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  • 151.
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image Analysis in Support of Computer-Assisted Cervical Cancer Screening2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Cervical cancer is a disease that annually claims the lives of over a quarter of a million women. A substantial number of these deaths could be prevented if population wide cancer screening, based on the Papanicolaou test, were globally available. The Papanicolaou test involves a visual review of cellular material obtained from the uterine cervix. While being relatively inexpensive from a material standpoint, the test requires highly trained cytology specialists to conduct the analysis. There is a great shortage of such specialists in developing countries, causing these to be grossly overrepresented in the mortality statistics. For the last 60 years, numerous attempts at constructing an automated system, able to perform the screening, have been made. Unfortunately, a cost-effective, automated system has yet to be produced.

    In this thesis, a set of methods, aimed to be used in the development of an automated screening system, are presented. These have been produced as part of an international cooperative effort to create a low-cost cervical cancer screening system. The contributions are linked to a number of key problems associated with the screening: Deciding which areas of a specimen that warrant analysis, delineating cervical cell nuclei, rejecting artefacts to make sure that only cells of diagnostic value are included when drawing conclusions regarding the final diagnosis of the specimen. Also, to facilitate efficient method development, two methods for creating synthetic images that mimic images acquired from specimen are described.

    Delarbeid
    1. Closing Curves with Riemannian Dilation: Application to Segmentation in Automated Cervical Cancer Screening
    Åpne denne publikasjonen i ny fane eller vindu >>Closing Curves with Riemannian Dilation: Application to Segmentation in Automated Cervical Cancer Screening
    2009 (engelsk)Inngår i: Advances in Visual Computing / [ed] George Bebis et al., Berlin / Heidelberg: Springer , 2009, s. 337-346Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    In this paper, we describe a nuclei segmentation algorithm for Pap smears that uses anisotropic dilation for curve closing. Edge detection methods often return broken edges that need to be closed to achieve a proper segmentation. Our method performs dilation using Riemannian distance maps that are derived from the local structure tensor field in the image. We show that our curve closing improve the segmentation along weak edges and significantly increases the overall performance of segmentation. This is validated in a thorough study on realistic synthetic cell images from our Pap smear simulator. The algorithm is also demonstrated on bright-field microscope images of real Pap smears from cervical cancer screening.

    sted, utgiver, år, opplag, sider
    Berlin / Heidelberg: Springer, 2009
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 5875
    Emneord
    Pap-smears, Riemannian dilation, Curve closing, Anisotropic dilation, Cell segmentation
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-111501 (URN)10.1007/978-3-642-10331-5_32 (DOI)978-3-642-10330-8 (ISBN)
    Konferanse
    ISVC
    Tilgjengelig fra: 2009-12-16 Laget: 2009-12-16 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    2. PAPSYNTH: Simulated Bright-field Images of Cervical Smears
    Åpne denne publikasjonen i ny fane eller vindu >>PAPSYNTH: Simulated Bright-field Images of Cervical Smears
    2010 (engelsk)Inngår i: 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    In this paper, we present a simulator for bright-field microscope imagesof ”Pap-smears”, which is the most common technique usedtoday for cervical cancer screening. Lacking a ground truth for realimages, these realistic synthetic images may be used to tune and validateimage analysis and processing algorithms. We demonstrate thisfor two tasks: uncorrelated noise removal and nucleus segmentation.The simulator is a part of a larger project, aiming at automatic, costefficient screening for cervical cancer in developing countries.In this paper, we present a simulator for bright-field microscope imagesof ”Pap-smears”, which is the most common technique usedtoday for cervical cancer screening. Lacking a ground truth for realimages, these realistic synthetic images may be used to tune and validateimage analysis and processing algorithms. We demonstrate thisfor two tasks: uncorrelated noise removal and nucleus segmentation.The simulator is a part of a larger project, aiming at automatic, costefficient screening for cervical cancer in developing countries.

    Serie
    Biomedical Imaging: From Nano to Macro, ISSN 1945-7936 ; 7
    Emneord
    Synthetic cell images, bright-field, cervical cancer
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-126066 (URN)978-1-4244-4126-6 (ISBN)
    Konferanse
    ISBI 2010
    Tilgjengelig fra: 2010-06-02 Laget: 2010-06-02 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    3. Debris removal in Pap-smear images
    Åpne denne publikasjonen i ny fane eller vindu >>Debris removal in Pap-smear images
    Vise andre…
    2013 (engelsk)Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 111, nr 1, s. 128-138Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Since its introduction in the 1940s the Pap-smear test has helped reduce the incidence of cervical cancer dramatically in countries where regular screening is standard. The automation of this procedure is an open problem that has been ongoing for over fifty years without reaching satisfactory results. Existing systems are discouragingly expensive and yet they are only able to make a correct distinction between normal and abnormal samples in a fraction of cases. Therefore, they are limited to acting as support for the cytotechnicians as they perform their manual screening. The main reason for the current limitations is that the automated systems struggle to overcome the complexity of the cell structures. Samples are covered in artefacts such as blood cells, overlapping and folded cells, and bacteria, that hamper the segmentation processes and generate large number of suspicious objects. The classifiers designed to differentiate between normal cells and pre-cancerous cells produce unpredictable results when classifying artefacts. In this paper, we propose a sequential classification scheme focused on removing unwanted objects, debris, from an initial segmentation result, intended to be run before the actual normal/abnormal classifier. The method has been evaluated using three separate datasets obtained from cervical samples prepared using both the standard Pap-smear approach as well as the more recent liquid based cytology sample preparation technique. We show success in removing more than 99% of the debris without loosing more than around one percent of the epithelial cells detected by the segmentation process.

    Emneord
    Debris removal, Pap-smear, Cervical cancer screening, LBC
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-204092 (URN)10.1016/j.cmpb.2013.02.008 (DOI)000320346400013 ()
    Tilgjengelig fra: 2013-07-22 Laget: 2013-07-22 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    4. Cluster detection and field-of-view quality rating: Applied to automated Pap-smear analysis
    Åpne denne publikasjonen i ny fane eller vindu >>Cluster detection and field-of-view quality rating: Applied to automated Pap-smear analysis
    2013 (engelsk)Inngår i: Proc. 2nd International Conference on Pattern Recognition Applications and Methods, SciTePress, 2013, s. 355-364Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    Automated cervical cancer screening systems require high resolution analysis of a large number of epithelial cells, involving complex algorithms, mainly analysing the shape and texture of cell nuclei. This can be a very time consuming process. An initial selection of relevant fields-of-view in low resolution images could limit the number of fields to be further analysed at a high resolution. In particular, the detection of cell clusters is of interest for nuclei segmentation improvement, and for diagnostic purpose, malignant and endometrial cells being more prone to stick together in clusters than other cells. In this paper, we propose methods aiming at evaluating the quality of fields-of-view in bright-field microscope images of cervical cells. The approach consists in the construction of neighbourhood graphs using the nuclei as the set of vertices. Transformations are then applied on such graphs in order to highlight the main structures in the image. The methods result in the delineation of regions with varying cell density and the identification of cell clusters. Clustering methods are evaluated using a dataset of manually delineated clusters and compared to a related work.

    sted, utgiver, år, opplag, sider
    SciTePress, 2013
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-212509 (URN)978-989-8565-41-9 (ISBN)
    Konferanse
    2nd International Conference on Pattern Recognition Applications and Methods (ICPRAM), February 15-18, 2013, Barcelona, Spain
    Tilgjengelig fra: 2013-12-11 Laget: 2013-12-11 Sist oppdatert: 2018-01-11bibliografisk kontrollert
    5. Simulation of bright-field microscopy images depicting pap-smear specimen
    Åpne denne publikasjonen i ny fane eller vindu >>Simulation of bright-field microscopy images depicting pap-smear specimen
    2015 (engelsk)Inngår i: Cytometry Part A, ISSN 1552-4922, E-ISSN 1552-4930, Vol. 87, nr 3, s. 212-226Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    As digital imaging is becoming a fundamental part of medical and biomedical research, the demand for computer-based evaluation using advanced image analysis is becoming an integral part of many research projects. A common problem when developing new image analysis algorithms is the need of large datasets with ground truth on which the algorithms can be tested and optimized. Generating such datasets is often tedious and introduces subjectivity and interindividual and intraindividual variations. An alternative to manually created ground-truth data is to generate synthetic images where the ground truth is known. The challenge then is to make the images sufficiently similar to the real ones to be useful in algorithm development. One of the first and most widely studied medical image analysis tasks is to automate screening for cervical cancer through Pap-smear analysis. As part of an effort to develop a new generation cervical cancer screening system, we have developed a framework for the creation of realistic synthetic bright-field microscopy images that can be used for algorithm development and benchmarking. The resulting framework has been assessed through a visual evaluation by experts with extensive experience of Pap-smear images. The results show that images produced using our described methods are realistic enough to be mistaken for real microscopy images. The developed simulation framework is very flexible and can be modified to mimic many other types of bright-field microscopy images.

    Emneord
    Synthetic image generation, Pap-smear, brightfield microscopy
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-212514 (URN)10.1002/cyto.a.22624 (DOI)000349984200005 ()25573002 (PubMedID)
    Tilgjengelig fra: 2015-01-08 Laget: 2013-12-11 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    6. Multi-resolution Cervical Cell Dataset
    Åpne denne publikasjonen i ny fane eller vindu >>Multi-resolution Cervical Cell Dataset
    2013 (engelsk)Rapport (Annet vitenskapelig)
    sted, utgiver, år, opplag, sider
    Uppsala, Sweden: Centre for Image Analysis, Swedish University of Agricultural Sciences, 2013. s. 9
    Serie
    External report (Blue series) ; 37
    Emneord
    Pap smear, multi-resolution, cervical cancer
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-212505 (URN)
    Tilgjengelig fra: 2013-12-11 Laget: 2013-12-11 Sist oppdatert: 2018-01-11bibliografisk kontrollert
  • 152.
    Malm, Patrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Balakrishnan, Byju N.
    Sujathan, Vilayil K.
    Kumar, Rajesh
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Debris removal in Pap-smear images2013Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 111, nr 1, s. 128-138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Since its introduction in the 1940s the Pap-smear test has helped reduce the incidence of cervical cancer dramatically in countries where regular screening is standard. The automation of this procedure is an open problem that has been ongoing for over fifty years without reaching satisfactory results. Existing systems are discouragingly expensive and yet they are only able to make a correct distinction between normal and abnormal samples in a fraction of cases. Therefore, they are limited to acting as support for the cytotechnicians as they perform their manual screening. The main reason for the current limitations is that the automated systems struggle to overcome the complexity of the cell structures. Samples are covered in artefacts such as blood cells, overlapping and folded cells, and bacteria, that hamper the segmentation processes and generate large number of suspicious objects. The classifiers designed to differentiate between normal cells and pre-cancerous cells produce unpredictable results when classifying artefacts. In this paper, we propose a sequential classification scheme focused on removing unwanted objects, debris, from an initial segmentation result, intended to be run before the actual normal/abnormal classifier. The method has been evaluated using three separate datasets obtained from cervical samples prepared using both the standard Pap-smear approach as well as the more recent liquid based cytology sample preparation technique. We show success in removing more than 99% of the debris without loosing more than around one percent of the epithelial cells detected by the segmentation process.

  • 153.
    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 progress2011Inngår i: Proceedings SSBA 2011, 2011Konferansepaper (Annet vitenskapelig)
    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.

  • 154.
    Malm, Patrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Brun, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Simulation of bright-field microscopy images depicting pap-smear specimen2015Inngår i: Cytometry Part A, ISSN 1552-4922, E-ISSN 1552-4930, Vol. 87, nr 3, s. 212-226Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As digital imaging is becoming a fundamental part of medical and biomedical research, the demand for computer-based evaluation using advanced image analysis is becoming an integral part of many research projects. A common problem when developing new image analysis algorithms is the need of large datasets with ground truth on which the algorithms can be tested and optimized. Generating such datasets is often tedious and introduces subjectivity and interindividual and intraindividual variations. An alternative to manually created ground-truth data is to generate synthetic images where the ground truth is known. The challenge then is to make the images sufficiently similar to the real ones to be useful in algorithm development. One of the first and most widely studied medical image analysis tasks is to automate screening for cervical cancer through Pap-smear analysis. As part of an effort to develop a new generation cervical cancer screening system, we have developed a framework for the creation of realistic synthetic bright-field microscopy images that can be used for algorithm development and benchmarking. The resulting framework has been assessed through a visual evaluation by experts with extensive experience of Pap-smear images. The results show that images produced using our described methods are realistic enough to be mistaken for real microscopy images. The developed simulation framework is very flexible and can be modified to mimic many other types of bright-field microscopy images.

