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- Fakhrzadeh, Azadeh, et al.
(författare)
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Analyzing Tubular Tissue in Histopathological Thin Sections
- 2012
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Ingår i: 2012 INTERNATIONAL CONFERENCE ON DIGITAL IMAGE COMPUTING TECHNIQUES AND APPLICATIONS (DICTA). - : IEEE conference proceedings. ; , s. 1-6
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Konferensbidrag (refereegranskat)abstract
- 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.
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| 2. |
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| 3. |
- Fakhrzadeh, Azadeh, 1981-
(författare)
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Computerized Cell and Tissue Analysis
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The latest advances in digital cameras combined with powerful computer software enable us to store high-quality microscopy images of specimen. Studying hundreds of images manually is very time consuming and has the problem of human subjectivity and inconsistency. Quantitative image analysis is an emerging field and has found its way into analysis of microscopy images for clinical and research purposes. When developing a pipeline, it is important that its components are simple enough to be generalized and have predictive value. This thesis addresses the automation of quantitative analysis of tissue in two different fields: pathology and plant biology.Testicular tissue is a complex structure consisting of seminiferous tubules. The epithelial layer of a seminiferous tubule contains cells that differentiate from primitive germ cells to spermatozoa in a number of steps. These steps are combined in 12 stages in the cycle of the seminiferous epithelium in the mink. The society of toxicological pathology recommends classifying the testicular epithelial into different stages when assessing tissue damage to determine if the dynamics in the spermatogenic cycle have been disturbed. This thesis presents two automated methods for fast and robust segmentation of tubules, and an automated method of staging them. For better accuracy and statistical analysis, we proposed to pool stages into 5 groups. This pooling is suggested based on the morphology of tubules. In the 5 stage case, the overall number of correctly classified tubules is 79.6%.Contextual information on the localization of fluorescence in microscopy images of plant specimen help us to better understand differentiation and maturation of stem cells into tissues. We propose a pipeline for automated segmentation and classification of the cells in a whole cross-section of Arabidopsis hypocotyl, stem, or root. As proof-of-concept that the classification provides a meaningful basis to group cells for fluorescence characterization, we probed tissues with an antibody specific to xylem vessels in the secondary cell wall. Fluorescence intensity in different classes of cells is measured by the pipeline. The measurement results clearly show that the xylem vessels are the dominant cell type that exhibit a fluorescence signal.
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| 5. |
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| 6. |
- Fakhrzadeh, Azadeh, et al.
(författare)
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Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut
- 2013
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Ingår i: Image Analysis and Processing – ICIAP 2013. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783642411830 - 9783642411847 ; 8157, s. 201-208
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Konferensbidrag (refereegranskat)abstract
- 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.
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| 7. |
- Fakhrzadeh, Azadeh, et al.
(författare)
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New computerized staging method to analyze mink testicular tissue in environmental research
- 2017
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Ingår i: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 36:1, s. 156-164
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Hall, Hardy, et al.
(författare)
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Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images
- 2016
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 9. |
- Spörndly-Nees, Ellinor, et al.
(författare)
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Basic Exploratory Study of Bisphenol A (BPA) Dietary Administration to Istrian Pramenka Rams and Male Toxicity Investigation
- 2022
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Ingår i: Toxics. - : MDPI AG. - 2305-6304. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Bisphenol A (BPA), an endocrine-disrupting chemical and environmental pollutant, has been reported by many researchers to induce male reproductive toxicity in different experimental models. In this study, we investigated whether long-term exposure for two months to 25 mu g/kg body weight (low dose) of BPA affects spermatogenesis or sperm quality in young Istrian Pramenka rams exposed via diet. We evaluated body and testicular weights, histopathology of testes and epididymides, and sperm analyses, and compared these parameters between the group of treated rams and the control group of rams. Although there were some differences between the two groups, these differences were not large or statistically significant. The only statistically significant difference was the lower epithelial height of seminiferous tubules in treated rams, compared to control rams. In addition to assessing toxicity, BPA concentrations in the blood plasma of treated rams were determined after the first administration, and the toxicokinetic parameters of total BPA were calculated. In this study, no major signs of altered reproduction in rams were detected.
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| 10. |
- Spörndly-Nees, Ellinor, et al.
(författare)
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Effect of Pre-Fixation Delay and Freezing on Mink Testicular Endpoints for Environmental Research
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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