capture the multi-scale variability. In this instance of siliceous type II source rock, we find that micro-XRM was insufficient to visualize porosity, nano-XRM was sufficient for visualization of only limited porosity, whereas FIB-SEM yielded the resolved pore network. We further find that discrimination of the pore types, with the aid of image segmentation, helps define the connectivity and nature of the transport system. Collectively, the application of imaging across scales with appropriate image processing is required to adequately understand the transport-governing microstructure.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
We explore development of an extensible programmatic workflow combining automated adaptive CNC backside deprocessing with automated plasma FIB Gas-Assisted Delayering and montage SEM imaging. “Intelligent automation” is realized by... more
We explore development of an extensible programmatic workflow combining automated adaptive CNC backside deprocessing with automated plasma FIB Gas-Assisted Delayering and montage SEM imaging. “Intelligent automation” is realized by bridging FIB-SEM instrument control with a “computational image processing engine” using a python scripting API. Tomographic reconstruction via automated back-side ultra-thinning coupled to automated gas-assisted plasma FIB delayering and automated SEM imaging is demonstrated for the first time. Further, we outline and promote development of an instrument control interface which permits secure rapid development of custom proprietary application specific modules without absolute reliance on OEM FIB-SEM hardware or software. Implementation of compressed sensing and dynamic stage scanning to allow arbitrarily large area delayering is
The complexity of unconventional reservoirs is manifested both in compositional variance of the matrix and the vast heterogeneity of the pore geometry. These complications confound proper understanding of transport properties and,... more
The complexity of unconventional reservoirs is manifested both in compositional variance of the matrix and the vast heterogeneity of the pore geometry. These complications confound proper understanding of transport properties and, consequently, recoverability for all stages in the production life cycle. Imaging techniques have emerged as a technical solution to aid how we decipher these complexities at the appropriate scales. In this study, we use the Woodford Shale as a representative of a commercially viable unconventional reservoir, and we apply multi-scale imaging analytics to a core sample. Our observations across four different length scales from imaging results of micro-x-ray microscopy (micro-XRM), nano-x-ray microscopy (nano-XRM), and focused ion-beam scanning electron microscopy (FIB-SEM) demonstrate both heterogeneity and anisotropy at every scale. We describe our multi-scale imaging workflow, which proved necessary to capture the multi-scale variability. In this instance of siliceous type II source rock, we find that micro-XRM was insufficient to visualize porosity, nano-XRM was sufficient for visualization of only limited porosity, whereas FIB-SEM yielded the resolved pore network. We further find that discrimination of the pore types, with the aid of image segmentation, helps define the connectivity and nature of the transport system. Collectively, the application of imaging across scales with appropriate image processing is required to adequately understand the transport-governing microstructure.
Research Interests:
This paper discusses the development of an extensible programmatic workflow that leverages evolving technologies in 2D/3D imaging, distributed instrument control, image processing, and automated mechanical/chemical deprocessing... more
This paper discusses the development of an extensible programmatic workflow that leverages evolving technologies in 2D/3D imaging, distributed instrument control, image processing, and automated mechanical/chemical deprocessing technology. Initial studies involve automated backside mechanical ultra-thinning of 65nm node IC processor chips in combination with SEM imaging and X-ray tomography. Areas as large as 800μm x 800μm were deprocessed using gas-assisted plasma FIB delayering. Ongoing work involves enhancing the workflow with “intelligent automation” by bridging FIB-SEM instrument control and near real-time data analysis to establish a computationally guided microscopy suite.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
It is well established that rocks contain a hierarchically-porous microstructure, with transport phenomena occurring over a range of length scales. Equally, it has been demonstrated that there is no single technique capable of capturing a... more
It is well established that rocks contain a hierarchically-porous microstructure, with transport phenomena occurring over a range of length scales. Equally, it has been demonstrated that there is no single technique capable of capturing a representative volume for a single rock type, or, more appropriately, of a single formation. Here, we demonstrate the union of XRM and FIB-SEM for a comprehensive 3D dataset, representing a porous rock microstructure as viewed across multiple length scales. Further, we show how this information is complementary to traditional laboratory analysis which can provide detailed chemical, mineral, and pore size information, but with spatial averaging over relevant length scales. Using both sets of information gives a more complete understanding of one formation, representing a new paradigm in digital rock analysis. INTRODUCTION One of the classic challenges facing the characterization of hierarchical materials is that of length scale. In the digital analy...