  • 155.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sandberg-Melin, Camilla
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Oftalmiatrik. Center for Research and Development, Region Gävleborg.
    Söderberg, Per G.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Oftalmiatrik.
    Estimating a structural bottle neck for eye–brain transfer of visual information from 3D-volumes of the optic nerve head from a commercial OCT device2016Inngår i: Ophthalmic Technologies XXVI, Bellingham, WA: SPIE - International Society for Optical Engineering, 2016, artikkel-id 96930NKonferansepaper (Fagfellevurdert)
  • 156.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ahlström, Håkan
    Kullberg, Joel
    A Toolbox for Non-parametric Deformable Registration of Volume Images2016Konferansepaper (Annet vitenskapelig)
  • 157.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Kullberg, Joel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Radiologi.
    Interactive Deformation of Volume Images for Image Registration2015Inngår i: Proc. Interactive Medical Image Computing Workshop, 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Deformable image registration, the task of nding a spatial transformation that aligns two or more images with each other, is an important task in medical image analysis. To a large extent, research on image registration has been focused on automatic methods. This is in contrast to, e.g., image segmentation, where interactive semi-automatic methods are common. Here, we propose a method for interactive editing of a deformation eld aligning two volume images. The method has been implemented in a software that allows the user to click and drag points in the deformed image to a new location, while smoothly deforming surrounding points. The method is fast enough to allow real-time display of the deformed volume image during user interaction, on standard hardware. The resulting tool is useful for initializing automatic methods, and to correct errors in automatically generated registrations.

  • 158.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Kullberg, Joel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Nordenskjöld, Richard
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Smart Paint: A New Interactive Segmentation Method\\ Applied to MR Prostate Segmentation2012Inngår i: Prostate MR Image Segmentation Grand Challenge (PROMISE'12), a MICCAI 2012 workshop, 2012Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper describes a general method for interactive segmentation, Smart Paint. The user interaction is inspired by the way an airbrush is used, objects are segmented by "sweeping" with the mouse cursor in the image. The user adds or removes details in 3D by the proposed segmentation tool and the user interface shows the segmentation result in 2D slices through the object. We use the novel method for prostate segmentation in transversal T2-weighted MR images from multiple centers and vendors and with differences in scanning protocol.

    The method was evaluated on the training set obtained from http://promise12.grand-challenge.org. In the first round, all 50 volumes were segmented and the mean of Dice's coefficient was 0.82 with standard deviation 0.09. In a second round, the first 30 volumes were re-segmented by the same user and the result was slightly improved -- Dice's coefficient 0.86 $\pm$ 0.05 was obtained. For the training data, the mean time to segment a volume was 3 minutes and 30 seconds.

    The proposed method is a generic tool for interactive image segmentation and this paper illustrates that it is well-suited for prostate segmentation.

  • 159.
    Malmberg, Filip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Strand, Robin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nordenskjöld, Richard
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Kullberg, Joel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    An interactive tool for deformable registration of volume images2014Inngår i: Symposium of the Swedish Society for Automated Image Analysis (SSBA), 2014Konferansepaper (Annet vitenskapelig)
  • 160.
    Malmberg, Filip
    et al.
    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, Avdelningen för visuell information och interaktion.
    Strand, Robin
    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, Avdelningen för visuell information och interaktion.
    Nordenskjöld, Richard
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Kullberg, Joel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Seeded Segmentation Based on Object Homogeneity2012Inngår i: Proceedings of the 21st International Conference on Pattern Recognition (ICPR), 2012, s. 21-24Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Seeded segmentation methods attempt to solve the segmentation problem in the presence of prior knowledge in the form of a partial segmentation, where a small subset of the image elements (seed-points) have been assigned correct segmentation labels. Common for most of the leading methods in this area is that they seek to find a segmentation where the boundaries of the segmented regions coincide with sharp edges in the image. Here, we instead propose a method for seeded segmentation that seeks to divide the image into areas of homogeneous pixel values. The method is based on the computation of minimal cost paths in a discrete representation of the image, using a novel path-cost function. The utility of the proposed method is demonstrated in a case study on segmentation of white matter hyperintensitities in MR images of the human brain.

  • 161.
    Matuszewski, Damian J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Image and Data Analysis for Biomedical Quantitative Microscopy2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis presents automatic image and data analysis methods to facilitate and improve microscopy-based research and diagnosis. New technologies and computational tools are necessary for handling the ever-growing amounts of data produced in life science. The thesis presents methods developed in three projects with different biomedical applications.

    In the first project, we analyzed a large high-content screen aimed at enabling personalized medicine for glioblastoma patients. We focused on capturing drug-induced cell-cycle disruption in fluorescence microscopy images of cancer cell cultures. Our main objectives were to identify drugs affecting the cell-cycle and to increase the understanding of different drugs’ mechanisms of action.  Here we present tools for automatic cell-cycle analysis and identification of drugs of interest and their effective doses.

    In the second project, we developed a feature descriptor for image matching. Image matching is a central pre-processing step in many applications. For example, when two or more images must be matched and registered to create a larger field of view or to analyze differences and changes over time. Our descriptor is rotation-, scale-, and illumination-invariant and it has a short feature vector which makes it computationally attractive. The flexibility to combine it with any feature detector and the customization possibility make it a very versatile tool.

    In the third project, we addressed two general problems for bridging the gap between deep learning method development and their use in practical scenarios. We developed a method for convolutional neural network training using minimally annotated images. In many biomedical applications, the objects of interest cannot be accurately delineated due to their fuzzy shape, ambiguous morphology, image quality, or the expert knowledge and time it requires. The minimal annotations, in this case, consist of center-points or centerlines of target objects of approximately known size. We demonstrated our training method in a challenging application of a multi-class semantic segmentation of viruses in transmission electron microscopy images. We also systematically explored the influence of network architecture hyper-parameters on its size and performance and show the possibility to substantially reduce the size of a network without compromising its performance.

    All methods in this thesis were designed to work with little or no input from biomedical experts but of course, require fine-tuning for new applications. The usefulness of the tools has been demonstrated by collaborators and other researchers and has inspired further development of related algorithms.

    Delarbeid
    1. Comparison of Flow Cytometry and Image-Based Screening for Cell Cycle Analysis
    Åpne denne publikasjonen i ny fane eller vindu >>Comparison of Flow Cytometry and Image-Based Screening for Cell Cycle Analysis
    2016 (engelsk)Inngår i: Image Analysis And Recognition (ICIAR 2016) / [ed] Aurélio Campilho, Fakhri Karray, Springer, 2016, Vol. 9730, s. 623-630Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    Quantitative cell state measurements can provide a wealth of information about mechanism of action of chemical compounds and gene functionality. Here we present a comparison of cell cycle disruption measurements from commonly used flow cytometry (generating onedimensional signal data) and bioimaging (producing two-dimensional image data). Our results show high correlation between the two approaches indicating that image-based screening can be used as an alternative to flow cytometry. Furthermore, we discuss the benefits of image informatics over conventional single-signal flow cytometry.

    sted, utgiver, år, opplag, sider
    Springer, 2016
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 9730
    Emneord
    Quantitative microscopy, DNA content histogram
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-307245 (URN)10.1007/978-3-319-41501-7_70 (DOI)000386604000070 ()
    Konferanse
    13th International Conference, ICIAR 2016, in Memory of Mohamed Kamel, Póvoa de Varzim, Portugal, July 13-15, 2016
    Tilgjengelig fra: 2016-11-11 Laget: 2016-11-11 Sist oppdatert: 2019-10-09bibliografisk kontrollert
    2. PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data
    Åpne denne publikasjonen i ny fane eller vindu >>PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data
    2016 (engelsk)Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 3, artikkel-id e0151554Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Image-based screening typically produces quantitative measurements of cell appearance. Large-scale screens involving tens of thousands of images, each containing hundreds of cells described by hundreds of measurements, result in overwhelming amounts of data. Reducing per-cell measurements to the averages across the image(s) for each treatment leads to loss of potentially valuable information on population variability. We present PopulationProfiler-a new software tool that reduces per-cell measurements to population statistics. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. We validate the tool by showing how PopulationProfiler can be used to analyze the effect of drugs that disturb the cell cycle, and compare the results to those obtained with flow cytometry.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-282026 (URN)10.1371/journal.pone.0151554 (DOI)000372580300085 ()26987120 (PubMedID)
    Forskningsfinansiär
    Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council, 2012-4968; 2014-6075
    Tilgjengelig fra: 2016-03-17 Laget: 2016-04-01 Sist oppdatert: 2019-10-09bibliografisk kontrollert
    3. Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma
    Åpne denne publikasjonen i ny fane eller vindu >>Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma
    Vise andre…
    2018 (engelsk)Inngår i: SLAS Discovery: Advancing Life Sciences R&D, ISSN 2472-5552, Vol. 23, nr 10, s. 1030-1039Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Image-based analysis is an increasingly important tool to characterize the effect of drugs in large-scale chemical screens. Herein, we present image and data analysis methods to investigate population cell-cycle dynamics in patient-derived brain tumor cells. Images of glioblastoma cells grown in multiwell plates were used to extract per-cell descriptors, including nuclear DNA content. We reduced the DNA content data from per-cell descriptors to per-well frequency distributions, which were used to identify compounds affecting cell-cycle phase distribution. We analyzed cells from 15 patient cases representing multiple subtypes of glioblastoma and searched for clusters of cell-cycle phase distributions characterizing similarities in response to 249 compounds at 11 doses. We show that this approach applied in a blind analysis with unlabeled substances identified drugs that are commonly used for treating solid tumors as well as other compounds that are well known for inducing cell-cycle arrest. Redistribution of nuclear DNA content signals is thus a robust metric of cell-cycle arrest in patient-derived glioblastoma cells.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-368698 (URN)10.1177/2472555218791414 (DOI)000452283500003 ()30074852 (PubMedID)
    Forskningsfinansiär
    AstraZenecaSwedish Research Council, 2012-4968; 2014-6075eSSENCE - An eScience Collaboration
    Tilgjengelig fra: 2018-12-06 Laget: 2018-12-06 Sist oppdatert: 2019-10-09bibliografisk kontrollert
    4. A short feature vector for image matching: The Log-Polar Magnitude feature descriptor
    Åpne denne publikasjonen i ny fane eller vindu >>A short feature vector for image matching: The Log-Polar Magnitude feature descriptor
    2017 (engelsk)Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 11, artikkel-id e0188496Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The choice of an optimal feature detector-descriptor combination for image matching often depends on the application and the image type. In this paper, we propose the Log-Polar Magnitude feature descriptor—a rotation, scale, and illumination invariant descriptor that achieves comparable performance to SIFT on a large variety of image registration problems but with much shorter feature vectors. The descriptor is based on the Log-Polar Transform followed by a Fourier Transform and selection of the magnitude spectrum components. Selecting different frequency components allows optimizing for image patterns specific for a particular application. In addition, by relying only on coordinates of the found features and (optionally) feature sizes our descriptor is completely detector independent. We propose 48- or 56-long feature vectors that potentially can be shortened even further depending on the application. Shorter feature vectors result in better memory usage and faster matching. This combined with the fact that the descriptor does not require a time-consuming feature orientation estimation (the rotation invariance is achieved solely by using the magnitude spectrum of the Log-Polar Transform) makes it particularly attractive to applications with limited hardware capacity. Evaluation is performed on the standard Oxford dataset and two different microscopy datasets; one with fluorescence and one with transmission electron microscopy images. Our method performs better than SURF and comparable to SIFT on the Oxford dataset, and better than SIFT on both microscopy datasets indicating that it is particularly useful in applications with microscopy images.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-335460 (URN)10.1371/journal.pone.0188496 (DOI)000416841900060 ()
    Forskningsfinansiär
    EU, European Research Council, ERC-CoG-2015Swedish Research Council, 2014-6075
    Tilgjengelig fra: 2017-12-05 Laget: 2017-12-05 Sist oppdatert: 2019-10-09bibliografisk kontrollert
    5. Minimal annotation training for segmentation of microscopy images
    Åpne denne publikasjonen i ny fane eller vindu >>Minimal annotation training for segmentation of microscopy images
    2018 (engelsk)Inngår i: Proc. 15th International Symposium on Biomedical Imaging, IEEE, 2018, s. 387-390Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    IEEE, 2018
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-368701 (URN)10.1109/ISBI.2018.8363599 (DOI)000455045600088 ()978-1-5386-3636-7 (ISBN)
    Konferanse
    ISBI 2018, April 4–7, Washington, DC
    Tilgjengelig fra: 2018-12-06 Laget: 2018-12-06 Sist oppdatert: 2019-10-09bibliografisk kontrollert
    6. Reducing the U-Net size for practical scenarios: Virus recognition in electron microscopy images
    Åpne denne publikasjonen i ny fane eller vindu >>Reducing the U-Net size for practical scenarios: Virus recognition in electron microscopy images
    2019 (engelsk)Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 178, s. 31-39Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Background and objective: Convolutional neural networks (CNNs) offer human experts-like performance and in the same time they are faster and more consistent in their prediction. However, most of the proposed CNNs require an expensive state-of-the-art hardware which substantially limits their use in practical scenarios and commercial systems, especially for clinical, biomedical and other applications that require on-the-fly analysis. In this paper, we investigate the possibility of making CNNs lighter by parametrizing the architecture and decreasing the number of trainable weights of a popular CNN: U-Net. Methods: In order to demonstrate that comparable results can be achieved with substantially less trainable weights than the original U-Net we used a challenging application of a pixel-wise virus classification in Transmission Electron Microscopy images with minimal annotations (i.e. consisting only of the virus particle centers or centerlines). We explored 4 U-Net hyper-parameters: the number of base feature maps, the feature maps multiplier, the number of the encoding-decoding levels and the number of feature maps in the last 2 convolutional layers. Results: Our experiments lead to two main conclusions: 1) the architecture hyper-parameters are pivotal if less trainable weights are to be used, and 2) if there is no restriction on the trainable weights number using a deeper network generally gives better results. However, training larger networks takes longer, typically requires more data and such networks are also more prone to overfitting. Our best model achieved an accuracy of 82.2% which is similar to the original U-Net while using nearly 4 times less trainable weights (7.8 M in comparison to 31.0 M). We also present a network with < 2M trainable weights that achieved an accuracy of 76.4%. Conclusions: The proposed U-Net hyper-parameter exploration can be adapted to other CNNs and other applications. It allows a comprehensive CNN architecture designing with the aim of a more efficient trainable weight use. Making the networks faster and lighter is crucial for their implementation in many practical applications. In addition, a lighter network ought to be less prone to over-fitting and hence generalize better. (C) 2019 Published by Elsevier B.V.

