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  • 1.
    Aiesh, Basel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Measurement of dispersion barriers through SEM images2015Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    In this thesis digital image analysis is applied to Scanning Electron Microscope imagesof dispersion barriers to measure specific properties. The thin barriers are used asprotection for paperboard packaging and are made of polymers and fillers. The orientation, area, length and density distributions of the fillers determine the functionality and quality of the barrier. Methods built on image analysis tools are developed with the objective to measure these quantities. Input for the methods are Scanning Electron Microscope images showing the cross-section of the barriers. To make the images relevant for the methods they are preprocessed by reducing noise and distinguishing fillers from the background.

    For measuring the orientation distribution of the fillers two different methods are implemented and compared. The first one is based on a structure tensor and the other one applies a covariance matrix. The structure tensor is preferable because of its flexibility and better performance for complex images. The area and length distributions are measured by applying mathematical morphology together withsoft-clipping. The density distribution is obtained by filtering the underlying image twice with a uniform filter which creates a heat map.

    The developed methods are evaluated by applying them on fabricated binary test images with known properties. The methods are very accurate when applied on simple test images but for more complex test images with greater variation the accuracy decreases. However, for most applications the results are still on an acceptable level.

  • 2.
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Methods for 2D and 3D Quantitative Microscopy of Biological Samples2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. 

    It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that  produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. 

    HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.

    Delarbeten
    1. A detailed analysis of 3D subcellular signal localization
    Öppna denna publikation i ny flik eller fönster >>A detailed analysis of 3D subcellular signal localization
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    2009 (Engelska)Ingår i: Cytometry Part A, ISSN 1552-4922, Vol. 75A, nr 4, s. 319-328Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Detection and localization of fluorescent signals in relation to other subcellular structures is an important task in various biological studies. Many methods for analysis of fluorescence microscopy image data are limited to 2D. As cells are in fact 3D structures, there is a growing need for robust methods for analysis of 3D data. This article presents an approach for detecting point-like fluorescent signals and analyzing their subnuclear position. Cell nuclei are delineated using marker-controlled (seeded) 3D watershed segmentation. User-defined object and background seeds are given as input, and gradient information defines merging and splitting criteria. Point-like signals are detected using a modified stable wave detector and localized in relation to the nuclear membrane using distance shells. The method was applied to a set of biological data studying the localization of Smad2-Smad4 protein complexes in relation to the nuclear membrane. Smad complexes appear as early as 1 min after stimulation while the highest signal concentration is observed 45 min after stimulation, followed by a concentration decrease. The robust 3D signal detection and concentration measures obtained using the proposed method agree with previous observations while also revealing new information regarding the complex formation.

    Nyckelord
    3D image analysis, fluorescence signal segmentation, subcellular positioning, Smad detection
    Nationell ämneskategori
    Data- och informationsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-98014 (URN)10.1002/cyto.a.20663 (DOI)000264513800006 ()
    Tillgänglig från: 2009-02-05 Skapad: 2009-02-05 Senast uppdaterad: 2018-01-13Bibliografiskt granskad
    2. Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis
    Öppna denna publikation i ny flik eller fönster >>Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis
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    2007 (Engelska)Ingår i: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 55, nr 11, s. 1159-1166Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Segregation of mitochondrial DNA (mtDNA) is an important underlying pathogenic factor in mtDNA mutation accumulation in mitochondrial diseases and aging, but the molecular mechanisms of mtDNA segregation are elusive. Lack of high-throughput single-cell mutation load assays lies at the root of the paucity of studies in which, at the single-cell level, mitotic mtDNA segregation patterns have been analyzed. Here we describe development of a novel fluorescence-based, non-gel PCR restriction fragment length polymorphism method for single-cell A3243G mtDNA mutation load measurement. Results correlated very well with a quantitative in situ Padlock/rolling circle amplification–based genotyping method. In view of the throughput and accuracy of both methods for single-cell A3243G mtDNA mutation load determination, we conclude that they are well suited for segregation analysis.

    Nyckelord
    A3243G mtDNA, Aging, Heteroplasmy, Mitochondrial diseases, Mutation load, Padlock probing, PCR-RFLP, Segregation
    Nationell ämneskategori
    Medicin och hälsovetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-12658 (URN)10.1369/jhc.7A7282.2007 (DOI)000250320100009 ()17679731 (PubMedID)
    Tillgänglig från: 2008-01-09 Skapad: 2008-01-09 Senast uppdaterad: 2017-12-11Bibliografiskt granskad
    3. BlobFinder, a tool for fluorescence microscopy image cytometry
    Öppna denna publikation i ny flik eller fönster >>BlobFinder, a tool for fluorescence microscopy image cytometry
    2009 (Engelska)Ingår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 94, nr 1, s. 58-65Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Images can be acquired at high rates with modern fluorescence microscopy hardware, giving rise to a demand for high-speed analysis of image data. Digital image cytometry, i.e., automated measurements and extraction of quantitative data from images of cells, provides valuable information for many types of biomedical analysis. There exists a number of different image analysis software packages that can be programmed to perform a wide array of useful measurements. However, the multi-application capability often compromises the simplicity of the tool. Also, the gain in speed of analysis is often compromised by time spent learning complicated software. We provide a free software called BlobFinder that is intended for a limited type of application, making it easy to use, easy to learn and optimized for its particular task. BlobFinder can perform batch processing of image data and quantify as well as localize cells and point like source signals in fluorescence microscopy images, e.g., from FISH, in situ PLA and padlock probing, in a fast and easy way.

    Nyckelord
    Image cytometry, Single cell analysis, FISH, Software
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-87971 (URN)10.1016/j.cmpb.2008.08.006 (DOI)000264282400006 ()18950895 (PubMedID)
    Tillgänglig från: 2009-01-22 Skapad: 2009-01-16 Senast uppdaterad: 2018-06-26Bibliografiskt granskad
    4. Robust signal detection in 3D fluorescence microscopy
    Öppna denna publikation i ny flik eller fönster >>Robust signal detection in 3D fluorescence microscopy
    2010 (Engelska)Ingår i: Cytometry. Part A, ISSN 1552-4922, Vol. 77A, nr 1, s. 86-96Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Robust detection and localization of biomolecules inside cells is of great importance to better understand the functions related to them. Fluorescence microscopy and specific staining methods make biomolecules appear as point-like signals on image data, often acquired in 3D. Visual detection of such point-like signals can be time consuming and problematic if the 3D images are large, containing many, sometimes overlapping, signals. This sets a demand for robust automated methods for accurate detection of signals in 3D fluorescence microscopy. We propose a new 3D point-source signal detection method that is based on Fourier series. The method consists of two parts, a detector, which is a cosine filter to enhance the point-like signals, and a verifier, which is a sine filter to validate the result from the detector. Compared to conventional methods, our method shows better robustness to noise and good ability to resolve signals that are spatially close. Tests on image data show that the method has equivalent accuracy in signal detection in comparison to Visual detection by experts. The proposed method can be used as an efficient point-like signal detection tool for various types of biological 3D image data.

    Nationell ämneskategori
    Bioinformatik och systembiologi
    Identifikatorer
    urn:nbn:se:uu:diva-98015 (URN)10.1002/cyto.a.20795 (DOI)000273384700011 ()
    Tillgänglig från: 2009-02-05 Skapad: 2009-02-05 Senast uppdaterad: 2011-11-04Bibliografiskt granskad
    5. High-throughput in vivo optical projection tomography of small vertebrates
    Öppna denna publikation i ny flik eller fönster >>High-throughput in vivo optical projection tomography of small vertebrates
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    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-159203 (URN)
    Tillgänglig från: 2011-09-25 Skapad: 2011-09-25 Senast uppdaterad: 2011-11-04
    6. Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
    Öppna denna publikation i ny flik eller fönster >>Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
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    2012 (Engelska)Ingår i: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 12, nr 4, s. 711-716Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The zebrafish larva is an optically-transparent vertebrate model with complex organs that is widelyused to study genetics, developmental biology, and to model various human diseases. In this article, wepresent a set of novel technologies that significantly increase the throughput and capabilities of ourpreviously described vertebrate automated screening technology (VAST). We developed a robustmulti-thread system that can simultaneously process multiple animals. System throughput is limitedonly by the image acquisition speed rather than by the fluidic or mechanical processes. We developedimage recognition algorithms that fully automate manipulation of animals, including orienting andpositioning regions of interest within the microscope’s field of view. We also identified the optimalcapillary materials for high-resolution, distortion-free, low-background imaging of zebrafish larvae.

