Azadeh Fakhrzadeh

Analyzing Tubular Tissue in Histopathological Thin Sections

We propose a method for automatic segmentation of tubules in the stained thin sections of various tissue types. Tubules consist of one or more layers of cells surrounding a cavity. The segmented tubules can be used to study the morphology of the tissue. Some research has been done to automatically estimate the density of tubules. To the best of our knowledge, no one has been able to, fully automatically, segment the whole tubule. Usually the border between tubules is subtle and appears broken in a straight-forward segmentation. Here we suggest delineating these borders using the geodesic distance transform. We apply this method on images of Periodic Acid Shiffs (PAS) stained thin sections of testicular tissue, delineating 89% of the tubules correctly.

Precision Automation of Cell Type Classification and Sub-Cellular Fluorescence Quantification from Laser Scanning Confocal Images

While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to (1) segment radial plant organs into individual cells, (2) classify cells into cell type categories based upon Random Forest classification, (3) divide each cell into sub-regions, and (4) quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.

Effect of Pre-Fixation Delay and Freezing on Mink Testicular Endpoints for Environmental Research

There is growing interest in using wild animals to monitor the real-life cocktail effect of environmental chemicals on male reproduction. However, practical difficulties, such as long distances to the laboratory, generally prolong the time between euthanisation and specimen handling. For instance, tissue fixation is often performed on frozen material or on material where deterioration has started, which may affect tissue morphology. This study examined the effect of pre-fixation delay and freezing on mink testicular endpoints in order to determine robust endpoints in suboptimally handled specimens. Sexually mature farmed mink (n=30) selected at culling were divided into six groups and subjected to different time intervals between euthanisation and fixation or freezing: 0 hours (fixed immediately post mortem), 6 hours, 18 hours, 30 hours, 42 hours, or frozen 6 hours post mortem and thawed overnight. Unaffected endpoints when pre-fixation storage was extended to 30 hours included: area and diameter of the seminiferous tubules, length and weight of the testes, and acrosomes marked with Gata-4. Epithelial height, Sertoli cells marked with Gata-4 and cell morphology were affected endpoints after 6 hours of storage. Freezing the tissue prior to fixation severely altered cell morphology and reduced testicular weight, tubular diameter and area. Morphological changes seen after 6 hours included shredded germ cells and excess cytoplasm in seminiferous tubular lumen, chromatin rearrangements and increased germ cell death. Extended delay before fixation and freezing affected many endpoints in the mink testicular tissue. Some of these endpoints may mimic chemically induced effects, which is important to consider when evaluating specimens from wild animals for environmental toxicity.

Minimum Noiseless Description Length (MNDL) Thresholding

In this paper, a new thresholding approach for data denoising is presented. The approach is based minimum noiseless description length (MNDL), a new method for optimum sub-space selection in data representation. By using the observed noisy data, this information theoretic approach provides the optimum threshold that minimizes the description length of the noiseless signal. Comparison of the new method with the existing thresholding methods is provided

Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut

Computerized image processing has provided us with valuable tools for analyzing histology images. However, histology images are complex, and the algorithm which is developed for a data set may not work for a new and unseen data set. The preparation procedure of the tissue before imaging can significantly affect the resulting image. Even for the same staining method, factors like delayed fixation may alter the image quality. In this paper we face the challenging problem of designing a method that works on data sets with strongly varying quality. In environmental research, due to the distance between the site where the wild animals are caught and the laboratory, there is always a delay in fixation. Here we suggest a segmentation method based on the structural information of epithelium cell layer in testicular tissue. The cell nuclei are detected using the fast radial symmetry filter. A graph is constructed on top of the epithelial cells. Graph-cut optimization method is used to cut the links between cells of different tubules. The algorithm is tested on five different groups of animals. Group one is fixed immediately, three groups were left at room temperature for 18, 30 and 42 hours respectively, before fixation. Group five was frozen after 6 hours in room temperature and thawed. The suggested algorithm gives promising results for the whole data set.

Low-dose exposure to Bisphenol A during development has limited effects on male reproduction in midpubertal and aging Fischer 344 rats

Low doses of Bisphenol A (BPA) during development may affect reproduction. In this study, Fischer 344 rats were exposed to 0.5 or 50 μg BPA/kg bw/day via drinking water from gestational day 3.5 to postnatal day 22. Anogenital distance, organ weight, histopathology of reproductive organs, hormone analysis and sperm morphology were evaluated in male offspring. In this study no major effects of BPA on male reproduction in midpubertal (postnatal day 35) or adult (12-month-old) rats were revealed, apart from a higher prevalence of mild inflammatory cell infiltrate in cauda epididymis in adult rats exposed to 50 μg BPA/kg bw/day. No BPA-related effects on sexual development were seen but care should be taken when evaluating histopathology in midpuberty testis due to large morphological variation. Results from the present study show no major signs of altered male reproduction in rats exposed to low doses of BPA during gestation and lactation.

New computerized staging method to analyze mink testicular tissue in environmental research

Histopathology of testicular tissue is considered to be the most sensitive tool to detect adverse effects on male reproduction. When assessing tissue damage, seminiferous epithelium needs to be classified into different stages to detect certain cell damages; but stage identification is a demanding task. The authors present a method to identify the 12 stages in mink testicular tissue. The staging system uses Gata-4 immunohistochemistry to visualize acrosome development and proved to be both intraobserver-reproducible and interobserver-reproducible with a substantial agreement of 83.6% (kappa = 0.81) and 70.5% (kappa = 0.67), respectively. To further advance and objectify this method, they present a computerized staging system that identifies these 12 stages. This program has an agreement of 52.8% (kappa 0.47) with the consensus staging by 2 investigators. The authors propose a pooling of the stages into 5 groups based on morphology, stage transition, and toxicologically important endpoints. The computerized program then reached a substantial agreement of 76.7% (kappa = 0.69). The computerized staging tool uses local ternary patterns to describe the texture of the tubules and a support vector machine classifier to learn which textures correspond to which stages. The results have the potential to modernize the tedious staging process required in toxicological evaluation of testicular tissue, especially if combined with whole-slide imaging and automated tubular segmentation. Environ Toxicol Chem 2017;36:156-164.

Noiseless codelength in wavelet denoising

We propose an adaptive, data-driven thresholding method based on a recently developed idea of Minimum Noiseless Description Length (MNDL). MNDL Subspace Selection (MNDL-SS) is a novel method of selecting an optimal subspace among the competing subspaces of the transformed noisy data. Here we extend the application of MNDL-SS for thresholding purposes. The approach searches for the optimum threshold for the data coefficients in an orthonormal basis. It is shown that the optimum threshold can be extracted from the noisy coefficients themselves. While the additive noise in the available data is assumed to be independent, the main challenge in MNDL thresholding is caused by the dependence of the additive noise in the sorted coefficients. The approach provides new hard and soft thresholds. Simulation results are presented for orthonormal wavelet transforms. While the method is comparable with the existing thresholding methods and in some cases outperforms them, the main advantage of the new approach is that it provides not only the optimum threshold but also an estimate of the associated mean-square error (MSE) for that threshold simultaneously.