    sted, utgiver, år, opplag, sider
    ELSEVIER IRELAND LTD, 2019
    Emneord
    Deep learning, Hyper parameter optimization, Hardware integration, Transmission Electron Microscopy
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-393644 (URN)10.1016/j.cmpb.2019.05.026 (DOI)000480432000004 ()31416558 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 2014-6075
    Tilgjengelig fra: 2019-09-26 Laget: 2019-09-26 Sist oppdatert: 2019-10-09bibliografisk kontrollert
  • 162.
    Matuszewski, Damian J.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Minimal annotation training for segmentation of microscopy images2018Inngår i: Proc. 15th International Symposium on Biomedical Imaging, IEEE, 2018, s. 387-390Konferansepaper (Fagfellevurdert)
  • 163.
    Matuszewski, Damian J.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Carreras Puigvert, Jordi
    Karolinska Inst, Dept Med Biochem & Biophys, Div Translat Med & Chem Biol, Stockholm, Sweden; ] Sci Life Lab, Stockholm, Sweden .
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data2016Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 3, artikkel-id e0151554Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Image-based screening typically produces quantitative measurements of cell appearance. Large-scale screens involving tens of thousands of images, each containing hundreds of cells described by hundreds of measurements, result in overwhelming amounts of data. Reducing per-cell measurements to the averages across the image(s) for each treatment leads to loss of potentially valuable information on population variability. We present PopulationProfiler-a new software tool that reduces per-cell measurements to population statistics. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. We validate the tool by showing how PopulationProfiler can be used to analyze the effect of drugs that disturb the cell cycle, and compare the results to those obtained with flow cytometry.

  • 164. Mehnert, Andrew
    et al.
    Moshavegh, Ramin
    Sujathan, Vilayil K.
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    A Structural Texture Approach for Characterising Malignancy Associated Changes in Pap Smears Based on Mean-Shift and the Watershed Transform2014Inngår i: Proc. 22nd International Conference on Pattern Recognition, IEEE Computer Society, 2014, s. 1189-1193Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper presents a novel structural approach to quantitatively characterising nuclear chromatin texture in light microscope images of Pap smears. The approach is based on segmenting the chromatin into blob-like primitives and characterising their properties and arrangement. The segmentation approach makes use of multiple focal planes. It comprises two basic steps: (i) mean-shift filtering in the feature space formed by concatenating pixel spatial coordinates and intensity values centred around the best all-in-focus plane; and (ii) hierarchical marker-based watershed segmentation. The paper also presents an empirical evaluation of the approach based on the classification of 43 routine clinical Pap smears. Two variants of the approach were compared to a reference approach (employing extended depth-of-field rather than mean-shift) in a feature selection/classification experiment, involving 138 segmentation-based features, for discriminating normal and abnormal slides. The results demonstrate improved performance over the reference approach. The results of a second feature selection/classification experiment, including additional classes of features from the literature, show that a combination of the proposed structural and conventional features yields a classification performance of 0.919 +/- 0.015 (AUC +/- Std.Dev.). Overall the results demonstrate the efficacy of the proposed structural approach and confirm that it is indeed possible to detect malignancy associated changes (MACs) in conventional Papanicolaou stain.

  • 165. Mehre, Shrikant A.
    et al.
    Dhara, Ashis Kumar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Garg, Mandeep
    Kalra, Naveen
    Khandelwal, Niranjan
    Mukhopadhyay, Sudipta
    Content-Based Image Retrieval System for Pulmonary Nodules Using Optimal Feature Sets and Class Membership-Based Retrieval2019Inngår i: Journal of digital imaging, ISSN 0897-1889, E-ISSN 1618-727X, Vol. 32, s. 362-385Artikkel i tidsskrift (Fagfellevurdert)
  • 166.
    Mei, Xueshuang
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Öron-, näs- och halssjukdomar. Peking Univ, Shenzhen Hosp, Dept Otolaryngol, Beijing, Peoples R China.
    Atturo, Francesca
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Öron-, näs- och halssjukdomar.
    Wadin, Karin
    Uppsala Univ Hosp, Dept Diagnost Radiol, Uppsala, Sweden.
    Larsson, Sune
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Ortopedi.
    Agrawal, Sumit
    Western Univ, Dept Otolaryngol Head & Neck Surg, London, ON, Canada.
    Ladak, Hanif M.
    Western Univ, Dept Otolaryngol Head & Neck Surg, London, ON, Canada;Western Univ, Dept Med Biophys, London, ON, Canada;Western Univ, Dept Elect & Comp Engn, London, ON, Canada.
    Li, Hao
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Öron-, näs- och halssjukdomar.
    Rask-Andersen, Helge
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Öron-, näs- och halssjukdomar.
    Human inner ear blood supply revisited: the Uppsala collection of temporal bone - an international resource of education and collaboration2018Inngår i: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 123, nr 3, s. 131-142Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The Uppsala collection of human temporal bones and molds is a unique resource for education and international research collaboration. Micro-computerized tomography (micro-CT) and synchrotron imaging are used to investigate the complex anatomy of the inner ear. Impaired microcirculation is etiologically linked to various inner ear disorders, and recent developments in inner ear surgery promote examination of the vascular system. Here, for the first time, we present three-dimensional (3D) data from investigations of the major vascular pathways and corresponding bone channels.

    Methods: We used the archival Uppsala collection of temporal bones and molds consisting of 324 inner ear casts and 113 macerated temporal bones. Micro-CT was used to investigate vascular bone channels, and 26 fresh human temporal bones underwent synchrotron radiation phase contrast imaging (SR-PCI). Data were processed by volume-rendering software to create 3D reconstructions allowing orthogonal sectioning, cropping, and soft tissue analyses.

    Results: Micro-CT with 3D rendering was superior in reproducing the anatomy of the vascular bone channels, while SR-PCI replicated soft tissues. Arterial bone channels were traced from scala vestibuli (SV) arterioles to the fundus, cochlea, and vestibular apparatus. Drainage routes along the aqueducts were examined.

    Conclusion: Human inner ear vessels are difficult to study due to the adjoining hard bone. Micro-CT and SR-PCI with 3D reconstructions revealed large portions of the micro-vascular system in un-decalcified specimens. The results increase our understanding of the organization of the vascular system in humans and how altered microcirculation may relate to inner ear disorders. The findings may also have surgical implications.

  • 167.
    Mignardi, Marco
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Ishaq, Omer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Qian, Xiaoyan
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-17165 Stockholm, Sweden..
    Wählby, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bridging Histology and Bioinformatics: Computational analysis of spatially resolved transcriptomics2017Inngår i: Proceedings of the IEEE, ISSN 0018-9219, E-ISSN 1558-2256, Vol. 105, nr 3, s. 530-541Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well known that cells in tissue display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment. Traditional methods that analyze gene expression from bulk RNA extracts fail to accurately describe this heterogeneity because of their intrinsic limitation in cellular and spatial resolution. Also, information on histology in the form of tissue architecture and organization is lost in the process. Recently, new transcriptome-wide analysis technologies have enabled the study of RNA molecules directly in tissue samples, thus maintaining spatial resolution and complementing histological information with molecular information important for the understanding of many biological processes and potentially relevant for the clinical management of cancer patients. These new methods generally comprise three levels of analysis. At the first level, biochemical techniques are used to generate signals that can be imaged by different means of fluorescence microscopy. At the second level, images are subject to digital image processing and analysis in order to detect and identify the aforementioned signals. At the third level, the collected data are analyzed and transformed into interpretable information by statistical methods and visualization techniques relating them to each other, to spatial distribution, and to tissue morphology. In this review, we describe state-of-the-art techniques used at all three levels of analysis. Finally, we discuss future perspective in this fast-growing field of spatially resolved transcriptomics.

  • 168. Moshavegh, R.
    et al.
    Bejnordi, B. E.
    Mehnert, A.
    Sujathan, K.
    Malm, P.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automated segmentation of free-lying cell nuclei in Pap smears for malignancy-associated change analysis2012Inngår i: Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE, 2012, s. 5372-5375Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper presents an automated algorithm for robustly detecting and segmenting free-lying cell nuclei in bright-field microscope images of Pap smears. This is an essential initial step in the development of an automated screening system for cervical cancer based on malignancy associated change (MAC) analysis. The proposed segmentation algorithm makes use of gray-scale annular closings to identify free-lying nuclei-like objects together with marker-based watershed segmentation to accurately delineate the nuclear boundaries. The algorithm also employs artifact rejection based on size, shape, and granularity to ensure only the nuclei of intermediate squamous epithelial cells are retained. An evaluation of the performance of the algorithm relative to expert manual segmentation of 33 fields-of-view from 11 Pap smear slides is also presented. The results show that the sensitivity and specificity of nucleus detection is 94.71% and 85.30% respectively, and that the accuracy of segmentation, measured using the Dice coefficient, of the detected nuclei is 97.30 #x00B1;1.3%.

  • 169. Moshavegh, R.
    et al.
    Bejnordi, B. E.
    Mehnert, A.
    Sujathan, K.
    Malm, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Automated segmentation of free-lying cell nuclei in Pap smears for malignancy-associated change analysis2012Inngår i: Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2012, s. 5372-5375Konferansepaper (Fagfellevurdert)
    Abstract [en]

    This paper presents an automated algorithm for robustly detecting and segmenting free-lying cell nuclei in bright-field microscope images of Pap smears. This is an essential initial step in the development of an automated screening system for cervical cancer based on malignancy associated change (MAC) analysis. The proposed segmentation algorithm makes use of gray-scale annular closings to identify free-lying nuclei-like objects together with marker-based watershed segmentation to accurately delineate the nuclear boundaries. The algorithm also employs artifact rejection based on size, shape, and granularity to ensure only the nuclei of intermediate squamous epithelial cells are retained. An evaluation of the performance of the algorithm relative to expert manual segmentation of 33 fields-of-view from 11 Pap smear slides is also presented. The results show that the sensitivity and specificity of nucleus detection is 94.71% and 85.30% respectively, and that the accuracy of segmentation, measured using the Dice coefficient, of the detected nuclei is 97.30±1.3%.

  • 170. Motevakel, Amir
    et al.
    Medvedev, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    Localization of deep brain stimulation electrodes via metal artifacts in CT images2014Inngår i: Proc. 36th International Conference of the IEEE Engineering in Medicine and Biology Society, Curran Associates, Inc., 2014, s. 1055-1058Konferansepaper (Fagfellevurdert)
    Abstract [en]

    In Deep Brain Stimulation (DBS), the location of implanted electrodes in the brain has direct influence on the therapeutic effect of the treatment. This work deals with estimating the position of the implanted DBS electrodes from the images registered by X-ray Computed Tomography (CT) scanners. A technique named junction method that takes advantage of the streak artifacts created by the metal parts of the electrodes in CT images is proposed for this purpose. To start with, the brain image is extracted by defining a brain mask. Next, the edges are intensified by applying a Gaussian convolution operator followed by a measure of the second derivative of the image along all directions in the image plane. Criteria of adjacency and length are applied to the lines detected by the Hough transform to distinguish between tracks of streak artifacts and the brain structure. At some points, straight lines are distorted by noise. To handle this issue, all lines that fit same line equation are merged. The horizontal line connecting the two DBS electrodes (one in each cerebral hemisphere) is called electrode line. To specify the electrodes position, intersections of the electrode line with every other line are marked. Finally, to obtain the vertical position estimate, the above algorithm is applied to the image stack.