    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Identifikatorer
    urn:nbn:se:uu:diva-159202 (URN)10.1039/c1lc20849g (DOI)000299380800007 ()
    Tillgänglig från: 2011-09-25 Skapad: 2011-09-25 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    7. Image based measurements of single cell mtDNA mutation load MTD 2007
    Öppna denna publikation i ny flik eller fönster >>Image based measurements of single cell mtDNA mutation load MTD 2007
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    2007 (Engelska)Ingår i: Medicinteknikdagarna 2007, 2007Konferensbidrag, Publicerat paper (Övrig (populärvetenskap, debatt, mm))
    Abstract [en]

    Cell cultures as well as cells in tissue always display a certain degree of variability,and measurements based on cell averages will miss important information contained in a heterogeneous population. These differences among cells in a population may be essential to quantify when looking at, e.g., protein expression and mutations in tumor cells which often show high degree of heterogeneity.

    Single nucleotide mutations in the mithochondrial DNA (mtDNA) can accumulate and later be present in large proportions of the mithocondria causing devastating diseases. To study mtDNA accumulation and segregation one needs to measure the amount of mtDNA mutations in each cell in multiple serial cell culture passages. The different degrees of mutation in a cell culture can be quantified by making measurements on individual cells as an alternative to looking at an average of a population. Fluorescence microscopy in combination with automated digital image analysis provides an efficient approach to this type of single cell analysis.

    Image analysis software for these types of applications are often complicated and not easy to use for persons lacking extensive knowledge in image analysis, e.g., laboratory personnel. This paper presents a user friendly implementation of an automated method for image based measurements of mtDNA mutations in individual cells detected with padlock probes and rolling-circle amplification (RCA). The mitochondria are present in the cell’s cytoplasm, and here each cytoplasm has to be delineated without the presence of a cytoplasmic stain. Three different methods for segmentation of cytoplasms are compared and it is shown that automated cytoplasmic delineation can be performed 30 times faster than manual delineation, with an accuracy as high as 87%. The final image based measurements of mitochondrial mutation load are also compared to, and show high agreement with, measurements made using biochemical techniques.

    Nationell ämneskategori
    Annan data- och informationsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-12745 (URN)
    Tillgänglig från: 2008-01-11 Skapad: 2008-01-11 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    8. Increasing the dynamic range of in situ PLA
    Öppna denna publikation i ny flik eller fönster >>Increasing the dynamic range of in situ PLA
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    2011 (Engelska)Ingår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 8, nr 11, s. 892-893Artikel i tidskrift, Editorial material (Refereegranskat) Published
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-159199 (URN)10.1038/nmeth.1743 (DOI)000296891800004 ()
    Tillgänglig från: 2011-09-25 Skapad: 2011-09-25 Senast uppdaterad: 2017-12-08Bibliografiskt granskad
    9. High-throughput cellular-resolution in vivo vertebrate screening
    Öppna denna publikation i ny flik eller fönster >>High-throughput cellular-resolution in vivo vertebrate screening
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    2011 (Engelska)Ingår i: Proc. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011Konferensbidrag, Publicerat paper (Refereegranskat)
    Nationell ämneskategori
    Medicinsk bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-159201 (URN)
    Tillgänglig från: 2011-09-25 Skapad: 2011-09-25 Senast uppdaterad: 2011-11-04
  • 3.
    Allalou, Amin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Curic, Vladimir
    Pardo-Martin, Carlos
    Massachusetts Institute of Technology, USA.
    Yanik, Mehmet Fatih
    Massachusetts Institute of Technology, USA.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Approaches for increasing throughput andinformation content of image-based zebrafishscreens2011Ingår i: Proceeding of SSBA 2011, 2011Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    Microscopy in combination with image analysis has emerged as one of the most powerful and informativeways to analyze cell-based high-throughput screening (HTS) samples in experiments designed to uncover novel drugs and drug targets. However, many diseases and biological pathways can be better studied in whole animals, particularly diseases and pathways that involve organ systems and multicellular interactions, such as organ development, neuronal degeneration and regeneration, cancer metastasis, infectious disease progression and pathogenesis. The zebrafish is a wide-spread and popular vertebrate model of human organfunction and development, and it is unique in the sense that large-scale in vivo genetic and chemical studies are feasible due in part to its small size, optical transparency,and aquatic habitat. To improve the throughput and complexity of zebrafish screens, a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae has been developed at Yanik lab at Research Laboratory of Electronics, MIT, USA. The system loads live zebrafish from reservoirs or multiwell plates, positions and rotates them for high-speed confocal imaging of organs,and dispenses the animals without damage. We present two improvements to the described system, including automation of positioning of the animals and a novel approach for brightfield microscopy tomographic imaging of living animals.

  • 4.
    Blom, Elisabeth
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Velikyan, Irina
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för biomedicinsk strålningsvetenskap.
    Monazzam, Azita
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Endokrin tumörbiologi.
    Razifar, Pasha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nair, Manoj
    Razifar, Payam
    Vanderheyden, Jean-Luc
    Krivoshein, Arcadius V.
    Backer, Marina
    Backer, Joseph
    Långström, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Synthesis and characterization of scVEGF-PEG-[68Ga]NOTA and scVEGF-PEG-[68Ga]DOTA PET tracers2011Ingår i: Journal of labelled compounds & radiopharmaceuticals, ISSN 0362-4803, E-ISSN 1099-1344, Vol. 54, nr 11, s. 685-692Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vascular endothelial growth factor (VEGF) signaling via vascular endothelial growth factor receptor 2 (VEGFR-2) on tumor endothelial cells is a critical driver of tumor angiogenesis. Novel anti-angiogenic drugs target VEGF/VEGFR-2 signaling and induce changes in VEGFR-2 prevalence. To monitor VEGFR-2 prevalence in the course of treatment, we are evaluating (68)Ga positron emission tomography imaging agents based on macrocyclic chelators, site-specifically conjugated via polyethylene glycol (PEG) linkers to engineered VEGFR-2 ligand, single-chain (sc) VEGF. The (68)Ga-labeling was performed at room temperature with NOTA (2,2', 2 ''-(1,4,7-triazonane-1,4,7-triyl) triacetic acid) conjugates or at 90 degrees C by using either conventional or microwave heating with NOTA and DOTA (2,2', 2 '', 2'''-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl) tetraacetic acid) conjugates. The fastest (similar to 2min) and the highest incorporation (>90%) of (68)Ga into conjugate that resulted in the highest specific radioactivity (similar to 400MBq/nmol) was obtained with microwave heating of the conjugates. The bioactivity of the NOTA-and DOTA-containing tracers was validated in 3-D tissue culture model of 293/KDR cells engineered to express high levels of VEGFR-2. The NOTA-containing tracer also displayed a rapid accumulation (similar to 20s after intravenous injection) to steady-state level in xenograft tumor models. A combination of high specific radioactivity and maintenance of functional activity suggests that scVEGF-PEG-[(68)Ga] NOTA and scVEGF-PEG-[(68)Ga] DOTA might be promising tracers for monitoring VEGFR-2 prevalence and should be further explored.

  • 5.
    Byström, Anna
    et al.
    Swedish University of Agricultural Sciences, Department of Anatomy, Physiology and Biochemistry.
    Roepstorff, Lars
    Swedish University of Agricultural Sciences, Department of Anatomy, Physiology and Biochemistry.
    Brun, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image Analysis of Saddle Pressure Data2011Konferensbidrag (Övrigt vetenskapligt)
  • 6.
    Chinga-Carrasco, Gary
    et al.
    Paper and Fibre Research Institute (PFI), Norway.
    Miettinen, Arttu
    Department of Physics, University of Jyväskylä, Finland.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Gamstedt, E. Kristofer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Tillämpad mekanik.
    Kataja, Markku
    Department of Physics, University of Jyväskylä, Finland.
    Structural Characterisation of Kraft Pulp Fibres and Their Nanofibrillated Materials for Biodegradable Composite Applications2011Ingår i: Nanocomposites and Polymers with Analytical Methods / [ed] Cuppoletti, John, InTech , 2011, s. 243-260Kapitel i bok, del av antologi (Refereegranskat)
  • 7.
    Clausson, Carl-Magnus
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Weibrecht, Irene
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Mahmoudi, Salah
    Farnebo, Marianne
    Landegren, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Söderberg, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Increasing the dynamic range of in situ PLA2011Ingår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 8, nr 11, s. 892-893Artikel i tidskrift (Refereegranskat)
  • 8.
    Curic, Vladimir
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sladoje, Natasa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Faculty of Technical Sciences, University of Novi Sad, Serbia.
    Distance measures between digital fuzzy objects and their applicability in image processing2011Ingår i: Combinatorial Image Analysis / [ed] Jake Aggarwal, Reneta Barneva, Valentin Brimkov, Kostadin Koroutchev, Elka Koroutcheva, Springer Berlin/Heidelberg, 2011, s. 385-397Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present two different extensions of the Sum of minimal distances and the Complement weighted sum of minimal distances to distances between fuzzy sets. We evaluate to what extent the proposed distances show monotonic behavior with respect to increasing translation and rotation of digital objects, in noise free, as well as in noisy conditions. Tests show that one of the extension approaches leads to distances exhibiting very good performance. Furthermore, we evaluate distance based classification of crisp and fuzzy representations of objects at a range of resolutions. We conclude that the proposed distances are able to utilize the additional information available in a fuzzy representation, thereby leading to improved performance of related image processing tasks.

