Segmentation of biological images containing multitarget labeling using the jelly filling framework

Biomedical imaging when combined with digital image analysis is capable of quantitative morphological and physiological characterizations of biological structures. Recent fluorescence microscopy techniques can collect hundreds of focal plane images from deeper tissue volumes, thus enabling characterization of three-dimensional (3-D) biological structures at subcellular resolution. Automatic analysis methods are required to obtain quantitative, objective, and reproducible measurements of biological quantities. However, these images typically contain many artifacts such as poor edge details, nonuniform brightness, and distortions that vary along different axes, all of which complicate the automatic image analysis. Another challenge is due to "multitarget labeling," in which a single probe labels multiple biological entities in acquired images. We present a "jelly filling" method for segmentation of 3-D biological images containing multitarget labeling. Intuitively, our iterative segmentation method is based on filling disjoint tubule regions of an image with a jelly-like fluid. This helps in the detection of components that are "floating" within a labeled jelly. Experimental results show that our proposed method is effective in segmenting important biological quantities

Error Resilient Video Coding Using Bitstream Syntax And Iterative Microscopy Image Segmentation

There has been a dramatic increase in the amount of video traffic over the Internet in past several years. For applications like real-time video streaming and video conferencing, retransmission of lost packets is often not permitted. Popular video coding standards such as H.26x and VPx make use of spatial-temporal correlations for compression, typically making compressed bitstreams vulnerable to errors. We propose several adaptive spatial-temporal error concealment approaches for subsampling-based multiple description video coding. These adaptive methods are based on motion and mode information extracted from the H.26x video bitstreams. We also present an error resilience method using data duplication in VPx video bitstreams. A recent challenge in image processing is the analysis of biomedical images acquired using optical microscopy. Due to the size and complexity of the images, automated segmentation methods are required to obtain quantitative, objective and reproducible measurements of biological entities. In this thesis, we present two techniques for microscopy image analysis. Our first method, “Jelly Filling” is intended to provide 3D segmentation of biological images that contain incompleteness in dye labeling. Intuitively, this method is based on filling disjoint regions of an image with jelly-like fluids to iteratively refine segments that represent separable biological entities. Our second method selectively uses a shape-based function optimization approach and a 2D marked point process simulation, to quantify nuclei by their locations and sizes. Experimental results exhibit that our proposed methods are effective in addressing the aforementioned challenges

Automatic Hotspots Detection for Intracellular Calcium Analysis in Fluorescence Microscopic Videos

In recent years, life-cell imaging techniques and their software applications have become powerful tools to investigate complex biological mechanisms such as calcium signalling. In this paper, we propose an automated framework to detect areas inside cells that show changes in their calcium concentration i.e. the regions of interests or hotspots, based on videos taken after loading living mouse cardiomyocytes with fluorescent calcium reporter dyes. The proposed system allows an objective and efficient analysis through the following four key stages: (1) Pre-processing to enhance video quality, (2) First level segmentation to detect candidate hotspots based on adaptive thresholding on the frame level, (3) Second-level segmentation to fuse and identify the best hotspots from the entire video by proposing the concept of calcium fluorescence hit-ratio, and (4) Extraction of the changes of calcium fluorescence over time per hotspot. From the extracted signals, different measurements are calculated such as maximum peak amplitude, area under the curve, peak frequency, and inter-spike interval of calcium changes. The system was tested using calcium imaging data collected from Heart muscle cells. The paper argues that the automated proposal offers biologists a tool to speed up the processing time and mitigate the consequences of inter-intra observer variability

New Techniques in Gastrointestinal Endoscopy

As result of progress, endoscopy has became more complex, using more sophisticated devices and has claimed a special form. In this moment, the gastroenterologist performing endoscopy has to be an expert in macroscopic view of the lesions in the gut, with good skills for using standard endoscopes, with good experience in ultrasound (for performing endoscopic ultrasound), with pathology experience for confocal examination. It is compulsory to get experience and to have patience and attention for the follow-up of thousands of images transmitted during capsule endoscopy or to have knowledge in physics necessary for autofluorescence imaging endoscopy. Therefore, the idea of an endoscopist has changed. Examinations mentioned need a special formation, a superior level of instruction, accessible to those who have already gained enough experience in basic diagnostic endoscopy. This is the reason for what these new issues of endoscopy are presented in this book of New techniques in Gastrointestinal Endoscopy

Mechanisms of Early Brain Morphogenesis

In structures with obvious mechanical function, like the heart and bone, the relationship of mechanical forces to growth and development has been well studied. In contrast, other than the problem of neurulation: formation of the neural tube), developmental mechanisms in the nervous system have received relatively little attention. The central aim of this research is to characterize the biophysical mechanisms that shape the early embryonic brain. Experiments were performed primarily in the chicken brain, which is morphologically similar to humans during early stages of development. Proposed mechanisms were tested using computational models to ensure that hypotheses are consistent with physical law. The brain initially forms as a straight epithelial tube in the embryo: approximately 3 weeks gestation in humans). We first investigated a potential role for mechanical feedback in regulating the development of this structure. We find that the neuroepithelium actively stiffens under decreased loading and softens under increased loading. Nuclear shapes are elongated in stiffer brains and circular in softer brains, consistent with changes in cytoskeletal contractility and wall stress. These results suggest a role for stress-based mechanical feedback in regulating epithelial development. We next investigated the more specific role of cytoskeletal contraction in forming the primary brain vesicles and rhombomeres that subdivide the primitive brain tube. We show that a combination of circumferential contraction in the boundary regions and isotropic contraction between boundaries can generate realistic vesicle morphologies, whereas longitudinal contraction between boundaries likely causes rhombomere formation. Models are used to show how regional variations in contraction may be a function of brain geometry and morphogenetic plasticity. As an extension of the previous study, we show that enhancing contractility in the embryonic chicken brain induces morphologies reminiscent of more primitive species such as frog and fish. In particular, brain cross sections that are relatively circular transform into diamonds, triangles, and narrow slits, shapes that are present in normal zebrafish and Xenopus brains at comparable stages of development. Models show that these shapes are likely produced by locally elevated cytoskeletal contraction, indicating a potential role for differential contractility in early brain development and evolution. In summary, results from this thesis should improve our understanding of the biophysical mechanisms that establish and regulate phenotype in the developing brain. The research begins to establish the framework necessary to connect early-stage mechanisms to interspecies differences in brain morphogenesis that occur during later development