  • 171.
    Nedelcu, Robert
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Olsson, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Thor, Andreas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Finish line distinctness and accuracy in 7 intraoral scanners versus conventional impression: an in vitro descriptive comparison2018Inngår i: BMC Oral Health, ISSN 1472-6831, E-ISSN 1472-6831, Vol. 18, artikkel-id 27Artikkel i tidsskrift (Fagfellevurdert)
  • 172.
    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 Applications2011Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

     

    Delarbeid
    1. An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    Åpne denne publikasjonen i ny fane eller vindu >>An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling; Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-158673 (URN)
    Tilgjengelig fra: 2011-09-13 Laget: 2011-09-13 Sist oppdatert: 2011-10-04
    2. Bias field correction using grey-weighted distance transform applied on MR volumes
    Åpne denne publikasjonen i ny fane eller vindu >>Bias field correction using grey-weighted distance transform applied on MR volumes
    2011 (engelsk)Inngår i: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, s. 357-360Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    Piscataway, NJ: IEEE conference proceedings, 2011
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-144827 (URN)10.1109/ISBI.2011.5872423 (DOI)000298849400082 ()978-1-4244-4127-3 (ISBN)
    Konferanse
    8th IEEE International Symposium on Biomedical Imaging (ISBI)
    Tilgjengelig fra: 2011-06-09 Laget: 2011-02-02 Sist oppdatert: 2012-06-09bibliografisk kontrollert
    3. Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Åpne denne publikasjonen i ny fane eller vindu >>Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Vise andre…
    2011 (engelsk)Inngår i: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, s. 523-530Konferansepaper, Publicerat paper (Fagfellevurdert)
    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.

    sted, utgiver, år, opplag, sider
    Springer-Verlag, 2011
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 6855
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-155123 (URN)000300567300062 ()978-3-642-23677-8 (ISBN)
    Konferanse
    14th International Conference on Computer Analysis of Images and Patterns (CAIP) AUG 29-31, 2011 Seville, SPAIN
    Tilgjengelig fra: 2011-06-16 Laget: 2011-06-16 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    4. Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    Åpne denne publikasjonen i ny fane eller vindu >>Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    2009 (engelsk)Inngår i: Transactions on Mass-Data Analysis of Images and Signals, ISSN 1868-6451, Vol. 1, nr 2, s. 132-146Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    Leipzig, Germany: IBAI Publishing, 2009
    Emneord
    heart detection, absolute central moments, embryo culture, directional analysis, edge delineation
    HSV kategori
    Forskningsprogram
    Signalbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-111495 (URN)
    Tilgjengelig fra: 2009-12-15 Laget: 2009-12-15 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    5. Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Åpne denne publikasjonen i ny fane eller vindu >>Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Vise andre…
    2010 (engelsk)Inngår i: Reproductive Toxicology, ISSN 0890-6238, E-ISSN 1873-1708, Vol. 29, nr 2, s. 156-163Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    Elsevier, 2010
    Emneord
    Astemizole, hERG channel, IKr, Teratogenicity, Hypoxia, Embryonic cardiac adverse effects, Embryotoxicity, Toxicology
    HSV kategori
    Forskningsprogram
    Toxikologi; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-118335 (URN)10.1016/j.reprotox.2010.01.014 (DOI)000276326900004 ()20144703 (PubMedID)
    Tilgjengelig fra: 2010-02-23 Laget: 2010-02-23 Sist oppdatert: 2019-04-29bibliografisk kontrollert
    6. A Modified Particle Swarm Optimization Applied in Image Registration
    Åpne denne publikasjonen i ny fane eller vindu >>A Modified Particle Swarm Optimization Applied in Image Registration
    2010 (engelsk)Inngår i: Proceedings of 20th International Conference on Pattern Recognition, IEEE computer society , 2010, s. 2302-2305Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    IEEE computer society, 2010
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-141213 (URN)
    Konferanse
    20th International Conference on Pattern Recognition (ICPR 2010)
    Tilgjengelig fra: 2011-01-11 Laget: 2011-01-11 Sist oppdatert: 2018-01-12bibliografisk kontrollert
  • 173.
    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) (Annet vitenskapelig)
  • 174.
    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 volumes2011Inngår i: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, s. 357-360Konferansepaper (Fagfellevurdert)
  • 175.
    Nilsson, Johanna
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    On Virtual Surgical Planning in Cranio-Maxillofacial Surgery2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The complex three-dimensional (3D) anatomy of the cranio-maxillofacial (CMF) region makes surgery a challenging task. Virtual surgical planning (VSP) has the potential to increase accuracy, reproducibility and shorten operation time. Key challenges in VSP are to accurately separate, or segment, certain structures of interest, such as the orbit, from the rest of the image, as well as to create an accurate 3D model of the facial bones and dentition for orthognathic surgery planning. The time required for planning and fabrication of guides for trauma surgery is another challenge. The overall aim of this thesis was to develop and evaluate new virtual planning tools for CMF-surgery and to investigate their usefulness. Study I, II discuss and evaluate image fusion of CT/CBCT and intraoral scanning for orthognathic surgery. A method for virtual bite registration in centric relation (CR) was also proposed. The workflow has the potential to eliminate traditional laboratory work, and may facilitate 3D computer-assisted-planning in orthognathic surgery. Study III deals with orbit segmentation and presents a semi-automatic method, using a deformable model tracing the inside of the orbit via haptic 3D interaction. The method was validated in retrospective unilateral orbital fracture cases. The fractured orbits were compared to the intact side by volume and shape analyses. The method showed high accuracy, precision, time-efficiency and thereby potential to be a powerful tool for planning and evaluating reconstruction of orbital fractures. Study IV evaluates an in-house haptic-assisted VSP system for complex mandibular fractures on a series of retrospective cases and an artificial case. The system showed high precision and time-efficiency, but relatively low accuracy. This study proposes a novel, fast and user-friendly way of integrating VSP into planning mandible trauma surgery and could help in reducing operating time and increase accuracy. Study V is a systematic review and meta-analysis studying potential time benefits using VSP in CMF surgery. The study suggests that VSP shortens the operating time and ischemia time for reconstructive surgery. VSP also appears to shorten the preoperative planning time for orthognathic surgery.

    Delarbeid
    1. Development of workflow for recording virtual bite in the planning of orthognathic operations
    Åpne denne publikasjonen i ny fane eller vindu >>Development of workflow for recording virtual bite in the planning of orthognathic operations
    2015 (engelsk)Inngår i: British Journal of Oral & Maxillofacial Surgery, ISSN 0266-4356, E-ISSN 1532-1940, Vol. 53, nr 4, s. 384-386Artikkel i tidsskrift (Fagfellevurdert) Published
    Emneord
    Orthognathic surgery, 3-Dimensional computer model, Virtual planning, Digital scanner, Computed tomography, Cone beam computed tomography
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-252180 (URN)10.1016/j.bjoms.2014.12.017 (DOI)000352083800017 ()25631397 (PubMedID)
    Eksternt samarbeid:
    Tilgjengelig fra: 2015-05-06 Laget: 2015-05-04 Sist oppdatert: 2019-02-25bibliografisk kontrollert
    2. Virtual bite registration using intraoral digital scanning, CT and CBCT: In vitro evaluation of a new method and its implication for orthognathic surgery
    Åpne denne publikasjonen i ny fane eller vindu >>Virtual bite registration using intraoral digital scanning, CT and CBCT: In vitro evaluation of a new method and its implication for orthognathic surgery
    2016 (engelsk)Inngår i: Journal of Cranio-Maxillofacial Surgery, ISSN 1010-5182, E-ISSN 1878-4119, Vol. 44, nr 9, s. 1194-1200Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Three-dimensional (3D) computer-assisted planning requires detailed visualisation of the craniomaxillofacial region and interocclusal relationship. The aim of this study was to establish and evaluate a method to create a 3D model of the craniomaxillofacial region and to adopt intraoral digital scanning to place the lower jaw into a centric relation (CR) without the need of additional plaster casts and model surgery. A standard plastic skull modified by metallic dental wires and brackets was subjected to computed tomography (CT), cone beam computed tomography (CBCT), and intraoral digital scanning. We evaluated two different virtual bite registrations, a digital scan of the buccal dental surfaces and scanning of the wax bites to position the lower jaw into a CR, and assessed the accuracy of the integration of intraoral scanning to the CT/CBCT scans. The mean registration error of corresponding mesh points for the CT and intraoral scanned images was 0.15 ± 0.12 mm, while this error was 0.18 ± 0.13 mm for the CBCT and intraoral scanned images. The mean accuracy of the two virtual bite registrations ranged from 0.41 to 0.49 mm (buccal scan technique) and from 0.65 to 1.3 mm (virtualised wax bite technique). A method for virtual bite registration was developed. It has the potential to eliminate plaster casts and model surgery and may facilitate 3D computer-assisted planning of orthognathic surgery cases.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-302047 (URN)10.1016/j.jcms.2016.06.013 (DOI)000384776400013 ()27423538 (PubMedID)
    Tilgjengelig fra: 2016-08-29 Laget: 2016-08-29 Sist oppdatert: 2019-02-25bibliografisk kontrollert
    3. Comparison analysis of orbital shape and volume in unilateral fractured orbits
    Åpne denne publikasjonen i ny fane eller vindu >>Comparison analysis of orbital shape and volume in unilateral fractured orbits
    2018 (engelsk)Inngår i: Journal of Cranio-Maxillofacial Surgery, ISSN 1010-5182, E-ISSN 1878-4119, Vol. 46, nr 3, s. 381-387Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Facial fractures often result in changes of the orbital volume. These changes can be measured in three-dimensional (3D) computed tomography (CT) scans for preoperative planning and postoperative evaluation. The aim of this study was to analyze the orbital volume and shape before and after surgical treatment of unilateral orbital fractures using semi-automatic image segmentation and registration techniques. The orbital volume in 21 patients was assessed by a semi-automatic model-based segmentation method. The fractured orbit was compared relative to the contralateral orbit. The same procedure was performed for the postoperative evaluation. Two observers performed the segmentation procedure, and the inter- and intraobserver variability was evaluated. The interobserver variability (mean volume difference ± 1.96 SD) was −0.6 ± 1.0 ml in the first trial and 0.7 ± 0.8 ml in the second trial. The intra-observer variability was −0.2 ± 0.7 ml for the first observer and 1.1 ± 0.9 ml for the second observer. The average volume overlap (Dice similarity coefficient) between the fractured and contralateral side increased after surgery, while the mean and maximum surface distance decreased, indicating that the surgery contributed to a re-establishment of size and shape. In conclusion, our study shows that the semi-automatic segmentation method has precision for detecting volume differences down to 1.0 ml. The combination of semi-automatic segmentation and 3D shape analysis provides a powerful tool for planning and evaluating treatment of orbital fractures.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-341456 (URN)10.1016/j.jcms.2017.12.012 (DOI)000425712500002 ()29325886 (PubMedID)
    Tilgjengelig fra: 2017-12-21 Laget: 2018-02-09 Sist oppdatert: 2019-02-25bibliografisk kontrollert
    4. Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures.
    Åpne denne publikasjonen i ny fane eller vindu >>Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures.
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The management of complex mandible fractures, i.e severely comminuted or fractures of edentulous/atrophic mandibles, can be challenging. This is due to the three-dimensional loss of bone, which limits the possibility for accurate anatomic reduction. Virtual surgery planning (VSP) can provide improved accuracy and shorter operating times, but is often not employed for trauma cases because of time constraints and complex user interfaces limited to two-dimensional interaction with three-dimensional data. In this study, we evaluate the accuracy, precision, and time efficiency of the Haptic Assisted Surgery Planning system (HASP), an in-house VSP system that supports stereo graphics, six degrees-of-freedom input and haptics, to improve the surgical planning. Three operators performed planning in HASP on Computed Tomography (CT) and Come Beam Computed Tomography (CBCT) images of a plastic skull model and on twelve retrospective cases with complex mandible fractures. The result shows an accuracy and reproducibility of less than 2mm when using HASP, with an average planning time of 15 minutes, including time for segmentation in the software BoneSplit. This study presents an in-house haptic assisted planning tool for cranio-maxillofacial surgery with high usability that can be used for preoperative planning and evaluation of complex mandible fractures. 