  • 9.
    Dražić, Slobodan
    et al.
    Faculty of Technical Sciences, University of Novi Sad, Serbia.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sladoje, Natasa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Faculty of Technical Sciences, University of Novi Sad, Serbia.
    Precise Estimation of the Projection of a Shape from a Pixel Coverage Representation2011Ingår i: Proceedings of the 7th IEEE International Symposium on Image and Signal Processing and Analysis (ISPA), IEEE Computer Society, 2011, s. 569-574Konferensbidrag (Refereegranskat)
    Abstract [en]

    Measuring width and diameter of a shape areproblems well studied in the literature. A pixel coverage repre-sentation is one specific type of digital fuzzy representation of acontinuous image object, where the (membership) value of eachpixel is (approximately) equal to the relative area of the pixelwhich is covered by the continuous object. Lately a number ofmethods for shape analysis use pixel coverage for reducing errorof estimation. We introduce a novel method for estimating theprojection of a shape in a given direction. The method is based onutilizing pixel coverage representation of a shape. Performance ofthe method is evaluated by a number of tests on synthetic objects,confirming high precision and applicability for calculation ofdiameter and elongation of a shape.

  • 10.
    Fowlkes, Charless C.
    et al.
    Department of Computer Science, University of California Irvine.
    Eckenrode, Kelly B.
    Department of Systems Biology, Harvard Medical School.
    Bragdon, Meghan D.
    Department of Systems Biology, Harvard Medical School.
    Meyer, Miriah
    School of Engineering and Applied Sciences, Harvard University.
    Wunderlich, Zeba
    Department of Systems Biology, Harvard Medical School.
    Simirenko, Lisa
    California Institute for Quantitative Biosciences, University of California Berkeley.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Keränen, Soile V. E.
    Genomics and Life Sciences Division, Lawrence Berkeley National Laboratory.
    Henriquez, Clara
    Genomics and Life Sciences Division, Lawrence Berkeley National Laboratory.
    Knowles, David W.
    Genomics and Life Sciences Division, Lawrence Berkeley National Laboratory.
    Biggin, Mark D.
    Genomics and Life Sciences Division, Lawrence Berkeley National Laboratory.
    Eisen, Michael B.
    California Institute for Quantitative Biosciences, University of California Berkeley.
    DePace, Angela H.
    Department of Systems Biology, Harvard Medical School.
    A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila2011Ingår i: PLoS Genetics, ISSN 1553-7390, Vol. 7, nr 10, s. e1002346-Artikel i tidskrift (Refereegranskat)
  • 11.
    Gavrilovic, Milan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Spectral Image Processing with Applications in Biotechnology and Pathology2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Color theory was first formalized in the seventeenth century by Isaac Newton just a couple of decades after the first microscope was built. But it was not until the twentieth century that technological advances led to the integration of color theory, optical spectroscopy and light microscopy through spectral image processing. However, while the focus of image processing often concerns modeling of how images are perceived by humans, the goal of image processing in natural sciences and medicine is the objective analysis. This thesis is focused on color theory that promotes quantitative analysis rather than modeling how images are perceived by humans.

    Color and fluorescent dyes are routinely added to biological specimens visualizing features of interest. By applying spectral image processing to histopathology, subjectivity in diagnosis can be minimized, leading to a more objective basis for a course of treatment planning. Also, mathematical models for spectral image processing can be used in biotechnology research increasing accuracy and throughput, and decreasing bias.

    This thesis presents a model for spectral image formation that applies to both fluorescence and transmission light microscopy. The inverse model provides estimates of the relative concentration of each individual component in the observed mixture of dyes. Parameter estimation for the model is based on decoupling light intensity and spectral information. This novel spectral decomposition method consists of three steps: (1) photon and semiconductor noise modeling providing smoothing parameters, (2) image data transformation to a chromaticity plane removing  intensity variation while maintaining chromaticity differences, and (3) a piecewise linear decomposition combining advantages of spectral angle mapping and linear decomposition yielding relative dye concentrations.

    The methods described herein were used for evaluation of molecular biology techniques as well as for quantification and interpretation of image-based measurements. Examples of successful applications comprise quantification of colocalization, autofluorescence removal, classification of multicolor rolling circle products, and color decomposition of histological images.

    Delarbeten
    1. Quantification of colocalization and cross-talk based on spectral angles
    Öppna denna publikation i ny flik eller fönster >>Quantification of colocalization and cross-talk based on spectral angles
    2009 (Engelska)Ingår i: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Vol. 234, nr 3, s. 311-324Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Common methods for quantification of colocalization in fluorescence microscopy typically require cross-talk free images or images where cross-talk has been eliminated by image processing, as they are based on intensity thresholding. Quantification of colocalization includes not only calculating a global measure of the degree of colocalization within an image, but also a classification of each image pixel as showing colocalized signals or not. In this paper, we present a novel, automated method for quantification of colocalization and classification of image pixels. The method, referred to as SpecDec, is based on an algorithm for spectral decomposition of multispectral data borrowed from the field of remote sensing. Pixels are classified based on hue rather than intensity. The hue distribution is presented as a histogram created by a series of steps that compensate for the quantization noise always present in digital image data, and classification rules are thereafter based on the shape of the angle histogram. Detection of colocalized signals is thus only dependent on the hue, making it possible to classify also low-intensity objects, and decoupling image segmentation from detection of colocalization. Cross-talk will show up as shifts of the peaks of the histogram, and thus a shift of the classification rules, making the method essentially insensitive to cross-talk. The method can also be used to quantify and compensate for cross-talk, independent of the microscope hardware.

    Ort, förlag, år, upplaga, sidor
    Oxford, UK: Blackwell Publishing, 2009
    Nyckelord
    Colocalization, cross-talk, fluorescence microscopy, image analysis
    Nationell ämneskategori
    Data- och informationsvetenskap
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-111376 (URN)10.1111/j.1365-2818.2009.03170.x (DOI)000266180400011 ()19493110 (PubMedID)
    Projekt
    EU-Strep project ENLIGHT (ENhanced LIGase based Histochemical Techniques)
    Tillgänglig från: 2009-12-15 Skapad: 2009-12-11 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    2. Suppression of Autofluorescence based on Fuzzy Classification by Spectral Angles
    Öppna denna publikation i ny flik eller fönster >>Suppression of Autofluorescence based on Fuzzy Classification by Spectral Angles
    2009 (Engelska)Ingår i: Optical Tissue Image analysis in Microscopy, Histopathology and Endoscopy (OPTIMHisE): A satellite workshop associated with MICCAI / [ed] Daniel Elson and Nasir Rajpoot, London, 2009, s. 135-146Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    Background fluorescence, also known as autofluorescence, and cross-talk are two problems in fluorescence microscopy that stem from similar phenomena. When biological specimens are imaged, the detected signal often contains contributions from fluorescence originating from sources other than the imaged fluorophore. This fluorescence could either come from the specimen itself (autofluorescence), or from fluorophores with partly overlapping emission spectra (cross-talk). In order to resolve spectral components at least two distinct wavelength intervals have to be imaged. This paper shows how autofluorescence can be presented statistically using a spectral angle histogram. Pixel classification by spectral angles was previously developed for detection and quantification of colocalization. Here we show how the spectral angle histogram can be employed to suppress autofluorescence. First, classical background subtraction (also referred to as linear unmixing) is presented in the form of a fuzzy classification by spectral angles. A modification of the fuzzy classification rules is also presented and we show that sigmoid membership functions lead to better suppression of background and amplification of true signals.

    Ort, förlag, år, upplaga, sidor
    London: , 2009
    Nyckelord
    autofluorescence, fluorescence microscopy, multispectral image analysis, fuzzy classification, dimensionality reduction
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-111374 (URN)978-0-9563776-0-9 (ISBN)
    Konferens
    MICCAI 2009, the 12th International Conference on Medical Image Computing and Computer Assisted Intervention
    Projekt
    EU-Strep project ENLIGHT (ENhanced LIGase based Histochemical Techniques)
    Tillgänglig från: 2009-12-16 Skapad: 2009-12-11 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    3. Automated Classification of Multicolored Rolling Circle Products in Dual-Channel Wide-Field Fluorescence Microscopy
    Öppna denna publikation i ny flik eller fönster >>Automated Classification of Multicolored Rolling Circle Products in Dual-Channel Wide-Field Fluorescence Microscopy
    Visa övriga...
    2011 (Engelska)Ingår i: Cytometry Part A, ISSN 1552-4922, Vol. 79A, nr 7, s. 518-527Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Specific single-molecule detection opens new possibilities in genomics and proteomics, and automated image analysis is needed for accurate quantification. This work presents image analysis methods for the detection and classification of single molecules and single-molecule interactions detected using padlock probes or proximity ligation. We use simple, widespread, and cost-efficient wide-field microscopy and increase detection multiplexity by labeling detection events with combinations of fluorescence dyes. The mathematical model presented herein can classify the resulting point-like signals in dual-channel images by spectral angles without discriminating between low and high intensity. We evaluate the methods on experiments with known signal classes and compare to classical classification algorithms based on intensity thresholding. We also demonstrate how the methods can be used as tools to evaluate biochemical protocols by measuring detection probe quality and accuracy. Finally, the method is used to evaluate single-molecule detection events in situ.

