Probabilistic Model-Based Cell Tracking

The study of cell behavior is of crucial importance in drug and disease research. The fields of bioinformatics and biotechnology rely on the collection, processing, and analysis of huge numbers of biocellular images, including cell features such as cell size, shape, and motility. However manual methods of inferring these values are so onerous that automated methods of cell tracking and segmentation are in high demand. In this paper, a novel model-based cell tracker is designed to locate and track individual cells. The proposed cell tracker has been successfully applied to track hematopoietic stem cells (HSCs) based on identified cell locations and probabilistic data association

Association Factor for Identifying Linear and Nonlinear Correlations in Noisy Conditions

Background: In data analysis and machine learning, we often need to identify and quantify the correlation between variables. Although Pearson’s correlation coefficient has been widely used, its value is reliable only for linear relationships and Distance correlation was introduced to address this shortcoming. Methods: Distance correlation can identify linear and nonlinear correlations. However, its performance drops in noisy conditions. In this paper, we introduce the Association Factor (AF) as a robust method for identification and quantification of linear and nonlinear associations in noisy conditions. Results: To test the performance of the proposed Association Factor, we modeled several simulations of linear and nonlinear relationships in different noise conditions and computed Pearson’s correlation, Distance correlation, and the proposed Association Factor. Conclusion: Our results show that the proposed method is robust in two ways. First, it can identify both linear and nonlinear associations. Second, the proposed Association Factor is reliable in both noiseless and noisy conditions

A combined Bayesshrink wavelet-ridgelet technique for image denoising

In this paper a combined BayesShrink Wavelet-Ridgelet denoising method is presented. In our previous work we have showed that BayesShrink Ridgelet performs better than VisuShrink Ridgelet and VisuShrink Wavelet. Although our BayesShrink Ridgelet technique performs somewhat poorer in comparison with BayesShrink Wavelet, based on SNR, visually it produces smoother results, especially for images with straight lines. In the proposed method BayesShrink Wavelet is combined with BayesShrink Ridgelet denoising method which performs better than each filter individually. The proposed combined denoising method gains the advantage of each filter in its specific domain, i.e., Wavelet for natural and Ridgelet for straight regions, and produces better and smoother results, both visually and in terms of SNR. 1

Optimized Multichannel Filter Bank with Flat Frequency Response for Texture Segmentation

<p/> <p>Previous approaches to texture analysis and segmentation use multichannel filtering by applying a set of filters in the frequency domain or a set of masks in the spatial domain. This paper presents two new texture segmentation algorithms based on multichannel filtering in conjunction with neural networks for feature extraction and segmentation. The features extracted by Gabor filters have been applied for image segmentation and analysis. Suitable choices of filter parameters and filter bank coverage in the frequency domain to optimize the filters are discussed. Here we introduce two methods to optimize Gabor filter bank. First, a Gabor filter bank with a flat response is implemented and the optimal feature dimension is extracted by competitive networks. Second, a subset of Gabor filter bank is selected to compose the best discriminative filters, so that each filter in this small set can discriminate a pair of textures in a given image. In both approaches, multilayer perceptrons are employed to segment the extracted features. The comparisons of segmentation results generated using the proposed methods and previous research using Gabor, discrete cosine transform (DCT), and Laws filters are presented. Finally, the segmentation results generated by applying the optimized filter banks to textured images are presented and discussed.</p

A Medical Texture Local Binary Pattern For TRUS Prostate Segmentation

Abstract — Prostate cancer diagnosis and treatment rely on segmentation of Transrectal Ultrasound (TRUS) prostate im-ages. This is a challenging and difficult task dut to weak prostate boundaries, speckle noise and the short range of gray levels. Advances in digital imaging techniques have made it possible the acquisition of large volumes of TRUS prostate images so that there is considerable demand for automated segmentation systems. Local Binary Pattern (LBP) has been used for texture segmentation and analysis. Despite its promising performance for texture classification it has not yet been considered for TRUS prostate segmentation. In this paper we introduce a medical texture local binary pattern operator designed for applications of medical imaging where different tissues or micro organisms might maintain extremely weak underlying textures that make it impossible or very difficult for ordinary texture analysis approaches to classify them. In the proposed method the deformations of a level set contour are controlled based on the medical texture local binary pattern operator. I

A probabilistic cell model in background corrected image sequences for single cell analysis

Abstract Background Methods of manual cell localization and outlining are so onerous that automated tracking methods would seem mandatory for handling huge image sequences, nevertheless manual tracking is, astonishingly, still widely practiced in areas such as cell biology which are outside the influence of most image processing research. The goal of our research is to address this gap by developing automated methods of cell tracking, localization, and segmentation. Since even an optimal frame-to-frame association method cannot compensate and recover from poor detection, it is clear that the quality of cell tracking depends on the quality of cell detection within each frame. Methods Cell detection performs poorly where the background is not uniform and includes temporal illumination variations, spatial non-uniformities, and stationary objects such as well boundaries (which confine the cells under study). To improve cell detection, the signal to noise ratio of the input image can be increased via accurate background estimation. In this paper we investigate background estimation, for the purpose of cell detection. We propose a cell model and a method for background estimation, driven by the proposed cell model, such that well structure can be identified, and explicitly rejected, when estimating the background. Results The resulting background-removed images have fewer artifacts and allow cells to be localized and detected more reliably. The experimental results generated by applying the proposed method to different Hematopoietic Stem Cell (HSC) image sequences are quite promising. Conclusion The understanding of cell behavior relies on precise information about the temporal dynamics and spatial distribution of cells. Such information may play a key role in disease research and regenerative medicine, so automated methods for observation and measurement of cells from microscopic images are in high demand. The proposed method in this paper is capable of localizing single cells in microwells and can be adapted for the other cell types that may not have circular shape. This method can be potentially used for single cell analysis to study the temporal dynamics of cells.</p