    Emneord
    Virtual surgical planning, Haptic technology, Complex mandible fractures.
    HSV kategori
    Forskningsprogram
    Kirurgi; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-377518 (URN)
    Tilgjengelig fra: 2019-02-25 Laget: 2019-02-25 Sist oppdatert: 2019-02-25
    5. Time matters - differences between virtual surgical planning and conventional planning in cranio-maxillofacial surgery: a systematic review and meta-analysis
    Åpne denne publikasjonen i ny fane eller vindu >>Time matters - differences between virtual surgical planning and conventional planning in cranio-maxillofacial surgery: a systematic review and meta-analysis
    (engelsk)Inngår i: International Journal of Oral and Maxillofacial Surgery, ISSN 0901-5027, E-ISSN 1399-0020Artikkel i tidsskrift (Fagfellevurdert) Submitted
    Abstract [en]

    The aim of the study was to assess if there is a time difference (operative time, ischemia time, planning time and hospitalization) between virtual surgical planning (VSP) and conventional planning in cranio-maxillofacial surgery (CMF). An electronic search was performed in June 2018. Studies comparing time difference between VSP and traditional planning were included. A meta-analysis was undertaken to demonstrate the difference between the groups regarding operative time, ischemia time and hospitalization duration for CMF reconstruction. 27 publications were included, with 524 patients in the VSP group and 770 in the control group. Most studies reported on mandible/maxilla reconstruction and the meta-analysis showed a decreased operative time for the VSP group with a mean difference of -84.61 min (95%CI -106.77, -62,45, p<0.00001). Ischemia time was also decreased, with a mean difference of -36.14 min (95% confidence interval -50.57, -21.71, p<0.00001). This systematic review and meta-analysis suggests that VSP is shortening the operation time and ischemia time for reconstructive CMF surgery. VSP also seems to shorten the preoperative planning time for orthognathic surgery.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-377725 (URN)
    Tilgjengelig fra: 2019-02-25 Laget: 2019-02-25 Sist oppdatert: 2019-02-25
  • 176.
    Nilsson, Johanna
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi. Department of Oral & Maxillofacial Surgery, Zealand University Hospital, Køge, Denmark.
    Nysjö, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Carlsson, Anders-Petter
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi. Department of Oral & Maxillofacial Surgery, Zealand University Hospital, Køge, Denmark.
    Thor, Andreas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Comparison analysis of orbital shape and volume in unilateral fractured orbits2018Inngår i: Journal of Cranio-Maxillofacial Surgery, ISSN 1010-5182, E-ISSN 1878-4119, Vol. 46, nr 3, s. 381-387Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Facial fractures often result in changes of the orbital volume. These changes can be measured in three-dimensional (3D) computed tomography (CT) scans for preoperative planning and postoperative evaluation. The aim of this study was to analyze the orbital volume and shape before and after surgical treatment of unilateral orbital fractures using semi-automatic image segmentation and registration techniques. The orbital volume in 21 patients was assessed by a semi-automatic model-based segmentation method. The fractured orbit was compared relative to the contralateral orbit. The same procedure was performed for the postoperative evaluation. Two observers performed the segmentation procedure, and the inter- and intraobserver variability was evaluated. The interobserver variability (mean volume difference ± 1.96 SD) was −0.6 ± 1.0 ml in the first trial and 0.7 ± 0.8 ml in the second trial. The intra-observer variability was −0.2 ± 0.7 ml for the first observer and 1.1 ± 0.9 ml for the second observer. The average volume overlap (Dice similarity coefficient) between the fractured and contralateral side increased after surgery, while the mean and maximum surface distance decreased, indicating that the surgery contributed to a re-establishment of size and shape. In conclusion, our study shows that the semi-automatic segmentation method has precision for detecting volume differences down to 1.0 ml. The combination of semi-automatic segmentation and 3D shape analysis provides a powerful tool for planning and evaluating treatment of orbital fractures.

  • 177.
    Nordenskjöld, Richard
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Analysis of Human Brain MRI: Contributions to Regional Volume Studies2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Many disorders are associated with regional brain volumes. The analysis of these volumes from MR images often requires sequential processing steps such as localization and delineation. It is common to perform volumetric normalization using intracranial volume (ICV, the total volume inside the cranial cavity) when comparing regional brain volumes, since head size varies considerably between individuals. Multiple methods for estimating ICV and procedures for volume normalization exist.

    A method for interhemispheric surface localization and extraction, using both intensity and symmetry information and without time consuming pre-processing, was developed. Evaluations of hemisphere division accuracy as well as suitability as a pre-processing step for interhemispheric structure localization were made. The performance of the method was comparable to that of methods focusing on either of these tasks, making it suited for use in many different studies.

    Automated ICV estimations from Freesurfer and SPM were evaluated using 399 reference segmentations. Both methods overestimated ICV and estimations using Freesurfer contained errors associated with skull-size. Estimations from SPM contained errors associated with gender and atrophy. An experiment showed that the choice of method can affect study results.

    Manual ICV estimation is very time consuming, but can be performed using only a subset of voxels in an image to increase speed and decrease manual labor. Segmenting every nth slice and stereology were evaluated in terms of required manual labor and estimation error, using the previously created ICV references. An illustration showing how much manual labor is required for a given estimation error using different combinations of n and stereology grid spacing was presented.

    Finally, different procedures for ICV normalization of regional brain volumes when investigating gender related volume differences were theoretically explained and evaluated using both simulated and real data. Resulting volume differences were seen to depend on the procedure used. A suggested workflow for procedure selection was presented.

    Methodological contributions that can aid the analysis of the human brain have been presented. The performed studies also contribute to the understanding of important methodological considerations for regional brain volume analysis.

    Delarbeid
    1. Automated interhemispheric surface extraction in T1-weighted MRI using intensity and symmetry information
    Åpne denne publikasjonen i ny fane eller vindu >>Automated interhemispheric surface extraction in T1-weighted MRI using intensity and symmetry information
    Vise andre…
    2014 (engelsk)Inngår i: Journal of Neuroscience Methods, ISSN 0165-0270, E-ISSN 1872-678X, Vol. 222, s. 97-105Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Background: Localizing the human interhemispheric region is of interest in image analysis mainly because it can be used for hemisphere separation and as a preprocessing step for interhemispheric structure localization. Many existing methods focus on only one of these applications. New method: Here a new Intensity and Symmetry based Interhemispheric Surface extraction method (ISIS) that enables both applications is presented. A combination of voxel intensity and local symmetry is used to optimize a surface from T1-weighted MRI. Results: ISIS was evaluated in regard to cerebral hemisphere separation using manual segmentations. It was also evaluated in regard to being a preprocessing step for interhemispheric structure localization using manually placed landmarks. Comparison with existing methods: Results were compared to cerebral hemisphere separations by Brain-Visa and Freesurfer as well as to a midsagittal plane (MSP) extraction method. ISIS had less misclassified voxels than BrainVisa (ISIS: 0.119+/-0.114%, BrainVisa: 0.138+/-0.084%, p=0.020). Freesurfer had less misclassified voxels than ISIS for one dataset (ISIS: 0.063+/-0.056%, Freesurfer: 0.049+/-0.044%, p=0.019), but failed to produce usable results for another. Total voxel distance from all manual landmarks did not differ significantly between ISIS and the MSP method (ISIS: 4.00+/-1.88, MSP: 4.47+/-4.97). Conclusions: ISIS was found successful in both cerebral hemisphere separation and as a preprocessing step for interhemispheric structure localization. It needs no time consuming preprocessing and extracts the interhemispheric surface in less than 30 s.

    Emneord
    Interhemispheric surface, Graph cut, Hemisphere separation, Midsagittal plane, Anterior commissure, Posterior commissure
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-221919 (URN)10.1016/j.jneumeth.2013.11.007 (DOI)000331672000012 ()
    Tilgjengelig fra: 2014-04-07 Laget: 2014-04-07 Sist oppdatert: 2017-12-05bibliografisk kontrollert
    2. Intracranial volume estimated with commonly used methods could introduce bias in studies including brain volume measurements
    Åpne denne publikasjonen i ny fane eller vindu >>Intracranial volume estimated with commonly used methods could introduce bias in studies including brain volume measurements
    Vise andre…
    2013 (engelsk)Inngår i: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, Vol. 83, s. 355-360Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    In brain volumetric studies, intracranial volume (ICV) is often used as an estimate of pre-morbid brain size as well as to compensate for inter-subject variations in head size. However, if the estimated ICV is biased by for example gender or atrophy, it could introduce errors in study results. To evaluate how two commonly used methods for ICV estimation perform, computer assisted reference segmentations were created and evaluated. Segmentations were created for 399 MRI volumes from 75-year-old subjects, with 53 of these subjects having an additional scan and segmentation created at age 80. ICV estimates from Statistical Parametric Mapping (SPM, version 8) and Freesurfer (FS, version 5.1.0) were compared to the reference segmentations, and bias related to skull size (approximated with the segmentation measure), gender or atrophy were tested for. The possible ICV related effect on associations between normalized hippocampal volume and factors gender, education and cognition was evaluated by normalizing hippocampal volume with different ICV measures. Excellent agreement was seen for inter- (r=0.999) and intra- (r=0.999) operator reference segmentations. Both SPM and FS overestimated ICV. SPM showed bias associated with gender and atrophy while FS showed bias dependent on skull size. All methods showed good correlation between time points in the longitudinal data (reference: 0.998, SPM: 0.962, FS: 0.995). Hippocampal volume showed different associations with cognition and gender depending on which ICV measure was used for hippocampal volume normalization. These results show that the choice of method used for ICV estimation can bias results in studies including brain volume measurements.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-207611 (URN)10.1016/j.neuroimage.2013.06.068 (DOI)000326953700032 ()23827332 (PubMedID)
    Tilgjengelig fra: 2013-09-17 Laget: 2013-09-17 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    3. Manual intracranial volume estimation from MRI: labor reduction and estimation error
    Åpne denne publikasjonen i ny fane eller vindu >>Manual intracranial volume estimation from MRI: labor reduction and estimation error
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-222374 (URN)
    Tilgjengelig fra: 2014-04-10 Laget: 2014-04-10 Sist oppdatert: 2014-06-30
    4. Intracranial volume normalization methods: considerations when investigating gender differences in regional brain volume
    Åpne denne publikasjonen i ny fane eller vindu >>Intracranial volume normalization methods: considerations when investigating gender differences in regional brain volume
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-222375 (URN)
    Tilgjengelig fra: 2014-04-10 Laget: 2014-04-10 Sist oppdatert: 2017-02-21
  • 178.
    Nordenskjöld, Richard
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Larsson, Elna-Marie
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Simmons, Andrew
    Brooks, Samantha J.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Lind, Lars
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Kardiovaskulär epidemiologi.
    Ahlström, Håkan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Johansson, Lars
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Kullberg, Joel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för radiologi, onkologi och strålningsvetenskap, Enheten för radiologi.
    Intracranial volume estimated with commonly used methods could introduce bias in studies including brain volume measurements2013Inngår i: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, Vol. 83, s. 355-360Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In brain volumetric studies, intracranial volume (ICV) is often used as an estimate of pre-morbid brain size as well as to compensate for inter-subject variations in head size. However, if the estimated ICV is biased by for example gender or atrophy, it could introduce errors in study results. To evaluate how two commonly used methods for ICV estimation perform, computer assisted reference segmentations were created and evaluated. Segmentations were created for 399 MRI volumes from 75-year-old subjects, with 53 of these subjects having an additional scan and segmentation created at age 80. ICV estimates from Statistical Parametric Mapping (SPM, version 8) and Freesurfer (FS, version 5.1.0) were compared to the reference segmentations, and bias related to skull size (approximated with the segmentation measure), gender or atrophy were tested for. The possible ICV related effect on associations between normalized hippocampal volume and factors gender, education and cognition was evaluated by normalizing hippocampal volume with different ICV measures. Excellent agreement was seen for inter- (r=0.999) and intra- (r=0.999) operator reference segmentations. Both SPM and FS overestimated ICV. SPM showed bias associated with gender and atrophy while FS showed bias dependent on skull size. All methods showed good correlation between time points in the longitudinal data (reference: 0.998, SPM: 0.962, FS: 0.995). Hippocampal volume showed different associations with cognition and gender depending on which ICV measure was used for hippocampal volume normalization. These results show that the choice of method used for ICV estimation can bias results in studies including brain volume measurements.

  • 179.
    Nordesjö, Olle
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Pontén, Victor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Herman, Stephanie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ås, Joel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Jamal, Sabri
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nyberg, Alona
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ett sannolikhetsbaserat kvalitetsmått förbättrar klassificeringen av oförväntade sekvenser i in situ sekvensering2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    In situ sekvensering är en metod som kan användas för att lokalisera differentiellt uttryck av mRNA direkt i vävnadssnitt, vilket kan ge viktiga ledtrådar om många sjukdomstillstånd. Idag förloras många av sekvenserna från in situ sekvensering på grund av det kvalitetsmått man använder för att säkerställa att sekvenser är korrekta. Det finns troligtvis möjlighet att förbättra prestandan av den nuvarande base calling-metoden eftersom att metoden är i ett tidigt utvecklingsskede. Vi har genomfört explorativ dataanalys för att undersöka förekomst av systematiska fel och korrigerat för dessa med hjälp av statistiska metoder. Vi har framförallt undersökt tre metoder för att korrigera för systematiska fel:

    I) Korrektion av överblödning som sker på grund avöverlappande emissionsspektra mellan fluorescenta prober.

    II) En sannolikhetsbaserad tolkningav intensitetsdata som resulterar i ett nytt kvalitetsmått och en alternativ klassificerare baseradpå övervakad inlärning.

    III) En utredning om förekomst av cykelberoende effekter, exempelvisofullständig dehybridisering av fluorescenta prober.

