Convolutional nets for reconstructing neural circuits from brain images acquired by serial section electron microscopy

Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional nets were first applied to neuronal boundary detection a dozen years ago, and have now achieved impressive accuracy on clean images. Robust handling of image defects is a major outstanding challenge. Convolutional nets are also being employed for other tasks in neural circuit reconstruction: finding synapses and identifying synaptic partners, extending or pruning neuronal reconstructions, and aligning serial section images to create a 3D image stack. Computational systems are being engineered to handle petavoxel images of cubic millimeter brain volumes

ZeVis: A Visual Analytics System for Exploration of a Larval Zebrafish Brain in Serial-Section Electron Microscopy Images

The automation and improvement of nano-scale electron microscopy imaging technologies have expanded a push in neuroscience to understand brain circuits at the scale of individual cells and their connections. Most of this research effort, called 'connectomics', has been devoted to handling, processing, and segmenting large-scale image data to reconstruct graphs of neuronal connectivity. However, connectomics datasets contain a wealth of high-resolution information about the brain that could be leveraged to understand its detailed anatomy beyond just the connections between neurons, such as cell morphologies and distributions. This study introduces a novel visualization system, ZeVis, for the interactive exploration of a whole larval zebrafish brain using a terabyte-scale serial-section electron microscopy dataset. ZeVis combines 2D cross-sectional views and 3D volumetric visualizations of the input serial-section electron microscopy data with overlaid segmentation results to facilitate the analyses of various brain structures and their interpretations. The system also provides a graph-based data processing interface to generate subsets of feature segmentation data easily. The segmentation data can be filtered by morphological features or anatomical constraints, allowing statistical analysis and comparisons across regions. We applied ZeVis to actual data of a terabyte-scale whole-brain larval zebrafish and analyzed cell nucleus distributions in several anatomical regions

Towards Fast and High-quality Biomedical Image Reconstruction

Department of Computer Science and EngineeringReconstruction is an important module in the image analysis pipeline with purposes of isolating the majority of meaningful information that hidden inside the acquired data. The term ???reconstruction??? can be understood and subdivided in several specific tasks in different modalities. For example, in biomedical imaging, such as Computed Tomography (CT), Magnetic Resonance Image (MRI), that term stands for the transformation from the, possibly fully or under-sampled, spectral domains (sinogram for CT and k-space for MRI) to the visible image domains. Or, in connectomics, people usually refer it to segmentation (reconstructing the semantic contact between neuronal connections) or denoising (reconstructing the clean image). In this dissertation research, I will describe a set of my contributed algorithms from conventional to state-of-the-art deep learning methods, with a transition at the data-driven dictionary learning approaches that tackle the reconstruction problems in various image analysis tasks.clos

Computer aided detection of natural reference markers in serial radiographs of growing bone

This thesis describes the theoretical and experimental development and testing of a computer-based image processing system for the detection of stable structural features in serial radiographs of growing bone. The study is divided into three parts. First, a simple theoretical model for the detection of stable structures in a radiographic sequence was developed together with a more detailed statistical model of the processes which hinder detection. Analysis of the models indicated that the processing procedures needed to perform the detection were those described by the so-called "matched filter equation". Secondly, the assumptions of the model were tested in a series of experiments using serial radiographs of 24 children with implanted tantalum markers, drawn from the files of the University of Washington, USA. Information gained from these experiments prompted changes to the detection method to allow the radiographic data to comply with these assumptions and provide robustness against image noise. The method was implemented as a semi-automatic image processing system on a Sun 3/160 computer. The system was tested in a further series of experiments using a second sample of radiographs of 28 children with implanted markers and with radiographs of dried human skulls. The results of these experiments indicated that the system could detect persistent structural features whose positions were consistent with the stable tantalum markers and that the system was robust against minor changes in projection between radiographs. Finally, the detection system was applied to the investigation of mandibular incisor eruption from intra-alveolar to pubertal eruption stages using serial lateral cephalometric radiographs of 11 children. This investigation revealed two new features of incisor eruption: first, the eruption paths deviated lingually at, or just prior to, alveolar emergence; and second, post-emergence eruption was characterised by a labio-lingual oscillation of the crowns of the incisors