    Nationell ämneskategori
    Cell- och molekylärbiologi Datorseende och robotik (autonoma system)
    Identifikatorer
    urn:nbn:se:uu:diva-156962 (URN)10.1002/cyto.a.21087 (DOI)000292947900004 ()
    Tillgänglig från: 2011-08-20 Skapad: 2011-08-11 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    4. Blind Color Decomposition of Histological Images
    Öppna denna publikation i ny flik eller fönster >>Blind Color Decomposition of Histological Images
    Visa övriga...
    2013 (Engelska)Ingår i: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 32, nr 6, s. 983-994Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Cancer diagnosis is based on visual examination under a microscope of tissue sections from biopsies. But whereas pathologists rely on tissue stains to identify morphological features, automated tissue recognition using color is fraught with problems that stem from image intensity variations due to variations in tissue preparation, variations in spectral signatures of the stained tissue, spectral overlap and spatial aliasing in acquisition, and noise at image acquisition. We present a blind method for color decomposition of histological images. The method decouples intensity from color information and bases the decomposition only on the tissue absorption characteristics of each stain. By modeling the charge-coupled device sensor noise, we improve the method accuracy. We extend current linear decomposition methods to include stained tissues where one spectral signature cannot be separated from all combinations of the other tissues' spectral signatures. We demonstrate both qualitatively and quantitatively that our method results in more accurate decompositions than methods based on non-negative matrix factorization and independent component analysis. The result is one density map for each stained tissue type that classifies portions of pixels into the correct stained tissue allowing accurate identification of morphological features that may be linked to cancer.

    Nationell ämneskategori
    Medicinsk bildbehandling
    Forskningsämne
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-160312 (URN)10.1109/TMI.2013.2239655 (DOI)000319701800002 ()
    Tillgänglig från: 2011-10-21 Skapad: 2011-10-21 Senast uppdaterad: 2018-12-02
  • 12.
    Gavrilovic, Milan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Jimmy, Azar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Busch, Christer
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylär och morfologisk patologi.
    Carlbom, Ingrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Tissue Separation for Quantitative Malignancy Grading of Prostate Cancer2011Ingår i: Abstracts of Medicinteknikdagarna 2011, 2011, s. 32-32Konferensbidrag (Övrigt vetenskapligt)
  • 13.
    Gavrilovic, Milan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Weibrecht, Irene
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Conze, Tim
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Söderberg, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automated Classification of Multicolored Rolling Circle Products in Dual-Channel Wide-Field Fluorescence Microscopy2011Ingår i: Cytometry Part A, ISSN 1552-4922, Vol. 79A, nr 7, s. 518-527Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Specific single-molecule detection opens new possibilities in genomics and proteomics, and automated image analysis is needed for accurate quantification. This work presents image analysis methods for the detection and classification of single molecules and single-molecule interactions detected using padlock probes or proximity ligation. We use simple, widespread, and cost-efficient wide-field microscopy and increase detection multiplexity by labeling detection events with combinations of fluorescence dyes. The mathematical model presented herein can classify the resulting point-like signals in dual-channel images by spectral angles without discriminating between low and high intensity. We evaluate the methods on experiments with known signal classes and compare to classical classification algorithms based on intensity thresholding. We also demonstrate how the methods can be used as tools to evaluate biochemical protocols by measuring detection probe quality and accuracy. Finally, the method is used to evaluate single-molecule detection events in situ.

  • 14.
    Gustavson, Stefan
    et al.
    Department of Science and Technology, Linköping University.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Anti-aliased Euclidean distance transform2011Ingår i: Pattern Recognition Letters, ISSN 0167-8655, E-ISSN 1872-7344, Vol. 32, nr 2, s. 252-257Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a modified distance measure for use with distance transforms of anti-aliased, area sampled grayscale images of arbitrary binary contours. The modified measure can be used in any vector-propagation Euclidean distance transform. Our test implementation in the traditional SSED8 algorithm shows a considerable improvement in accuracy and homogeneity of the distance field compared to a traditional binary image transform. At the expense of a 10× slowdown for a particular image resolution, we achieve an accuracy comparable to a binary transform on a supersampled image with 16 × 16 higher resolution, which would require 256 times more computations and memory.

  • 15.
    Hammarqvist, Ulf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Audio editing in the time-frequency domain using the Gabor Wavelet Transform2011Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Visualization, processing and editing of audio, directly on a time-frequency surface, is the scope of this thesis. More precisely the scalogram produced by a Gabor Wavelet transform is used, which is a powerful alternative to traditional techinques where the wave form is the main visual aid and editting is performed by parametric filters. Reconstruction properties, scalogram design and enhancements as well audio manipulation algorithms are investigated for this audio representation.The scalogram is designed to allow a flexible choice of time-frequency ratio, while maintaining high quality reconstruction. For this mean, the Loglet is used, which is observed to be the most suitable filter choice.  Re-assignmentare tested, and a novel weighting function using partial derivatives of phase is proposed.  An audio interpolation procedure is developed and shown to perform well in listening tests.The feasibility to use the transform coefficients directly for various purposes is investigated. It is concluded that Pitch shifts are hard to describe in the framework while noise thresh holding works well. A downsampling scheme is suggested that saves on operations and memory consumption as well as it speeds up real world implementations significantly. Finally, a Scalogram 'compression' procedure is developed, allowing the caching of an approximate scalogram.

  • 16. Ibrahim, Muhammad Talal
    et al.
    Niazi, M. Khalid Khan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Guan, Ling
    Horizontal features based illumination normalization method for face recognition2011Konferensbidrag (Refereegranskat)
  • 17.
    Kylberg, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Kylberg Texture Dataset v. 1.02011Rapport (Övrigt vetenskapligt)
  • 18.
    Kylberg, Gustaf
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Refinement of Segmented Virus Particel Candidates in TEM Images2011Konferensbidrag (Övrigt vetenskapligt)
  • 19.
    Kylberg, Gustaf
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Uppström, Mats
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Virus texture analysis using local binary patterns and radial density profiles2011Ingår i: Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications / [ed] San Martin, César; Kim, Sang-Woon, Springer Berlin/Heidelberg, 2011, s. 573-580Konferensbidrag (Refereegranskat)
    Abstract [en]

    We investigate the discriminant power of two local and two global texture measures on virus images. The viruses are imaged using negative stain transmission electron microscopy. Local binary patterns and a multi scale extension are compared to radial density profiles in the spatial domain and in the Fourier domain. To assess the discriminant potential of the texture measures a Random Forest classifier is used. Our analysis shows that the multi scale extension performs better than the standard local binary patterns and that radial density profiles in comparison is a rather poor virus texture discriminating measure. Furthermore, we show that the multi scale extension and the profiles in Fourier domain are both good texture measures and that they complement each other well, that is, they seem to detect different texture properties. Combining the two, hence, improves the discrimination between virus textures.

  • 20.
    Luengo Hendriks, Cris L.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Rapid prototyping of image analysis applications2011Ingår i: Medical Image Processing: Techniques and Applications / [ed] G. Dougherty, Springer , 2011, s. 5-25Kapitel i bok, del av antologi (Refereegranskat)
  • 21.
    Lukic, Tibor
    et al.
    University of Novi Sad, Faculty of technical sciences.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia.
    Sladoje, Natasa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbia.
    Regularized image denoising based on spectral gradient optimization2011Ingår i: Inverse Problems, ISSN 0266-5611, E-ISSN 1361-6420, Vol. 27, nr 8, s. 085010:1-17Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Image restoration methods, such as denoising, deblurring, inpainting, etc, are often based on the minimization of an appropriately defined energy function. We consider energy functions for image denoising which combine a quadratic data-fidelity term and a regularization term, where the properties of the latter are determined by a used potential function. Many potential functions are suggested for different purposes in the literature. We compare the denoising performance achieved by ten different potential functions. Several methods for efficient minimization of regularized energy functions exist. Most are only applicable to particular choices of potential functions, however. To enable a comparison of all the observed potential functions, we propose to minimize the objective function using a spectral gradient approach; spectral gradient methods put very weak restrictions on the used potential function. We present and evaluate the performance of one spectral conjugate gradient and one cyclic spectral gradient algorithm, and conclude from experiments that both are well suited for the task. We compare the performance with three total variation-based state-of-the-art methods for image denoising. From the empirical evaluation, we conclude that denoising using the Huber potential (for images degraded by higher levels of noise; signal-to-noise ratio below 10 dB) and the Geman and McClure potential (for less noisy images), in combination with the spectral conjugate gradient minimization algorithm, shows the overall best performance.