    Vi föreslår att man gör följande saker:

    • Implementerar och utvärderar det sannolikhetsbaserade kvalitetsmåttet
    • Utvecklar och implementerar den föreslagna klassificeraren
    • Genomför ytterligare experiment för att påvisa eller bestrida förekomst av ofullständigdehybridisering
  • 180.
    Nordin, Bo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för teknisk databehandling.
    The Development of an Automated Prescreener for the Early Detection of Cervical Cancer: Algorithms and Implementation1989Doktoravhandling, monografi (Annet vitenskapelig)
  • 181.
    Nordin, Bo
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Bengtsson, Ewert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Dahlqvist, Bengt
    Eriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Jarkrans, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Centrum för bildanalys.
    Stenkvist, Björn
    Object Oriented Cell Image Segmentation1982Inngår i: Proceedings of the IEEE International Symposium on Medical Imaging and Image Interpretation, 1982, s. 140-145Konferansepaper (Fagfellevurdert)
  • 182.
    Nysjö, Fredrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Olsson, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Hirsch, Jan-Michaél
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Carlbom, Ingrid B.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Custom Mandibular Implant Design with Deformable Models and Haptics2014Inngår i: Proc. Computer Assisted Radiology and Surgery (CARS). Fukuoka, Japan, June 25-28, Springer Berlin/Heidelberg, 2014, s. 246-247Konferansepaper (Fagfellevurdert)
  • 183.
    Nysjö, Fredrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Olsson, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Carlbom, Ingrid B.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Signed Distance Fields for Modeling Surgical Guides and Plates from CT Images2016Inngår i: Proc, Swedish Symposium on Image Analysis: SSBA 2016, 2016Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    User-friendly virtual surgery planning(VSP) systems for reconstructive surgery, such as cranio-maxillofacial (CMF) surgery, that can be used by the surgeons themselves without help of a technician have the potential to shorten the pre-operative planning from days to hours. An important part of such systems is the design of surgical guides and plates for osteosynthesis. We describe a method for generating surgical guide and plate models from computed tomography (CT) images, using signed distance fields and constructive solidgeometry (CSG). We implement the method as an extension to our Haptics-Assisted Surgery Plan-ning (HASP) system that enables a user to quickly design guide and plate models with stereo graphics and haptic feedback. We find that surgical guide and plate models can be efficiently generated from segmented CT images with our method. We also find that an anti-aliased distance transform can improve the accuracy and precision of the modelingin this application.

  • 184.
    Nysjö, Fredrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Olsson, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Carlbom, Ingrid B.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Using anti-aliased signed distance fields for generating surgical guides and plates from CT images2017Inngår i: Journal of WSCG, ISSN 1213-6972, E-ISSN 1213-6964, Vol. 25, nr 1, s. 11-20Artikkel i tidsskrift (Fagfellevurdert)
  • 185.
    Nysjö, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Interactive 3D Image Analysis for Cranio-Maxillofacial Surgery Planning and Orthopedic Applications2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Modern medical imaging devices are able to generate highly detailed three-dimensional (3D) images of the skeleton. Computerized image processing and analysis methods, combined with real-time volume visualization techniques, can greatly facilitate the interpretation of such images and are increasingly used in surgical planning to aid reconstruction of the skeleton after trauma or disease. Two key challenges are to accurately separate (segment) bone structures or cavities of interest from the rest of the image and to interact with the 3D data in an efficient way. This thesis presents efficient and precise interactive methods for segmenting, visualizing, and analysing 3D computed tomography (CT) images of the skeleton. The methods are validated on real CT datasets and are primarily intended to support planning and evaluation of cranio-maxillofacial (CMF) and orthopedic surgery.

    Two interactive methods for segmenting the orbit (eye-socket) are introduced. The first method implements a deformable model that is guided and fitted to the orbit via haptic 3D interaction, whereas the second method implements a user-steered volumetric brush that uses distance and gradient information to find exact object boundaries.

    The thesis also presents a semi-automatic method for measuring 3D angulation changes in wrist fractures. The fractured bone is extracted with interactive mesh segmentation, and the angulation is determined with a technique based on surface registration and RANSAC.

    Lastly, the thesis presents an interactive and intuitive tool for segmenting individual bones and bone fragments. This type of segmentation is essential for virtual surgery planning, but takes several hours to perform with conventional manual methods. The presented tool combines GPU-accelerated random walks segmentation with direct volume rendering and interactive 3D texture painting to enable quick marking and separation of bone structures. It enables the user to produce an accurate segmentation within a few minutes, thereby removing a major bottleneck in the planning procedure.

    Delarbeid
    1. Visualization and Haptics for Interactive Medical Image Analysis: Image Segmentation in Cranio-Maxillofacial Surgery Planning
    Åpne denne publikasjonen i ny fane eller vindu >>Visualization and Haptics for Interactive Medical Image Analysis: Image Segmentation in Cranio-Maxillofacial Surgery Planning
    2011 (engelsk)Inngår i: Visual Informatics: Sustaining Research and Innovations / [ed] H. Badioze Zaman, et al. (Eds.), Berlin Heidelberg: Springer-Verlag , 2011, s. 1-12Konferansepaper, Publicerat paper (Fagfellevurdert)
    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.

    sted, utgiver, år, opplag, sider
    Berlin Heidelberg: Springer-Verlag, 2011
    Serie
    Lecture Notes in Computer Science ; 7066
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-161227 (URN)10.1007/978-3-642-25191-7_1 (DOI)978-3-642-25190-0 (ISBN)
    Konferanse
    2nd International Visual Informatics Conference (IVIC 2011)
    Tilgjengelig fra: 2011-11-10 Laget: 2011-11-09 Sist oppdatert: 2016-09-06
    2. Towards User-Guided Quantitative Evaluation of Wrist Fractures in CT Images
    Åpne denne publikasjonen i ny fane eller vindu >>Towards User-Guided Quantitative Evaluation of Wrist Fractures in CT Images
    Vise andre…
    2012 (engelsk)Inngår i: Computer Vision and Graphics: ICCVG 2012 / [ed] Bolc, Leonard; Tadeusiewicz, Ryszard; Chmielewski, Leszek J; Wojciechowski, Konrad, Springer Berlin/Heidelberg, 2012, s. 204-211Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    The wrist is the most common location for long-bone fractures in humans. To evaluate the healing process of such fractures, it is of interest to measure the fracture displacement, particularly the angle between the joint line and the long axis of the fractured long bone. We propose to measure this angle in 3D computed tomography (CT) images of fractured wrists. As a first step towards this goal, we here present a fast and precise semi-automatic method for determining the long axis of the radius bone in CT images. To facilitate user interaction in 3D, we utilize stereo graphics, head tracking, 3D input, and haptic feedback.

    sted, utgiver, år, opplag, sider
    Springer Berlin/Heidelberg, 2012
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 7594
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys
    Identifikatorer
    urn:nbn:se:uu:diva-185557 (URN)10.1007/978-3-642-33564-8_25 (DOI)000313005700025 ()978-3-642-33563-1 (ISBN)
    Konferanse
    ICCVG 2012, September 24-26, 2012, Warsaw, Poland
    Tilgjengelig fra: 2012-11-26 Laget: 2012-11-26 Sist oppdatert: 2016-09-06bibliografisk kontrollert
    3. Shape and volume of craniofacial cavities in intentional skull deformations
    Åpne denne publikasjonen i ny fane eller vindu >>Shape and volume of craniofacial cavities in intentional skull deformations
    Vise andre…
    2013 (engelsk)Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 151, nr 1, s. 110-119Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Intentional cranial deformations (ICD) have been observed worldwide but are especially prevalent in preColombian cultures. The purpose of this study was to assess the consequences of ICD on three cranial cavities (intracranial cavity, orbits, and maxillary sinuses) and on cranial vault thickness, in order to screen for morphological changes due to the external constraints exerted by the deformation device. We acquired CT-scans for 39 deformed and 19 control skulls. We studied the thickness of the skull vault using qualitative and quantitative methods. We computed the volumes of the orbits, of the maxillary sinuses, and of the intracranial cavity using haptic-aided semi-automatic segmentation. We finally defined 3D distances and angles within orbits and maxillary sinuses based on 27 anatomical landmarks and measured these features on the 58 skulls. Our results show specific bone thickness patterns in some types of ICD, with localized thinning in regions subjected to increased pressure and thickening in other regions. Our findings confirm that volumes of the cranial cavities are not affected by ICDs but that the shapes of the orbits and of the maxillary sinuses are modified in circumferential deformations. We conclude that ICDs can modify the shape of the cranial cavities and the thickness of their walls but conserve their volumes. These results provide new insights into the morphological effects associated with ICDs and call for similar investigations in subjects with deformational plagiocephalies and craniosynostoses.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-198978 (URN)10.1002/ajpa.22263 (DOI)000318040200011 ()23553676 (PubMedID)
    Tilgjengelig fra: 2013-04-30 Laget: 2013-04-30 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    4. Precise 3D Angle Measurements in CT Wrist Images
    Åpne denne publikasjonen i ny fane eller vindu >>Precise 3D Angle Measurements in CT Wrist Images
    Vise andre…
    2013 (engelsk)Inngår i: Image Analysis and Processing – ICIAP 2013: Part II, Springer Berlin/Heidelberg, 2013, s. 479-488Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    The clinically established method to assess the displacement of a distal radius fracture is to manually measure two reference angles,the dorsal angle and the radial angle, in consecutive 2D X-ray images of the wrist. This approach has the disadvantage of being sensitive to operator errors since the measurements are performed on 2D projections of a 3D structure. In this paper, we present a semi-automatic system for measuring relative changes in the dorsal angle in 3D computed tomography (CT) images of fractured wrists. We evaluate the proposed 3D measurement method on 28 post-operative CT images of fractured wrists and compare it with the radiographic 2D measurement method used in clinical practice. The results show that our proposed 3D measurement method has a high intra- and inter-operator precision and is more precise and robust than the conventional 2D measurement method.

    sted, utgiver, år, opplag, sider
    Springer Berlin/Heidelberg, 2013
    Serie
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 8157
    Emneord
    Wrist fractures, CT, angle measurements, bone segmentation, interactive mesh segmentation, surface registration
    HSV kategori
    Forskningsprogram
    Datoriserad bildanalys; Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-211749 (URN)10.1007/978-3-642-41184-7_49 (DOI)000329811200049 ()978-3-642-41183-0 (ISBN)
    Konferanse
    17th International Conference on Image Analysis and Processing (ICIAP), Naples, Italy, September 9-13, 2013
    Tilgjengelig fra: 2013-11-30 Laget: 2013-11-30 Sist oppdatert: 2016-09-06bibliografisk kontrollert
    5. Optimal RANSAC - Towards a Repeatable Algorithm for Finding the Optimal Set
    Åpne denne publikasjonen i ny fane eller vindu >>Optimal RANSAC - Towards a Repeatable Algorithm for Finding the Optimal Set
    2013 (engelsk)Inngår i: Journal of WSCG, ISSN 1213-6972, E-ISSN 1213-6964, Vol. 21, nr 1, s. 21-30Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-200593 (URN)
    Konferanse
    International Conferences in Central Europe on Computer Graphics, Visualization and Computer Vision
    Tilgjengelig fra: 2013-05-31 Laget: 2013-05-31 Sist oppdatert: 2018-01-11bibliografisk kontrollert
    6. BoneSplit - A 3D Texture Painting Tool for Interactive Bone Separation in CT Images
    Åpne denne publikasjonen i ny fane eller vindu >>BoneSplit - A 3D Texture Painting Tool for Interactive Bone Separation in CT Images
    2015 (engelsk)Inngår i: Journal of WSCG, ISSN 1213-6972, E-ISSN 1213-6964, Vol. 23, nr 2, s. 157-166Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    We present an efficient interactive tool for separating collectively segmented bones and bone fragments in 3D computed tomography (CT) images. The tool, which is primarily intended for virtual cranio-maxillofacial (CMF) surgery planning, combines direct volume rendering with an interactive 3D texture painting interface to enable quick identification and marking of individual bone structures. The user can paint markers (seeds) directly on the rendered bone surfaces as well as on individual CT slices. Separation of the marked bones is then achieved through the random walks segmentation algorithm, which is applied on a graph constructed from the collective bone segmentation. The segmentation runs on the GPU and can achieve close to real-time update rates for volumes as large as 512^3. Segmentation editing can be performed both in the random walks segmentation stage and in a separate post-processing stage using a local 3D editing tool. In a preliminary evaluation of the tool, we demonstrate that segmentation results comparable with manual segmentations can be obtained within a few minutes.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-268818 (URN)
    Tilgjengelig fra: 2015-12-09 Laget: 2015-12-09 Sist oppdatert: 2018-05-30bibliografisk kontrollert
    7. Comparison of 2D radiography and a semi-automatic CT-based 3D method for measuring change in dorsal angulation over time in distal radius fractures
    Åpne denne publikasjonen i ny fane eller vindu >>Comparison of 2D radiography and a semi-automatic CT-based 3D method for measuring change in dorsal angulation over time in distal radius fractures
    Vise andre…
    2016 (engelsk)Inngår i: Skeletal Radiology, ISSN 0364-2348, E-ISSN 1432-2161, Vol. 45, nr 6, s. 763-769Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Objective The aim of the present study was to compare the reliability and agreement between a computer tomography-based method (CT) and digitalised 2D radiographs (XR) when measuring change in dorsal angulation over time in distal radius fractures. Materials and methods Radiographs from 33 distal radius fractures treated with external fixation were retrospectively analysed. All fractures had been examined using both XR and CT at six times over 6 months postoperatively. The changes in dorsal angulation between the first reference images and the following examinations in every patient were calculated from 133 follow-up measurements by two assessors and repeated at two different time points. The measurements were analysed using Bland-Altman plots, comparing intra- and inter-observer agreement within and between XR and CT. Results The mean differences in intra- and inter-observer measurements for XR, CT, and between XR and CT were close to zero, implying equal validity. The average intra- and inter-observer limits of agreement for XR, CT, and between XR and CT were +/- 4.4 degrees, +/- 1.9 degrees and +/- 6.8 degrees respectively. Conclusions For scientific purpose, the reliability of XR seems unacceptably low when measuring changes in dorsal angulation in distal radius fractures, whereas the reliability for the semi-automatic CT-based method was higher and is therefore preferable when a more precise method is requested.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-297776 (URN)10.1007/s00256-016-2350-6 (DOI)000374476200003 ()26922189 (PubMedID)
    Tilgjengelig fra: 2016-02-27 Laget: 2016-06-28 Sist oppdatert: 2018-05-14bibliografisk kontrollert
    8. Rapid and Precise Orbit Segmentation through Interactive 3D Painting
    Åpne denne publikasjonen i ny fane eller vindu >>Rapid and Precise Orbit Segmentation through Interactive 3D Painting
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    In this paper, we present an efficient interactive tool for segmenting and measuring the volume of the bony orbit (eye-socket) in computed tomography (CT) images. The tool implements a 3D painting interface that allows the user to quickly segment or "paint" the fat and soft-tissue content of the orbit by sweeping a volumetric brush over the image. The brush modifies and updates the segmentation result in real-time and takes distance and gradient information into account to fill out and find the exact boundaries of the orbit. A smooth and consistent delineation of the anterior boundary is obtained by fitting a thin-plate spline to user-selected landmarks. We evaluate the tool on 10 CT images of intact and fractured orbits and show that it achieves high intra- and inter-operator precision (mean spatial overlap 95%, less than 1 ml volume variability) and produces segmentation results that are similar to manually corrected reference segmentations, but only requires a few minutes of interaction time.

