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  • 1.
    Fakhrzadeh, Azadeh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Computerized Cell and Tissue Analysis2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    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.

    Delarbeid
    1. Analyzing Tubular Tissue in Histopathological Thin Sections
    Åpne denne publikasjonen i ny fane eller vindu >>Analyzing Tubular Tissue in Histopathological Thin Sections
    2012 (engelsk)Inngår i: 2012 INTERNATIONAL CONFERENCE ON DIGITAL IMAGE COMPUTING TECHNIQUES AND APPLICATIONS (DICTA), IEEE conference proceedings, 2012, s. 1-6Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    IEEE conference proceedings, 2012
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-188548 (URN)10.1109/DICTA.2012.6411735 (DOI)000316318400071 ()
    Konferanse
    International Conference on Digital Image Computing Techniques and Applications (DICTA), 3-5 Dec, 2012, Fremantle, AUSTRALIA
    Tilgjengelig fra: 2012-12-17 Laget: 2012-12-17 Sist oppdatert: 2015-06-03bibliografisk kontrollert
    2. Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut
    Åpne denne publikasjonen i ny fane eller vindu >>Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut
    2013 (engelsk)Inngår i: Image Analysis and Processing – ICIAP 2013: Part II, 2013, s. 201-208Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    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.

    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 8157
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-210299 (URN)10.1007/978-3-642-41184-7_21 (DOI)000329811200021 ()978-3-642-41183-0 (ISBN)978-3-642-41184-7 (ISBN)
    Konferanse
    17th International Conference on Image Analysis and Processing (ICIAP), Naples, Italy, September 9-13, 2013
    Tilgjengelig fra: 2013-11-05 Laget: 2013-11-05 Sist oppdatert: 2015-06-03bibliografisk kontrollert
    3. Computerized Study of Developmental Stages in Mink Testicular Tissue
    Åpne denne publikasjonen i ny fane eller vindu >>Computerized Study of Developmental Stages in Mink Testicular Tissue
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-252411 (URN)
    Tilgjengelig fra: 2015-05-06 Laget: 2015-05-06 Sist oppdatert: 2015-06-03
    4. Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images
    Åpne denne publikasjonen i ny fane eller vindu >>Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images
    2016 (engelsk)Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 119Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    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.

    Emneord
    automated image analysis; confocal microscopy; Arabidopsis; hypocotyl; automated phenotyping; code:matlab
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-252412 (URN)10.3389/fpls.2016.00119 (DOI)000369802700001 ()
    Forskningsfinansiär
    Bio4EnergyVINNOVA
    Tilgjengelig fra: 2016-02-09 Laget: 2015-05-06 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    5. Effect of pre-fixation delay and freezing on mink testicular endpoints for environmental research
    Åpne denne publikasjonen i ny fane eller vindu >>Effect of pre-fixation delay and freezing on mink testicular endpoints for environmental research
    Vise andre…
    2015 (engelsk)Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 5, artikkel-id e0125139Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-252410 (URN)10.1371/journal.pone.0125139 (DOI)000353887100081 ()25933113 (PubMedID)
    Tilgjengelig fra: 2015-05-01 Laget: 2015-05-06 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    Fulltekst (pdf)
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    Download (jpg)
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  • 2.
    Fakhrzadeh, Azadeh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sporndly-Nees, Ellinor
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Ekstedt, Elisabeth
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Holm, Lena
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. U.
    New computerized staging method to analyze mink testicular tissue in environmental research2017Inngår i: Environmental Toxicology and Chemistry, ISSN 0730-7268, E-ISSN 1552-8618, Vol. 36, nr 1, s. 156-164Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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.

    Fulltekst (pdf)
    fulltext
  • 3.
    Fakhrzadeh, Azadeh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Spörndly-Nees, Ellinor
    Swedish University of Agricultural Sciences.
    Holm, Lena
    Swedish University of Agricultural Sciences.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Analyzing Tubular Tissue in Histopathological Thin Sections2012Inngår i: 2012 INTERNATIONAL CONFERENCE ON DIGITAL IMAGE COMPUTING TECHNIQUES AND APPLICATIONS (DICTA), IEEE conference proceedings, 2012, s. 1-6Konferansepaper (Fagfellevurdert)
  • 4.
    Fakhrzadeh, Azadeh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Spörndly-Nees, Ellinor
    Swedish University of Agricultural Sciences.
    Holm, Lena
    Swedish University of Agricultural Sciences.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automated measurement of epithelial height of testicular tissue2012Inngår i: Proceedings of Swedish Society for Image Analysis, SSBA 2012, Stockholm: KTH Royal Institute of Technology, 2012Konferansepaper (Annet vitenskapelig)
  • 5.
    Fakhrzadeh, Azadeh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Spörndly-Nees, Ellinor
    Swedish University of Agricultural Sciences.
    Holm, Lena
    Swedish University of Agricultural Sciences.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Epithelial Cell Layer Segmentation UsingGraph-cut and Its Application in TesticularTissue2013Konferansepaper (Fagfellevurdert)
  • 6.
    Fakhrzadeh, Azadeh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Spörndly-Nees, Ellinor
    Swedish University of Agricultural Sciences.
    Holm, Lena
    Swedish University of Agricultural Sciences.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Epithelial Cell Segmentation in Histological Images of Testicular Tissue Using Graph-Cut2013Inngår i: Image Analysis and Processing – ICIAP 2013: Part II, 2013, s. 201-208Konferansepaper (Fagfellevurdert)
    Abstract [en]

    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.

  • 7. Hall, Hardy C.
    et al.
    Fakhrzadeh, Azadeh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Fischer, Urs
    Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 119Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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.

  • 8. Spörndly-Nees, Ellinor
    et al.
    Ekstedt, Elisabeth
    Magnusson, Ulf
    Fakhrzadeh, Azadeh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Holm, Lena
    Effect of pre-fixation delay and freezing on mink testicular endpoints for environmental research2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 5, artikkel-id e0125139Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    fulltext
1 - 8 of 8
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