Recombinant human adenovirus is a useful gene delivery vector for clinical gene therapy. Minor capsid protein IX of adenovirus has been of recent interest since multiple studies have shown that modifications can be made to its C terminus... more
Recombinant human adenovirus is a useful gene delivery vector for clinical gene therapy. Minor capsid protein IX of adenovirus has been of recent interest since multiple studies have shown that modifications can be made to its C terminus to alter viral tropism or add molecular tags and/or reporter proteins. We examined the structure of an engineered adenovirus displaying the enhanced green fluorescent protein (EGFP) fused to the C terminus of protein IX. Cryoelectron microscopy and reconstruction localized the C-terminal EGFP fusion between the H2 hexon and the H4 hexon, positioned between adjacent facets, directly above the density previously assigned as protein IIIa. The original assignment of IIIa was based largely on indirect evidence, and the data presented herein support the reassignment of the IIIa density as protein IX.
Research Interests:
Research Interests: Biology, Medicine, Software, Geometric model, Computer Simulation, and 15 moreFeature Detection, Data Display, Interactive Visualization, Protein structure, Proteins, Cryo Electron Microscopy, Interaction model, Protein Conformation, Amino Acid Sequence, Model Building, Atomic Resolution, Biochemistry and cell biology, Atomic model, Molecular Sequence Data, and Secondary structure prediction
SummaryTransmission electron microscopy imaging protocols required by structural scientists vary widely and can be laborious without tailor‐made applications. We present here the jeol automated microscopy expert system (james) api... more
SummaryTransmission electron microscopy imaging protocols required by structural scientists vary widely and can be laborious without tailor‐made applications. We present here the jeol automated microscopy expert system (james) api integrator, a programming library for computer control of transmission electron microscopy operations and equipment. james has been implemented on JEOL microscopes with Gatan CCDs but is designed to be modular so it can be adapted to run on different microscopes and detectors. We have used the james api integrator to develop two applications for low‐dose digital imaging: james imaging application and the mr t tomographic imaging application. Both applications have been widely used within our NCRR‐supported Center for routine data collection and are now made available for public download.
Research Interests: Materials Engineering, Computer Science, Condensed Matter Physics, Electron Microscopy, Microscopy, and 15 moreScanning Electron Microscopy, Transmission Electron Microscopy, Medicine, Software, Low Dose, Microscope, Data acquisition, expert System, Data Collection, Computer Control, Digital Image, X ray Computed Tomography, Modular Design, Reoviridae, and Biochemistry and cell biology
Research Interests:
Research Interests:
Research Interests:
Given the massive increase in the number of new sequences and struc-tures, a critical problem is how to integrate these raw data into meaning-ful biological information. One approach, the Evolutionary Trace, or ET, uses phylogenetic... more
Given the massive increase in the number of new sequences and struc-tures, a critical problem is how to integrate these raw data into meaning-ful biological information. One approach, the Evolutionary Trace, or ET, uses phylogenetic information to rank the residues in a protein sequence by evolutionary importance and then maps those ranked at the top onto a representative structure. If these residues form structural clusters, they can identify functional surfaces such as those involved in molecular rec-ognition. Now that a number of examples have shown that ET can ident-ify binding sites and focus mutational studies on their relevant functional determinants, we ask whether the method can be improved so as to be applicable on a large scale. To address this question, we introduce a new treatment of gaps resulting from insertions and deletions, which stream-lines the selection of sequences used as input. We also introduce objective statistics to assess the significance of the total num...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.