    Emneord
    interactive segmentation, volume rendering, computed tomography, orbit
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-301179 (URN)
    Tilgjengelig fra: 2016-08-19 Laget: 2016-08-19 Sist oppdatert: 2016-09-06
  • 186.
    Nysjö, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Christersson, Albert
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Ortopedi.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Towards User-Guided Quantitative Evaluation of Wrist Fractures in CT Images2012Inngår i: Computer Vision and Graphics: ICCVG 2012 / [ed] Bolc, Leonard; Tadeusiewicz, Ryszard; Chmielewski, Leszek J; Wojciechowski, Konrad, Springer Berlin/Heidelberg, 2012, s. 204-211Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The wrist is the most common location for long-bone fractures in humans. To evaluate the healing process of such fractures, it is of interest to measure the fracture displacement, particularly the angle between the joint line and the long axis of the fractured long bone. We propose to measure this angle in 3D computed tomography (CT) images of fractured wrists. As a first step towards this goal, we here present a fast and precise semi-automatic method for determining the long axis of the radius bone in CT images. To facilitate user interaction in 3D, we utilize stereo graphics, head tracking, 3D input, and haptic feedback.

  • 187.
    Nysjö, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Christersson, Albert
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Ortopedi.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Larsson, Sune
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Ortopedi.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Precise 3D Angle Measurements in CT Wrist Images2013Inngår i: Image Analysis and Processing – ICIAP 2013: Part II, Springer Berlin/Heidelberg, 2013, s. 479-488Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The clinically established method to assess the displacement of a distal radius fracture is to manually measure two reference angles,the dorsal angle and the radial angle, in consecutive 2D X-ray images of the wrist. This approach has the disadvantage of being sensitive to operator errors since the measurements are performed on 2D projections of a 3D structure. In this paper, we present a semi-automatic system for measuring relative changes in the dorsal angle in 3D computed tomography (CT) images of fractured wrists. We evaluate the proposed 3D measurement method on 28 post-operative CT images of fractured wrists and compare it with the radiographic 2D measurement method used in clinical practice. The results show that our proposed 3D measurement method has a high intra- and inter-operator precision and is more precise and robust than the conventional 2D measurement method.

  • 188.
    Nysjö, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Sintorn, Ida-Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    BoneSplit - A 3D Texture Painting Tool for Interactive Bone Separation in CT Images2015Inngår i: Journal of WSCG, ISSN 1213-6972, E-ISSN 1213-6964, Vol. 23, nr 2, s. 157-166Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present an efficient interactive tool for separating collectively segmented bones and bone fragments in 3D computed tomography (CT) images. The tool, which is primarily intended for virtual cranio-maxillofacial (CMF) surgery planning, combines direct volume rendering with an interactive 3D texture painting interface to enable quick identification and marking of individual bone structures. The user can paint markers (seeds) directly on the rendered bone surfaces as well as on individual CT slices. Separation of the marked bones is then achieved through the random walks segmentation algorithm, which is applied on a graph constructed from the collective bone segmentation. The segmentation runs on the GPU and can achieve close to real-time update rates for volumes as large as 512^3. Segmentation editing can be performed both in the random walks segmentation stage and in a separate post-processing stage using a local 3D editing tool. In a preliminary evaluation of the tool, we demonstrate that segmentation results comparable with manual segmentations can be obtained within a few minutes.

  • 189.
    Nysjö, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nilsson, Johanna
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Thor, Andreas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Nyström, Ingela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Rapid and Precise Orbit Segmentation through Interactive 3D PaintingManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    In this paper, we present an efficient interactive tool for segmenting and measuring the volume of the bony orbit (eye-socket) in computed tomography (CT) images. The tool implements a 3D painting interface that allows the user to quickly segment or "paint" the fat and soft-tissue content of the orbit by sweeping a volumetric brush over the image. The brush modifies and updates the segmentation result in real-time and takes distance and gradient information into account to fill out and find the exact boundaries of the orbit. A smooth and consistent delineation of the anterior boundary is obtained by fitting a thin-plate spline to user-selected landmarks. We evaluate the tool on 10 CT images of intact and fractured orbits and show that it achieves high intra- and inter-operator precision (mean spatial overlap 95%, less than 1 ml volume variability) and produces segmentation results that are similar to manually corrected reference segmentations, but only requires a few minutes of interaction time.

  • 190.
    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 representation2011Inngår i: Computerized Medical Imaging and Graphics, ISSN 0895-6111, E-ISSN 1879-0771, Vol. 35, nr 6, s. 460-471Artikkel i tidsskrift (Fagfellevurdert)
  • 191.
    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 Planning2011Inngår i: Visual Informatics: Sustaining Research and Innovations / [ed] H. Badioze Zaman, et al. (Eds.), Berlin Heidelberg: Springer-Verlag , 2011, s. 1-12Konferansepaper (Fagfellevurdert)
    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.

  • 192.
    Nyström, Ingela
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nysjö, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Thor, Andreas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Malmberg, Filip
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    BoneSplit – A 3D painting tool for interactive bone segmentation in CT images2017Inngår i: Pattern Recognition and Information Processing: PRIP 2016, Springer, 2017, s. 3-13Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We present an efficient interactive tool for segmenting individual bones and bone fragments in 3D computed tomography (CT) images. The tool, which is primarily intended for virtual craniomaxillofacial (CMF) surgery planning, combines direct volume rendering with interactive 3D texture painting to enable quick identification and marking of bone structures. The user can paint markers (seeds) directly on the rendered bone surfaces as well as on individual CT slices. Separation of the marked bones is then achieved through the random walks algorithm, which is applied on a graph constructed from the thresholded bones. The segmentation runs on the GPU and can achieve close to real-time update rates for volumes as large as 512x512x512 voxels. The user can perform segmentation editing to correct the result. An evaluation reports segmentation results comparable with manual segmentations, but obtained within a few minutes. In the invited PRIP talk, BoneSplit is presented and how the tool fits into our haptics-assisted surgery-planning system.

  • 193. Näppi, Janne
    et al.
    Frimmel, Hans
    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, Datoriserad bildanalys.
    Dachman, Abraham
    Yoshida, Hiroyuki
    A new high-performance CAD scheme for the detection of polyps in CT colonography2004Inngår i: Medical Imaging 2004: Image Processing, Bellingham, WA, 2004, s. 839-848Konferansepaper (Fagfellevurdert)
  • 194. Näppi, Janne
    et al.
    Frimmel, Hans
    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, Datoriserad bildanalys.
    Okamura, Akihiko
    Dachman, Abraham H.
    Yoshida, Hiroyuki
    Region-based supine-prone correspondence for reduction of false positives in CAD of CT colonography2004Inngår i: CARS 2004 – Computer Assisted Radiology and Surgery, Elsevier , 2004, s. 993-998Konferansepaper (Fagfellevurdert)
  • 195. Näppi, Janne
    et al.
    Frimmel, Hans
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för onkologi, radiologi och klinisk immunologi, Enheten för radiologi. 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, Datoriserad bildanalys.
    Yoshida, Hiroyuki
    Centerline-based colon segmentation for CAD of CT colonography2006Inngår i: Medical Imaging 2006: Image Processing, Bellingham, WA, 2006, s. 61445H:1-8Konferansepaper (Fagfellevurdert)
  • 196. Näppi, Janne
    et al.
    Frimmel, Hans
    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, Datoriserad bildanalys.
    Yoshida, Hiroyuki
    Virtual endoscopic visualization of the colon by shape-scale signatures2005Inngår i: IEEE transactions on information technology in biomedicine, ISSN 1089-7771, E-ISSN 1558-0032, Vol. 9, s. 120-131Artikkel i tidsskrift (Fagfellevurdert)
  • 197. Näppi, Janne
    et al.
    Okamura, Akihiko
    Frimmel, Hans
    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, Datoriserad bildanalys.
    Dachman, Abraham
    Yoshida, Hiroyuki
    Region-based supine-prone correspondence for the reduction of false-positive CAD polyp candidates in CT colonography2005Inngår i: Academic Radiology, ISSN 1076-6332, E-ISSN 1878-4046, Vol. 12, s. 695-707Artikkel i tidsskrift (Fagfellevurdert)
  • 198.
    Olofsson, Nils
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion.
    Kidney Dynamic Model Enrichment2015Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    This thesis explores and explains a method using discrete curvature as a feature to find regions of vertices that can be classified as being likely to indicate the presence of an underlying tumor on a kidney surface mesh. Vertices are tagged based on curvature type and mathematical morphology is used to form regions on the mesh. The size and location of the tumor is approximated by fitting a sphere to this region. The method is intended to be employed in noninvasive radiotherapy with a dynamic soft tissue model. It could also provide an alternative to volumetric methods used to segment tumors. A validation is made using the images from which the kidney mesh was constructed, the tumor is visible as a comparison to the method result.

    The dynamic kidney model is validated using the Hausdorff distance and it is explained how this can be computed in an effective way using bounding volume hierarchies.

    Both the tumor finding method and the dynamic model show promising results since they lie within the limit used by practitioners during therapy.

  • 199.
    Olsson, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Haptics with Applications to Cranio-Maxillofacial Surgery Planning2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Virtual surgery planning systems have demonstrated great potential to help surgeons achieve a better functional and aesthetic outcome for the patient, and at the same time reduce time in the operating room resulting in considerable cost savings. However, the two-dimensional tools employed in these systems today, such as a mouse and a conventional graphical display, are difficult to use for interaction with three-dimensional anatomical images. Therefore surgeons often outsource virtual planning which increases cost and lead time to surgery.

    Haptics relates to the sense of touch and haptic technology encompasses algorithms, software, and hardware designed to engage the sense of touch. To demonstrate how haptic technology in combination with stereo visualization can make cranio-maxillofacial surgery planning more efficient and easier to use, we describe our haptics-assisted surgery planning (HASP) system. HASP supports in-house virtual planning of reconstructions in complex trauma cases, and reconstructions with a fibula osteocutaneous free flap including bone, vessels, and soft-tissue in oncology cases. An integrated stable six degrees-of-freedom haptic attraction force model, snap-to-fit, supports semi-automatic alignment of virtual bone fragments in trauma cases. HASP has potential beyond this thesis as a teaching tool and also as a development platform for future research.

    In addition to HASP, we describe a surgical bone saw simulator with a novel hybrid haptic interface that combines kinesthetic and vibrotactile feedback to display both low frequency contact forces and realistic high frequency vibrations when a virtual saw blade comes in contact with a virtual bone model. 

    We also show that visuo-haptic co-location shortens the completion time, but does not improve the accuracy, in interaction tasks performed on two different visuo-haptic displays: one based on a holographic optical element and one based on a half-transparent mirror. 

    Finally, we describe two prototype hand-worn haptic interfaces that potentially may expand the interaction capabilities of the HASP system. In particular we evaluate two different types of piezo-electric motors, one walking quasi-static motor and one traveling-wave ultrasonic motor for actuating the interfaces.