  • 22. Maddah, Farzaneh
    et al.
    Soeria-Atmadja, Daniel
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Gustafsson, Mats G.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper.
    Hammerling, Ulf
    Interrogating health-related public databases from a food toxicology perspective: Computational analysis of scoring data2011Ingår i: Food and Chemical Toxicology, ISSN 0278-6915, E-ISSN 1873-6351, Vol. 49, nr 11, s. 2830-2840Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Over the last 15 years, an expanding number of databases with information on noxious effects of substances on mammalian organisms and the environment have been made available on the Internet. This set of databases is a key source of information for risk assessment within several areas of toxicology. Here we present features and relationships across a relatively wide set of publicly accessible databases broadly within toxicology, in part by clustering multi-score representations of such repositories, to support risk assessment within food toxicology. For this purpose 36 databases were each scrutinized, using 18 test substances from six different categories as probes. Results have been analyzed by means of various uni- and multi-variate statistical operations. The former included a special index devised to afford context-specific rating of databases across a highly heterogeneous data matrix, whereas the latter involved cluster analysis, enabling the identification of database assemblies with overall shared characteristics. One database – HSDB – was outstanding due to rich and qualified information for most test substances, but an appreciable fraction of the interrogated repositories showed good to decent scoring. Among the six chosen substance groups, Food contact materials had the most comprehensive toxicological information, followed by the Pesticides category.

  • 23.
    Malm, Patrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    The CerviSCAN project: Project description and current progress2011Ingår i: Proceedings SSBA 2011, 2011Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    Cervical cancer is the second most common type of cancer among women in spite of the fact that it through screening easily can be detected and cured before it becomes invasive. Current screening procedures are too complex and costly for use in developing countries. TheCerviSCAN project is an attempt to create a automated cervical cancer screening system that will lower the cost and increase the throughput of samples. This paper accounts for the current progress of the project as well as some of the planned future work.

  • 24.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Graph-based Methods for Interactive Image Segmentation2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The subject of digital image analysis deals with extracting relevant information from image data, stored in digital form in a computer. A fundamental problem in image analysis is image segmentation, i.e., the identification and separation of relevant objects and structures in an image. Accurate segmentation of objects of interest is often required before further processing and analysis can be performed.

    Despite years of active research, fully automatic segmentation of arbitrary images remains an unsolved problem. Interactive, or semi-automatic, segmentation methods use human expert knowledge as additional input, thereby making the segmentation problem more tractable. The goal of interactive segmentation methods is to minimize the required user interaction time, while maintaining tight user control to guarantee the correctness of the results. Methods for interactive segmentation typically operate under one of two paradigms for user guidance: (1) Specification of pieces of the boundary of the desired object(s). (2) Specification of correct segmentation labels for a small subset of the image elements. These types of user input are referred to as boundary constraints and regional constraints, respectively.

    This thesis concerns the development of methods for interactive segmentation, using a graph-theoretic approach. We view an image as an edge weighted graph, whose vertex set is the set of image elements, and whose edges are given by an adjacency relation among the image elements. Due to its discrete nature and mathematical simplicity, this graph based image representation lends itself well to the development of efficient, and provably correct, methods.

    The contributions in this thesis may be summarized as follows:

    • Existing graph-based methods for interactive segmentation are modified to improve their performance on images with noisy or missing data, while maintaining a low computational cost.
    • Fuzzy techniques are utilized to obtain segmentations from which feature measurements can be made with increased precision.
    • A new paradigm for user guidance, that unifies and generalizes regional and boundary constraints, is proposed.

    The practical utility of the proposed methods is illustrated with examples from the medical field.

    Delarbeten
    1. A 3D live-wire segmentation method for volume images using haptic interaction
    Öppna denna publikation i ny flik eller fönster >>A 3D live-wire segmentation method for volume images using haptic interaction
    2006 (Engelska)Ingår i: DISCRETE GEOMETRY FOR COMPUTER IMAGERY, PROCEEDINGS 4245, 2006, s. 663-673Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    Designing interactive segmentation methods for digital volume images is difficult, mainly because efficient 3D interaction is much

    harder to achieve than interaction with 2D images. To overcome this issue, we use a system that combines stereo graphics and haptics to facilitate efficient 3D interaction. We propose a new method, based on the 2D live-wire method, for segmenting volume images. Our method consists of two parts: an interface for drawing 3D live-wire curves onto the boundary of an object in a volume image, and an algorithm for connecting two such curves to create a discrete surface.

    Identifikatorer
    urn:nbn:se:uu:diva-19901 (URN)0302-9743 (ISBN)
    Tillgänglig från: 2006-12-04 Skapad: 2006-12-04 Senast uppdaterad: 2011-05-05
    2. Minimal Cost-Path for Path-Based Distances
    Öppna denna publikation i ny flik eller fönster >>Minimal Cost-Path for Path-Based Distances
    2007 (Engelska)Ingår i: Proceedings of 5th International Symposium on Image and Signal Processing and Analysis (ISPA 2007), 2007, s. 379-384Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    Distance functions defined by the minimal cost-path using weights and neighbourhood sequences (n.s.) are considered for the constrained distance transform (CDT). The CDT is then used to find one minimal cost-path between two points. The behaviour of some path-based distance functions is analyzed and a new error function is introduced. It is concluded that the weighted n.s.-distance with two weights (3 x 3 neighbourhood) and the weighted distance with three weights (5 x 5 neighbourhood) have similar properties in terms of minimal cost-path computation, while the former is more efficient to compute.

    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Identifikatorer
    urn:nbn:se:uu:diva-12585 (URN)doi:10.1109/ISPA.2007.4383723 (DOI)978-953-184-116-0 (ISBN)
    Tillgänglig från: 2008-01-07 Skapad: 2008-01-07 Senast uppdaterad: 2018-01-12
    3. Sub-pixel Segmentation with the Image Foresting Transform
    Öppna denna publikation i ny flik eller fönster >>Sub-pixel Segmentation with the Image Foresting Transform
    2009 (Engelska)Ingår i: Proceedings of International Workshop on Combinatorial Image Analysis: IWCIA 2009, Springer , 2009, s. 201-211Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    The Image Foresting Transform (IFT) is a framework forimage partitioning, commonly used for interactive segmentation. Givenan image where a subset of the image elements (seed-points) have beenassigned user-defined labels, the IFT completes the labeling by computingminimal cost paths from all image elements to the seed-points. Eachimage element is then given the same label as the closest seed-point. Inits original form, the IFT produces crisp segmentations, i.e., each imageelement is assigned the label of exactly one seed-point. Here, we proposea modified version of the IFT that computes region boundaries withsub-pixel precision by allowing mixed labels at region boundaries. Wedemonstrate that the proposed sub-pixel IFT allows properties of thesegmented object to be measured with higher precision.

    Ort, förlag, år, upplaga, sidor
    Springer, 2009
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 5852
    Nyckelord
    Image foresting transform, Interactive image segmentation, Sub-pixel precision
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-111261 (URN)10.1007/978-3-642-10210-3_16 (DOI)978-3-642-10208-0 (ISBN)
    Tillgänglig från: 2009-12-08 Skapad: 2009-12-08 Senast uppdaterad: 2018-12-02Bibliografiskt granskad
    4. Relaxed Image Foresting Transforms for Interactive Volume Image Segmentation
    Öppna denna publikation i ny flik eller fönster >>Relaxed Image Foresting Transforms for Interactive Volume Image Segmentation
    Visa övriga...
    2010 (Engelska)Ingår i: MEDICAL IMAGING 2010: IMAGE PROCESSING / [ed] Dawant BM, Haynor DR, 2010, Vol. 7623Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    The image Foresting (IFT) is a framework for image partitioning, commonly used for interactive segmentation. Given an image where a subset of the image elements (seed-points) have been assigned correct segmentation labels, the IFT completes the labeling by computing minimal cost paths from all image elements to the seed-points. Each image element is then given the same label as the closest seed-point. Here, we propose the relaxed IFT (RIFT). This modified version of the IFT features an additional parameter to control the smoothness of the segmentation boundary. The RIFT yields more intuitive segmentation results in the presence of noise and weak edges, while maintaining a low computational complexity. We show an application of the method to the refinement of manual segmentations of a thoracolumbar muscle in magnetic resonance images. The performed study shows that the refined segmentations are qualitatively similar to the manual segmentations, while intra-user variations are reduced by more than 50%.