Fluorescence Methods for Investigation of Living Cells and Microorganisms

Fluorescence methods play a leading role in the investigation of biological objects. They are the only non-destructive methods for investigating living cells and microorganisms in vivo. Using intrinsic and artificial fluorescence methods provides deep insight into mechanisms underlying physiological and biochemical processes. This book covers a wide range of modern methods involved in experimental biology. It illustrates the use of fluorescence microscopy and spectroscopy, confocal laser scanning microscopy, flow cytometry, delayed fluorescence, pulse-amplitude-modulation fluorometry, and fluorescent dye staining protocols. This book provides an overview of practical and theoretical aspects of fluorescence methods and their successful application in the investigation of static and dynamic processes in living cells and microorganisms

1994 OURE report, including the 4th Annual UMR Undergraduate Research Symposium -- Entire Proceedings

The Opportunities for Undergraduate Research Experience program began in 1990. This volume constitutes the proceedings of the fourth annual OURE program. The goals of the program are: (1) to expand opportunities for a more active form of learning by students; (2) to encourage the direct interaction of undergraduate students with faculty through research; (3) to expand the level of research activity on the campus; (4) to help encourage superior students to pursue graduate study; and (5) to reinforce the idea that teaching and research are compatible and mutually reinforcing at a research university. The OURE program continues to achieve its goals -- UMR students have performed research on a wide variety of topics, have worked closely with faculty and have experienced first-hand both the excitement and the frustration of performing research. This volume contains papers presented at the fourth annual UMR Undergraduate Research Symposium held on March 23, 1994, and final reports of students participating in the 1993-94 OURE program. Students in the OURE program are encouraged to participate in the Symposium and participation increased substantially this year. Through programs such as this, the University of Missouri--Rolla, Missouri’s Technological University, continues to provide opportunities for its undergraduate students to further their research experiences in preparation for their future endeavors

Molecular phylogeny of horseshoe crab using mitochondrial Cox1 gene as a benchmark sequence

An effort to assess the utility of 650 bp Cytochrome C oxidase subunit I (DNA barcode) gene in delineating the members horseshoe crabs (Family: xiphosura) with closely related sister taxa was made. A total of 33 sequences were extracted from National Center for Biotechnological Information (NCBI) which include horseshoe crabs, beetles, common crabs and scorpion sequences. Constructed phylogram showed beetles are closely related with horseshoe crabs than common crabs. Scorpion spp were distantly related to xiphosurans. Phylogram and observed genetic distance (GD) date were also revealed that Limulus polyphemus was closely related with Tachypleus tridentatus than with T.gigas. Carcinoscorpius rotundicauda was distantly related with L.polyphemus. The observed mean Genetic Distance (GD) value was higher in 3rd codon position in all the selected group of organisms. Among the horseshoe crabs high GC content was observed in L.polyphemus (38.32%) and lowest was observed in T.tridentatus (32.35%). We conclude that COI sequencing (barcoding) could be used in identifying and delineating evolutionary relatedness with closely related specie

Crab and cockle shells as heterogeneous catalysts in the production of biodiesel

In the present study, the waste crab and cockle shells were utilized as source of calcium oxide to transesterify palm olein into methyl esters (biodiesel). Characterization results revealed that the main component of the shells are calcium carbonate which transformed into calcium oxide upon activated above 700 °C for 2 h. Parametric studies have been investigated and optimal conditions were found to be catalyst amount, 5 wt.% and methanol/oil mass ratio, 0.5:1. The waste catalysts perform equally well as laboratory CaO, thus creating another low-cost catalyst source for producing biodiesel. Reusability results confirmed that the prepared catalyst is able to be reemployed up to five times. Statistical analysis has been performed using a Central Composite Design to evaluate the contribution and performance of the parameters on biodiesel purity