    Delarbeid
    1. Haptics-assisted Virtual Planning of Bone, Soft Tissue, and Vessels in Fibula Osteocutaneous Free Flaps
    Åpne denne publikasjonen i ny fane eller vindu >>Haptics-assisted Virtual Planning of Bone, Soft Tissue, and Vessels in Fibula Osteocutaneous Free Flaps
    Vise andre…
    2015 (engelsk)Inngår i: Plastic and Reconstructive Surgery - Global Open, ISSN 2169-7574, Vol. 3, nr 8, artikkel-id e479Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Background: Virtual surgery planning has proven useful for reconstructing head and neck defects by fibula osteocutaneous free flaps (FOFF). Benefits include improved healing, function, and aesthetics, as well as cost savings. But available virtual surgery planning systems incorporating fibula in craniomaxillofacial reconstruction simulate only bone reconstruction without considering vessels and soft tissue.

    Methods: The Haptics-Assisted Surgery Planning (HASP) system incorporates bone, vessels, and soft tissue of the FOFF in craniomaxillofacial defect reconstruction. Two surgeons tested HASP on 4 cases they had previously operated on: 3 with composite mandibular defects and 1 with a composite cervical spine defect. With the HASP stereographics and haptic feedback, using patient-specific computed tomography angiogram data, the surgeons planned the 4 cases, including bone resection, fibula design, recipient vessels selection, pedicle and perforator location selection, and skin paddle configuration.

    Results: Some problems encountered during the actual surgery could have been avoided as they became evident with HASP. In one case, the fibula reconstruction was incomplete because the fibula had to be reversed and thus did not reach the temporal fossa. In another case, the fibula had to be rotated 180 degrees to correct the plate and screw placement in relation to the perforator. In the spinal case, difficulty in finding the optimal fibula shape and position required extra ischemia time.

    Conclusions: The surgeons found HASP to be an efficient planning tool for FOFF reconstructions. The testing of alternative reconstructions to arrive at an optimal FOFF solution preoperatively potentially improves patient function and aesthetics and reduces operating room time.

    sted, utgiver, år, opplag, sider
    Wolters Kluwer, 2015
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-260771 (URN)10.1097/GOX.0000000000000447 (DOI)
    Tilgjengelig fra: 2015-08-24 Laget: 2015-08-24 Sist oppdatert: 2016-01-20bibliografisk kontrollert
    2. A haptics-assisted cranio-maxillofacial surgery planning system for restoring skeletal anatomy in complex trauma cases
    Åpne denne publikasjonen i ny fane eller vindu >>A haptics-assisted cranio-maxillofacial surgery planning system for restoring skeletal anatomy in complex trauma cases
    2013 (engelsk)Inngår i: International Journal of Computer Assisted Radiology and Surgery, ISSN 1861-6410, E-ISSN 1861-6429, Vol. 8, nr 6, s. 887-894Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Cranio-maxillofacial (CMF) surgery to restore normal skeletal anatomy in patients with serious trauma to the face can be both complex and time-consuming. But it is generally accepted that careful pre-operative planning leads to a better outcome with a higher degree of function and reduced morbidity in addition to reduced time in the operating room. However, today's surgery planning systems are primitive, relying mostly on the user's ability to plan complex tasks with a two-dimensional graphical interface. A system for planning the restoration of skeletal anatomy in facial trauma patients using a virtual model derived from patient-specific CT data. The system combines stereo visualization with six degrees-of-freedom, high-fidelity haptic feedback that enables analysis, planning, and preoperative testing of alternative solutions for restoring bone fragments to their proper positions. The stereo display provides accurate visual spatial perception, and the haptics system provides intuitive haptic feedback when bone fragments are in contact as well as six degrees-of-freedom attraction forces for precise bone fragment alignment. A senior surgeon without prior experience of the system received 45 min of system training. Following the training session, he completed a virtual reconstruction in 22 min of a complex mandibular fracture with an adequately reduced result. Preliminary testing with one surgeon indicates that our surgery planning system, which combines stereo visualization with sophisticated haptics, has the potential to become a powerful tool for CMF surgery planning. With little training, it allows a surgeon to complete a complex plan in a short amount of time.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-198977 (URN)10.1007/s11548-013-0827-5 (DOI)000326455900002 ()23605116 (PubMedID)
    Tilgjengelig fra: 2013-04-21 Laget: 2013-04-30 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    3. Visuohaptic bone saw simulator: Combining vibrotactile and kinesthetic feedback
    Åpne denne publikasjonen i ny fane eller vindu >>Visuohaptic bone saw simulator: Combining vibrotactile and kinesthetic feedback
    Vise andre…
    2015 (engelsk)Inngår i: Proc. 8th ACM SIGGRAPH Asia Technical Briefs, New York: ACM Press, 2015, s. 10:1-4Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    New York: ACM Press, 2015
    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling
    Identifikatorer
    urn:nbn:se:uu:diva-262369 (URN)10.1145/2820903.2820925 (DOI)978-1-4503-3930-8 (ISBN)
    Konferanse
    ACM SIGGRAPH Asia 2015, November 2–5, Kobe, Japan
    Tilgjengelig fra: 2015-11-02 Laget: 2015-09-14 Sist oppdatert: 2018-01-11bibliografisk kontrollert
    4. Snap-to-fit, a Haptic 6 DOF Alignment Tool for Virtual Assembly
    Åpne denne publikasjonen i ny fane eller vindu >>Snap-to-fit, a Haptic 6 DOF Alignment Tool for Virtual Assembly
    2013 (engelsk)Inngår i: Proc. World Haptics (WHC), 2013 IEEE, 2013, s. 205-210Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    Virtual assembly of complex objects has application in domains ranging from surgery planning to archaeology. In these domains the objective is to plan the restoration of skeletal anatomy or archaeological artifacts to achieve an optimal reconstruction without causing further damage. While graphical modeling plays a central role in virtual assembly, visual feedback alone is often insufficient since object contact and penetration is difficult to discern due to occlusion. Haptics can improve an assembly task by giving feedback when objects collide, but precise fitting of fractured objects guided by delicate haptic cues similar to those present in the physical world requires haptic display transparency beyond the performance of today’s systems. We propose a haptic alignment tool that combines a 6 Degrees of Freedom (DOF) attraction force with traditional 6 DOF contact forces to pull a virtual object towards a local stable fit with a fixed object. The object forces are integrated into a virtual coupling framework yielding a stable haptic tool. We demonstrate the use of our system on applications from both cranio-maxillofacial surgery and archaeology, and show that we can achieve haptic rates for fractured surfaces with over 5000 points.

    Emneord
    Virtual Assembly, Force Feedback, Haptic Rendering, Fractured Object, Virtual Environments, 3D puzzle
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-209551 (URN)10.1109/WHC.2013.6548409 (DOI)000325187400035 ()978-1-4799-0087-9 (ISBN)
    Konferanse
    IEEE World Haptics Conference (WHC), 14-18 April, 2013, Daejeon, SOUTH KOREA
    Tilgjengelig fra: 2013-10-21 Laget: 2013-10-21 Sist oppdatert: 2018-01-11bibliografisk kontrollert
    5. Comparison of walking and traveling-wave piezoelectric motors as actuators in kinesthetic haptic devices
    Åpne denne publikasjonen i ny fane eller vindu >>Comparison of walking and traveling-wave piezoelectric motors as actuators in kinesthetic haptic devices
    2016 (engelsk)Inngår i: IEEE Transactions on Haptics, ISSN 1939-1412, E-ISSN 2329-4051, Vol. 9, nr 3, s. 427-431Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Piezoelectric motors offer an attractive alternative to electromagnetic actuators in portable haptic interfaces: they are compact, have a high force-to-volume ratio, and can operate with limited or no gearing. However, the choice of a piezoelectric motor type is not obvious due to differences in performance characteristics. We present our evaluation of two commercial, operationally different, piezoelectric motors acting as actuators in two kinesthetic haptic grippers, a walking quasi-static motor and a traveling wave ultrasonic motor. We evaluate each gripper's ability to display common virtual objects including springs, dampers, and rigid walls, and conclude that the walking quasi-static motor is superior at low velocities. However, for applications where high velocity is required, traveling wave ultrasonic motors are a better option.

    HSV kategori
    Forskningsprogram
    Datoriserad bildbehandling; Teknisk fysik med inriktning mot mikrosystemteknik
    Identifikatorer
    urn:nbn:se:uu:diva-262371 (URN)10.1109/TOH.2016.2537803 (DOI)000384670000012 ()27046907 (PubMedID)
    Forskningsfinansiär
    Vårdal FoundationVINNOVA
    Tilgjengelig fra: 2016-03-30 Laget: 2015-09-14 Sist oppdatert: 2018-01-11bibliografisk kontrollert
    6. Rendering stiffness with a prototype haptic glove actuated by an integrated piezoelectric motor
    Åpne denne publikasjonen i ny fane eller vindu >>Rendering stiffness with a prototype haptic glove actuated by an integrated piezoelectric motor
    2012 (engelsk)Inngår i: Haptics: Perception, Devices, Mobility, and Communication: Part I, Springer Berlin/Heidelberg, 2012, s. 361-372Konferansepaper, Publicerat paper (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    Springer Berlin/Heidelberg, 2012
    Serie
    Lecture Notes in Computer Science ; 7282
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-183878 (URN)10.1007/978-3-642-31401-8_33 (DOI)978-3-642-31400-1 (ISBN)
    Konferanse
    EuroHaptics 2012, Tampere, Finland, June 13-15
    Prosjekter
    Whole Hand Haptics
    Tilgjengelig fra: 2012-05-30 Laget: 2012-11-05 Sist oppdatert: 2018-01-12bibliografisk kontrollert
    7. Physically Co-Located Haptic Interaction with 3D Displays
    Åpne denne publikasjonen i ny fane eller vindu >>Physically Co-Located Haptic Interaction with 3D Displays
    2012 (engelsk)Inngår i: Proc. Haptics Symposium (HAPTICS), 2012 IEEE, 2012, s. 267-272Konferansepaper, Poster (with or without abstract) (Fagfellevurdert)
    Abstract [en]

    Studies indicate that haptic interaction with a computer generated virtual scene may become more intuitive by aligning (co-locating) the visual and haptic workspaces so that the visual and haptic feedback coincide as they do in the real world. Co-located haptics may gain importance when more advanced haptic interfaces, such as high-fidelity whole hand devices, become available. We describe a user study that investigates the pros and cons with physically co-located versus non-collocated haptics on two different display types: a commercial half-transparent mirror 3D display with shutter glasses and a prototype autostereoscopic display based on a Holographic Optical Element (HOE). We use two accuracy tasks with spatial accuracy as the dependent variable and one manipulation task with time as the dependent variable. The study shows that on both displays co-location significantly improves completion time in the manipulation task. However, the study shows that co-location does not improve the accuracy in the spatial accuracy tasks.

    Emneord
    Haptics, Co-Location, 3D displays, Stereoscopy
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-175446 (URN)10.1109/HAPTIC.2012.6183801 (DOI)
    Konferanse
    Haptics Symposium (HAPTICS), 2012 IEEE
    Prosjekter
    Whole Hand Haptics
    Tilgjengelig fra: 2012-06-07 Laget: 2012-06-07 Sist oppdatert: 2018-01-12
  • 200.
    Olsson, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Nysjö, Fredrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Hirsch, Jan-Michaél
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Käkkirurgi.
    Carlbom, Ingrid B.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    A haptics-assisted cranio-maxillofacial surgery planning system for restoring skeletal anatomy in complex trauma cases2013Inngår i: International Journal of Computer Assisted Radiology and Surgery, ISSN 1861-6410, E-ISSN 1861-6429, Vol. 8, nr 6, s. 887-894Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cranio-maxillofacial (CMF) surgery to restore normal skeletal anatomy in patients with serious trauma to the face can be both complex and time-consuming. But it is generally accepted that careful pre-operative planning leads to a better outcome with a higher degree of function and reduced morbidity in addition to reduced time in the operating room. However, today's surgery planning systems are primitive, relying mostly on the user's ability to plan complex tasks with a two-dimensional graphical interface. A system for planning the restoration of skeletal anatomy in facial trauma patients using a virtual model derived from patient-specific CT data. The system combines stereo visualization with six degrees-of-freedom, high-fidelity haptic feedback that enables analysis, planning, and preoperative testing of alternative solutions for restoring bone fragments to their proper positions. The stereo display provides accurate visual spatial perception, and the haptics system provides intuitive haptic feedback when bone fragments are in contact as well as six degrees-of-freedom attraction forces for precise bone fragment alignment. A senior surgeon without prior experience of the system received 45 min of system training. Following the training session, he completed a virtual reconstruction in 22 min of a complex mandibular fracture with an adequately reduced result. Preliminary testing with one surgeon indicates that our surgery planning system, which combines stereo visualization with sophisticated haptics, has the potential to become a powerful tool for CMF surgery planning. With little training, it allows a surgeon to complete a complex plan in a short amount of time.

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