    Serie
    Proceedings of SPIE-The International Society for Optical Engineering, ISSN 0277-786X ; 7623
    Nyckelord
    Seeded segmentation, Interactive segmentation, Minimum cost paths, Image Foresting Transform
    Nationell ämneskategori
    Medicin och hälsovetenskap Datavetenskap (datalogi)
    Identifikatorer
    urn:nbn:se:uu:diva-140957 (URN)10.1117/12.840019 (DOI)000285048800137 ()978-0-8194-8024-8 (ISBN)
    Konferens
    Conference on Medical Imaging 2010 - Image Processing San Diego, CA, FEB 14-16, 2010
    Tillgänglig från: 2011-01-10 Skapad: 2011-01-10 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    5. A Graph-based Framework for Sub-pixel Image Segmentation
    Öppna denna publikation i ny flik eller fönster >>A Graph-based Framework for Sub-pixel Image Segmentation
    2011 (Engelska)Ingår i: Theoretical Computer Science, ISSN 0304-3975, E-ISSN 1879-2294, Vol. 412, nr 15, s. 1338-1349Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Many image segmentation methods utilize graph structures for representing images, where the flexibility and generality of the abstract structure is beneficial. By using a fuzzy object representation, i.e., allowing partial belongingness of elements to image objects, the unavoidable loss of information when representing continuous structures by finite sets is significantly reduced,enabling feature estimates with sub-pixel precision.This work presents a framework for object representation based on fuzzysegmented graphs. Interpreting the edges as one-dimensional paths betweenthe vertices of a graph, we extend the notion of a graph cut to that of a located cut, i.e., a cut with sub-edge precision. We describe a method for computing a located cut from a fuzzy segmentation of graph vertices. Further,the notion of vertex coverage segmentation is proposed as a graph theoretic equivalent to pixel coverage segmentations and a method for computing such a segmentation from a located cut is given. Utilizing the proposed framework,we demonstrate improved precision of area measurements of synthetic two-dimensional objects. We emphasize that although the experiments presented here are performed on two-dimensional images, the proposed framework is defined for general graphs and thus applicable to images of any dimension.

    Nyckelord
    Image segmentation, Graph labeling, Graph cuts, Coverage segmentation, Sub-pixel segmentation, Feature estimation
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-149256 (URN)10.1016/j.tcs.2010.11.030 (DOI)000288420900005 ()
    Tillgänglig från: 2011-03-16 Skapad: 2011-03-16 Senast uppdaterad: 2018-12-02Bibliografiskt granskad
    6. Image Foresting Transform: On-the-fly Computation of Segmentation Boundaries
    Öppna denna publikation i ny flik eller fönster >>Image Foresting Transform: On-the-fly Computation of Segmentation Boundaries
    2011 (Engelska)Ingår i: Image Analysis: 17th Scandinavian Conference, SCIA 2011, Springer , 2011Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    The Image Foresting Transform (IFT) is a framework for seeded image segmentation, based on the computation of minimal cost paths in a discrete representation of an image. In two recent publications, we have shown that the segmentations obtained by the IFT may be improved by refining the segmentation locally around the boundariesbetween segmented regions. Since these methods operate on a small subset of the image elements only, they may be implemented efficiently if the set of boundary elements is known. Here, we show that this set maybe obtained on-the-fly, at virtually no additional cost, as a by-product of the IFT algorithm.

    Ort, förlag, år, upplaga, sidor
    Springer, 2011
    Serie
    Lecture notes in computer science
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-149260 (URN)
    Tillgänglig från: 2011-03-16 Skapad: 2011-03-16 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    7. Generalized Hard Constraints for Graph Segmentation
    Öppna denna publikation i ny flik eller fönster >>Generalized Hard Constraints for Graph Segmentation
    2011 (Engelska)Ingår i: Image Analysis, 17th Scandinavian Conference. SCIA 2011., Springer , 2011Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    Graph-based methods have become well-established tools for image segmentation. Viewing the image as a weighted graph, these methods seek to extract a graph cut that best matches the image content.Many of these methods are interactive, in that they allow a human operator to guide the segmentation process by specifying a set of hard constraints that the cut must satisfy. Typically, these constraints are given in one of two forms: regional constraints (a set of vertices that must be separated by the cut) or boundary constraints (a set of edges that must be included in the cut). Here, we propose a new type of hard constraints,that includes both regional constraints and boundary constraints as special cases. We also present an efficient method for computing cuts that satisfy a set of generalized constraints, while globally minimizing a graph-cut measure.

    Ort, förlag, år, upplaga, sidor
    Springer, 2011
    Serie
    Lecture Notes in Computer Science
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-149259 (URN)
    Tillgänglig från: 2011-03-16 Skapad: 2011-03-16 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
  • 25.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image Foresting Transform: On-the-fly Computation of Segmentation Boundaries2011Ingår i: Image Analysis: 17th Scandinavian Conference, SCIA 2011, Springer , 2011Konferensbidrag (Refereegranskat)
    Abstract [en]

    The Image Foresting Transform (IFT) is a framework for seeded image segmentation, based on the computation of minimal cost paths in a discrete representation of an image. In two recent publications, we have shown that the segmentations obtained by the IFT may be improved by refining the segmentation locally around the boundariesbetween segmented regions. Since these methods operate on a small subset of the image elements only, they may be implemented efficiently if the set of boundary elements is known. Here, we show that this set maybe obtained on-the-fly, at virtually no additional cost, as a by-product of the IFT algorithm.

  • 26.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Sladoje, Natasa
    Faculty of Technical Sciences, University of Novi Sad.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    A Graph-based Framework for Sub-pixel Image Segmentation2011Ingår i: Theoretical Computer Science, ISSN 0304-3975, E-ISSN 1879-2294, Vol. 412, nr 15, s. 1338-1349Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Many image segmentation methods utilize graph structures for representing images, where the flexibility and generality of the abstract structure is beneficial. By using a fuzzy object representation, i.e., allowing partial belongingness of elements to image objects, the unavoidable loss of information when representing continuous structures by finite sets is significantly reduced,enabling feature estimates with sub-pixel precision.This work presents a framework for object representation based on fuzzysegmented graphs. Interpreting the edges as one-dimensional paths betweenthe vertices of a graph, we extend the notion of a graph cut to that of a located cut, i.e., a cut with sub-edge precision. We describe a method for computing a located cut from a fuzzy segmentation of graph vertices. Further,the notion of vertex coverage segmentation is proposed as a graph theoretic equivalent to pixel coverage segmentations and a method for computing such a segmentation from a located cut is given. Utilizing the proposed framework,we demonstrate improved precision of area measurements of synthetic two-dimensional objects. We emphasize that although the experiments presented here are performed on two-dimensional images, the proposed framework is defined for general graphs and thus applicable to images of any dimension.

  • 27.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Östlund, Catherine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Almgren, Karin
    Gamstedt, E. Kristofer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Tillämpad mekanik.
    Measurement of fibre–fibre contact in three-dimensional images of fibrous materials obtained from X-ray synchrotron microtomography2011Ingår i: Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, ISSN 0168-9002, E-ISSN 1872-9576, Vol. 637, nr 1, s. 143-148Artikel i tidskrift (Refereegranskat)
  • 28.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Generalized Hard Constraints for Graph Segmentation2011Ingår i: Image Analysis, 17th Scandinavian Conference. SCIA 2011., Springer , 2011Konferensbidrag (Refereegranskat)
    Abstract [en]

    Graph-based methods have become well-established tools for image segmentation. Viewing the image as a weighted graph, these methods seek to extract a graph cut that best matches the image content.Many of these methods are interactive, in that they allow a human operator to guide the segmentation process by specifying a set of hard constraints that the cut must satisfy. Typically, these constraints are given in one of two forms: regional constraints (a set of vertices that must be separated by the cut) or boundary constraints (a set of edges that must be included in the cut). Here, we propose a new type of hard constraints,that includes both regional constraints and boundary constraints as special cases. We also present an efficient method for computing cuts that satisfy a set of generalized constraints, while globally minimizing a graph-cut measure.

  • 29. Miles, Cecelia M.
    et al.
    Lott, Susan E.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ludwig, Michael Z.
    Manu,
    Williams, Calvin L.
    Kreitman, Martin
    Artificial selection on egg size perturbs early pattern formation in Drosophila melanogaster2011Ingår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 65, nr 1, s. 33-42Artikel i tidskrift (Refereegranskat)
  • 30. Nagy, Benedek
    et al.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Approximating Euclidean circles by neighbourhood sequences in a hexagonal grid2011Ingår i: Theoretical Computer Science, ISSN 0304-3975, E-ISSN 1879-2294, Vol. 412, nr 15, s. 1364-1377Artikel i tidskrift (Refereegranskat)
  • 31.
    Neytcheva, Maya
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Bängtsson, Erik
    Linnér, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Finite-element based sparse approximate inverses for block-factorized preconditioners2011Ingår i: Advances in Computational Mathematics, ISSN 1019-7168, E-ISSN 1572-9044, Vol. 35, s. 323-355Artikel i tidskrift (Refereegranskat)
  • 32.
    Niazi, M. Khalid Khan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image Filtering Methods for Biomedical Applications2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Filtering is a key step in digital image processing and analysis. It is mainly used for amplification or attenuation of some frequencies depending on the nature of the application. Filtering can either be performed in the spatial domain or in a transformed domain. The selection of the filtering method, filtering domain, and the filter parameters are often driven by the properties of the underlying image. This thesis presents three different kinds of biomedical image filtering applications, where the filter parameters are automatically determined from the underlying images.

    Filtering can be used for image enhancement. We present a robust image dependent filtering method for intensity inhomogeneity correction of biomedical images. In the presented filtering method, the filter parameters are automatically determined from the grey-weighted distance transform of the magnitude spectrum. An evaluation shows that the filter provides an accurate estimate of intensity inhomogeneity.

    Filtering can also be used for analysis. The thesis presents a filtering method for heart localization and robust signal detection from video recordings of rat embryos. It presents a strategy to decouple motion artifacts produced by the non-rigid embryonic boundary from the heart. The method also filters out noise and the trend term with the help of empirical mode decomposition. Again, all the filter parameters are determined automatically based on the underlying signal.

    Transforming the geometry of one image to fit that of another one, so called image registration, can be seen as a filtering operation of the image geometry. To assess the progression of eye disorder, registration between temporal images is often required to determine the movement and development of the blood vessels in the eye. We present a robust method for retinal image registration. The method is based on particle swarm optimization, where the swarm searches for optimal registration parameters based on the direction of its cognitive and social components. An evaluation of the proposed method shows that the method is less susceptible to becoming trapped in local minima than previous methods.

    With these thesis contributions, we have augmented the filter toolbox for image analysis with methods that adjust to the data at hand.

     

    Delarbeten
    1. An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    Öppna denna publikation i ny flik eller fönster >>An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Signalbehandling Medicinsk bildbehandling
    Forskningsämne
    Datoriserad bildbehandling; Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-158673 (URN)
    Tillgänglig från: 2011-09-13 Skapad: 2011-09-13 Senast uppdaterad: 2011-10-04
    2. Bias field correction using grey-weighted distance transform applied on MR volumes
    Öppna denna publikation i ny flik eller fönster >>Bias field correction using grey-weighted distance transform applied on MR volumes
    2011 (Engelska)Ingår i: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, s. 357-360Konferensbidrag, Publicerat paper (Refereegranskat)
    Ort, förlag, år, upplaga, sidor
    Piscataway, NJ: IEEE conference proceedings, 2011
    Nationell ämneskategori
    Medicinsk bildbehandling
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-144827 (URN)10.1109/ISBI.2011.5872423 (DOI)000298849400082 ()978-1-4244-4127-3 (ISBN)
    Konferens
    8th IEEE International Symposium on Biomedical Imaging (ISBI)
    Tillgänglig från: 2011-06-09 Skapad: 2011-02-02 Senast uppdaterad: 2012-06-09Bibliografiskt granskad
    3. Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Öppna denna publikation i ny flik eller fönster >>Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Visa övriga...
    2011 (Engelska)Ingår i: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, s. 523-530Konferensbidrag, Publicerat paper (Refereegranskat)
    Abstract [en]

    To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.

    Ort, förlag, år, upplaga, sidor
    Springer-Verlag, 2011
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 6855
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Identifikatorer
    urn:nbn:se:uu:diva-155123 (URN)000300567300062 ()978-3-642-23677-8 (ISBN)
    Konferens
    14th International Conference on Computer Analysis of Images and Patterns (CAIP) AUG 29-31, 2011 Seville, SPAIN
    Tillgänglig från: 2011-06-16 Skapad: 2011-06-16 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    4. Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    Öppna denna publikation i ny flik eller fönster >>Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    2009 (Engelska)Ingår i: Transactions on Mass-Data Analysis of Images and Signals, ISSN 1868-6451, Vol. 1, nr 2, s. 132-146Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location by using decimation free directional filter bank along with first absolute moment, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

    Ort, förlag, år, upplaga, sidor
    Leipzig, Germany: IBAI Publishing, 2009
    Nyckelord
    heart detection, absolute central moments, embryo culture, directional analysis, edge delineation
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Signalbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-111495 (URN)
    Tillgänglig från: 2009-12-15 Skapad: 2009-12-15 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
    5. Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Öppna denna publikation i ny flik eller fönster >>Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Visa övriga...
    2010 (Engelska)Ingår i: Reproductive Toxicology, ISSN 0890-6238, E-ISSN 1873-1708, Vol. 29, nr 2, s. 156-163Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Drugs blocking the potassium current IKr of the heart (via hERG channel-inhibition) have the potential to cause hypoxia-related teratogenic effects. However, this activity may be missed in conventional teratology studies because repeat dosing may cause resorptions. The aim of the present study was to investigate an alternative protocol to reveal the teratogenic potential of IKr-blocking drugs. The IKr blocker astemizole, given as a single dose (80mg/kg) on gestation day (GD) 13 to pregnant rats caused digital defects. In whole rat embryo culture (2h) on GD 13, astemizole caused a decrease in embryonic heart rate at 20nM, and arrhythmias at 200-400nM. Cetirizine, without IKr-blocking properties, did not affect the rat embryonic heart in vitro. The present study shows that single dose testing on sensitive days of development, together with whole embryo culture, can be a useful methodology to better characterize the teratogenic potential of IKr-blocking drugs.

    Ort, förlag, år, upplaga, sidor
    Elsevier, 2010
    Nyckelord
    Astemizole, hERG channel, IKr, Teratogenicity, Hypoxia, Embryonic cardiac adverse effects, Embryotoxicity, Toxicology
    Nationell ämneskategori
    Farmaceutiska vetenskaper Datorseende och robotik (autonoma system)
    Forskningsämne
    Toxikologi; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-118335 (URN)10.1016/j.reprotox.2010.01.014 (DOI)000276326900004 ()20144703 (PubMedID)
    Tillgänglig från: 2010-02-23 Skapad: 2010-02-23 Senast uppdaterad: 2019-04-29Bibliografiskt granskad
    6. A Modified Particle Swarm Optimization Applied in Image Registration
    Öppna denna publikation i ny flik eller fönster >>A Modified Particle Swarm Optimization Applied in Image Registration
    2010 (Engelska)Ingår i: Proceedings of 20th International Conference on Pattern Recognition, IEEE computer society , 2010, s. 2302-2305Konferensbidrag, Publicerat paper (Refereegranskat)
    Ort, förlag, år, upplaga, sidor
    IEEE computer society, 2010
    Nationell ämneskategori
    Datorseende och robotik (autonoma system)
    Forskningsämne
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-141213 (URN)
    Konferens
    20th International Conference on Pattern Recognition (ICPR 2010)
    Tillgänglig från: 2011-01-11 Skapad: 2011-01-11 Senast uppdaterad: 2018-01-12Bibliografiskt granskad
  • 33.
    Niazi, M Khalid Khan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Ibrahim, M Talal
    Guan, Ling
    Nyström, Ingela
    An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrumManuskript (preprint) (Övrigt vetenskapligt)
  • 34.
    Niazi, M. Khalid Khan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ibrahim, Muhammad Talal
    Nilsson, Mats F.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Sköld, Anna-Carin
    Guan, Ling
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition2011Ingår i: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, s. 523-530Konferensbidrag (Refereegranskat)
    Abstract [en]

    To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.

  • 35.
    Niazi, M. Khalid Khan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ibrahim, Muhammad Talal
    Guan, Ling
    Bias field correction using grey-weighted distance transform applied on MR volumes2011Ingår i: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, s. 357-360Konferensbidrag (Refereegranskat)
  • 36.
    Norell, Kristin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automatic counting of annual rings on Pinus sylvestris end faces in sawmill industry2011Ingår i: Computers and Electronics in Agriculture, ISSN 0168-1699, E-ISSN 1872-7107, Vol. 75, nr 2, s. 231-237Artikel i tidskrift (Refereegranskat)
  • 37.
    Normand, Nicolas
    et al.
    IRCCyN UMR CNRS 6597, University of Nantes, France and School of Physics, Monash University, Melbourne, Australia .
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Evenou, Pierre
    IRCCyN UMR CNRS 6597, University of Nantes, France .
    Arlicot, Aurore
    IRCCyN UMR CNRS 6597, University of Nantes, France .
    Path-Based Distance with Varying Weights andNeighborhood Sequences2011Ingår i: Proceedings, International Conference on Discrete Geometry for Computer Imagery (DGCI 2011): / [ed] Debled-Rennesson, Isabelle and Domenjoud, Eric and Kerautret, Bertrand and Even, Philippe, Berlin Heidelberg: Springer , 2011, s. 199-210Konferensbidrag (Refereegranskat)
    Abstract [en]

    This paper presents a path-based distance where local displacement costs vary both according to the displacement vector and with the travelled distance. The corresponding distance transform algorithm is similar in its form to classical propagation-based algorithms, but the more variable distance increments are either stored in look-up-tables or computed on-the-fly. These distances and distance transform extend neighborhood-sequence distances, chamfer distances and generalized distances based on Minkowski sums. We introduce algorithms to compute, in , a translated version of a neighborhood sequence distance map with a limited number of neighbors, both for periodic and aperiodic sequences. A method to recover the centered distance map from the translated one is also introduced. Overall, the distance transform can be computed with minimal delay, without the need to wait for the whole input image before beginning to provide the result image.

  • 38.
    Nyström, Ingela
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Grevera, George J.
    Hirsch, Bruce E.
    Udupa, Jayaram K.
    Efficient computation of enclosed volume and surface area from the same triangulated surface representation2011Ingår i: Computerized Medical Imaging and Graphics, ISSN 0895-6111, E-ISSN 1879-0771, Vol. 35, nr 6, s. 460-471Artikel i tidskrift (Refereegranskat)
  • 39.
    Nyström, Ingela
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nysjö, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Visualization and Haptics for Interactive Medical Image Analysis: Image Segmentation in Cranio-Maxillofacial Surgery Planning2011Ingår i: Visual Informatics: Sustaining Research and Innovations / [ed] H. Badioze Zaman, et al. (Eds.), Berlin Heidelberg: Springer-Verlag , 2011, s. 1-12Konferensbidrag (Refereegranskat)
    Abstract [en]

    A central problem in cranio-maxillofacial (CMF) surgery is to restore the normal anatomy of the skeleton after defects, e.g., trauma to the face. With careful pre-operative planning, the precision and predictability of the craniofacial reconstruction can be significantly improved. In addition, morbidity can be reduced thanks to shorter operation time. An important component in surgery planning is to be able to accurately measure the extent of anatomical structures. Of particular interest are the shape and volume of the orbits (eye sockets). These properties can be measured in 3D CT images of the skull, provided that an accurate segmentation of the orbits is available. Here, we present a system for interactive segmentation of the orbit in CT images. The system utilizes 3D visualization and haptic feedback to facilitate efficient exploration and manipulation of 3D data.

  • 40.
    Olsson, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Carlbom, Ingrid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Johansson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Mikrosystemteknik.
    Nysjö, Fredrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Whole Hand Haptics2011Ingår i: Medicinteknikdagarna Oktober 11-12 2011, Linköping, Sweden, 2011Konferensbidrag (Refereegranskat)
    Abstract [en]

    Our sense of touch is in many ways the most sophisticated of our senses with receptors throughout the body. Unlike vision and hearing, haptics provides bi-directional communication between an individual and his/her environment. Yet, our sense of touch has been exploited for computer interfaces mostly in primitive ways, with both input and output limited to contact with a single point on a virtual object or to signal an event. But a single point of contact is often insufficient for exploration and manipulation: try to pick up a small object with only one finger! Current multi-point interaction devices are built using mechanical tendons, which are large and bulky and provide neither the stiffness nor the dynamic range required for object manipulation. We present a first generation of a haptic glove that acts as an external skeleton where the hand and finger joints are controlled by actuators that are integrated in the glove. This first prototype allows for six degrees of freedom (DOF) movement of the hand, and one DOF gripping with the thumb and index finger. The six DOF movements are accomplished with a commercial haptic arm, which allows us to simulate physical object properties such as weight, friction and inertia. The gripping force is controlled by the most compact high precision piezoelectric motor that is commercially available today, using a separate force sensor in a feed-back loop. The high stiffness of the motor in combination with a high dynamic speed range allows for delicate control of the gripping force. Combined with emerging 3D display technology, the haptic glove opens up exciting possibilities of co-located visio-haptic interaction more closely resembling real-world interaction.

  • 41.
    Pardo-Martin, Carlos
    et al.
    Massachusetts Institute of Technology, USA.
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Eimon, Peter
    Massachusetts Institute of Technology, USA.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys.
    Yanik, Mehmet Fatih
    Massachusetts Institute of Technology, USA.
    High-throughput in vivo optical projection tomography of small vertebratesManuskript (preprint) (Övrigt vetenskapligt)
  • 42. Pardo-Martin, Carlos
    et al.
    Chang, Tsung-Yao
    Allalou, Amin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Yanik, Mehmet Fatih
    High-throughput cellular-resolution in vivo vertebrate screening2011Ingår i: Proc. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011Konferensbidrag (Refereegranskat)
  • 43.
    Sarve, Hamid
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Borgefors, Gunilla
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Johansson, Carina B.
    Extracting 3D information on bone remodeling in the proximity of titanium implants in SRμCT image volumes2011Ingår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 102, nr 1, s. 25-34Artikel i tidskrift (Refereegranskat)
  • 44.
    Seipel, Stefan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Jenke, Peter
    Högskolan i Gävle.
    Quantification of gaseous structures with volumetric reconstruction from visual hulls2011Ingår i: Proceedings of SIGRAD2011, 2011, s. 77-82Konferensbidrag (Refereegranskat)
  • 45. Sladoje, Natasa
    et al.
    Lindblad, Joakim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Defuzzification of spatial fuzzy sets by feature distance minimization2011Ingår i: Image and Vision Computing, ISSN 0262-8856, E-ISSN 1872-8138, Vol. 29, s. 127-141Artikel i tidskrift (Refereegranskat)
    Abstract
  • 46.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sparse Object Representations by Digital Distance Functions2011Ingår i: Proceedings, International Conference on Discrete Geometry for Computer Imagery (DGCI 2011) / [ed] Debled-Rennesson, Isabelle and Domenjoud, Eric and Kerautret, Bertrand and Even, Philippe, Berlin Heidelberg: Springer , 2011, s. 211-222Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this paper, some methods for representing objects usingpath-based distances are considered. The representations can be usedas anchor points when extracting medial representations of the objects.The distance transform (DT) is obtained by labeling each object elementwith the distance to the background. By local operations on the DT,different sets of anchor points can be obtained. We present two differentmethods based on local operations and prove that the representations arereversible, when this is the case. The methods are defined for weighteddistances based on neighborhood sequences, which includes for examplethe well known cityblock and chessboard distances.

  • 47.
    Strand, Robin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nagy, Benedek
    Faculty of Informatics, University of Debrecen, Debrecen, Hungary.
    A weighted neighbourhood sequence distance function with three local steps2011Ingår i: Proceedings of Image and Signal Processing and Analysis (ISPA), 2011 7th International Symposium on, IEEE Computer Society , 2011, s. 564-568Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present a combined weighted neighborhood sequence distance function on the square grid with three types of steps. For this general distance function, we compute parameters that optimize an error function for the asymptotic shape of digital disks. We also analyze approximations of the parameters that can be used in the digital grid used here. An algorithm that can be used for image processing applications is also presented.

  • 48.
    Strand, Robin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nagy, Benedek
    Borgefors, Gunilla
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Digital distance functions on three-dimensional grids2011Ingår i: Theoretical Computer Science, ISSN 0304-3975, E-ISSN 1879-2294, Vol. 412, nr 15, s. 1350-1363Artikel i tidskrift (Refereegranskat)
  • 49.
    Svensson, Lennart
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Brun, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Registration Parameter Spaces for Molecular Electron Tomography Images2011Ingår i: Image Analysis and Processing – ICIAP 2011: Part I / [ed] Maino, Giuseppe; Foresti, Gian Luca, Berlin: Springer-Verlag , 2011, s. 403-412Konferensbidrag (Refereegranskat)
  • 50.
    Svensson, Lennart
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Svensson, Stina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Centrum för bildanalys. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Investigating measures for transfer function generation for visualization of MET biomedical data2011Ingår i: WSCG '2011: Communication Papers Proceedings / [ed] Baranoski, Gladimir; Skala, Vaclav, Plzen, Czech Republic: Union Agency , 2011, s. 113-120Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this paper, the question of automatically setting transfer functions for volume images is further explored. Morespecifically, the focus is automatic visualization of Molecular Electron Tomography (MET) volume images usingone-dimensional transfer functions. We investigate how well a few general measures based on density, gradient,curvature and connected component information are suited for generating these transfer functions. To assessthis, an expert has set suitable transfer function levels manually and we have studied how these levels relate todifferent characteristics of the selected measures for 29 data sets. We have found that the measures can be used toautomatically generate a transfer function used to visualize MET data, to give the user an approximate view of thecomponents in the image.

12 1 - 50 av 56
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