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  • 301.
    Ilic, Vladimir
    et al.
    Faculty of Engineering, University of Novi Sad, Serbia.
    Lindblad, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Faculty of Engineering, University of Novi Sad, Serbia.
    Sladoje, Natasa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Faculty of Engineering, University of Novi Sad, Serbia.
    Precise Euclidean distance transforms in 3D from voxel coverage representation2015In: Pattern Recognition Letters, ISSN 0167-8655, E-ISSN 1872-7344, Vol. 65, p. 184-191Article in journal (Refereed)
    Abstract [en]

    Distance transforms (DTs) are, usually, defined on a binary image as a mapping from each background element to the distance between its centre and the centre of the closest object element. However, due to discretization effects, such DTs have limited precision, including reduced rotational and translational invariance. We show in this paper that a significant improvement in performance of Euclidean DTs can be achieved if voxel coverage values are utilized and the position of an object boundary is estimated with sub-voxel precision. We propose two algorithms of linear time complexity for estimating Euclidean DT with sub-voxel precision. The evaluation confirms that both algorithms provide 4-14 times increased accuracy compared to what is achievable from a binary object representation.

  • 302.
    Ilic, Vladimir
    et al.
    Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia.
    Lindblad, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbi.
    Sladoje, Nataša
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Mathematical Institute, Serbian Academy of Sciences and Arts, Belgrade, Serbi.
    Signature of a Shape Based on Its Pixel Coverage Representation2016In: Discrete Geometry for Computer Imagery, DGCI 2016. Lecture Notes in Computer Science, Vol. 9647, pp. 181-193, Springer 2016: 19th IAPR International Conference, DGCI 2016, Nantes, France, April 18-20, 2016. Proceedings / [ed] Normand, Nicolas, Guédon, Jeanpierre, Autrusseau, Florent, Springer Berlin/Heidelberg, 2016, Vol. 9647, p. 181-193Conference paper (Refereed)
    Abstract [en]

    Distance from the boundary of a shape to its centroid, a.k.a. signature of a shape, is a frequently used shape descriptor. Commonly, the observed shape results from a crisp (binary) segmentation of an image. The loss of information associated with binarization leads to a significant decrease in accuracy and precision of the signature, as well as its reduced invariance w.r.t. translation and rotation. Coverage information enables better estimation of edge position within a pixel. In this paper, we propose an iterative method for computing the signature of a shape utilizing its pixel coverage representation. The proposed method iteratively improves the accuracy of the computed signature, starting from a good initial estimate. A statistical study indicates considerable improvements in both accuracy and precision, compared to a crisp approach and a previously proposed approach based on averaging signatures over α-cuts of a fuzzy representation. We observe improved performance of the proposed descriptor in the presence of noise and reduced variation under translation and rotation.

  • 303.
    Isaksson-Lutteman, Gunnika
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Future Train Traffic Control: Development and deployment of new principles and systems in train traffic control2012Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The train traffic control system of the future requires new solutions and strategies in order to better meet tomorrow’s demands and goals. Uppsala University and Trafikverket have been collaborating for several years in research regarding train traffic control and how to improve traffic controllers’ support systems and working environment. At an early stage in the collaboration studies and analysis of important aspects of the traffic controller’s tasks, strategies, decision making, use of information and support systems were undertaken. This research resulted in new control paradigms, from control by exception to control by replanning. By using this paradigm we developed and designed prototype systems and interfaces that could better meet future goals and contribute to more optimal use of infrastructure capacity. Based on this research, a new operational traffic control system called STEG was developed in an iterative and user-centred design process. The system was deployed and tested operatively at a train traffic control centre in Sweden. The following evaluations focused on what happens when STEG is introduced in train traffic controllers’ work places. The evaluation of STEG showed satisfied users with a feeling of active involvement during the design and deployment processes, and gave confirmation that the new control strategies are functioning. STEG was seen as successful and was thereafter developed into MULTI-STEG, intended to be used by several users simultaneously, supporting them to share information in a new way. MULTI-STEG was deployed and tested at another train traffic control centre in Sweden. The following evaluations of MULTI-STEG focused on what happens when several users are involved and how train traffic controllers felt when sharing information, that before would have only been in their own minds, with each other. Some complications occurred due to mistakes in the deployment process, but altogether the evaluation showed positive attitudes towards the new system and MULTI-STEG was perceived as an efficient system for train traffic control.

    The main results are that STEG and MULTI-STEG can be used as an efficient train traffic control system and the new system can reduce the unnecessary cognitive load currently placed upon traffic controllers in today’s system. Also the deployment process is fundamental to the acceptance or non-acceptance of a new system by users. STEG was developed in a user-centred design process, but it is important that the deployment process is also user-centred.

    List of papers
    1. Development and implementation of new principles and systems for train traffic control in Sweden
    Open this publication in new window or tab >>Development and implementation of new principles and systems for train traffic control in Sweden
    2010 (English)In: Computers in Railways XII: Computer System Design and Operation in Railways and other Transit Systems, Southampton, UK: WIT Press , 2010, p. 441-450Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Southampton, UK: WIT Press, 2010
    National Category
    Computer and Information Sciences
    Identifiers
    urn:nbn:se:uu:diva-150562 (URN)10.2495/CR100411 (DOI)978-1-84564-468-0 (ISBN)
    Available from: 2011-03-31 Created: 2011-03-31 Last updated: 2018-01-12Bibliographically approved
    2. Operative tests of a new system for train traffic control
    Open this publication in new window or tab >>Operative tests of a new system for train traffic control
    Show others...
    2009 (English)In: Rail Human Factors around the World: Impacts on and of People for Successful Rail Operations / [ed] Dadashi, Nastaran, 2009, p. 424-433Conference paper, Published paper (Other academic)
    Abstract [en]

    Tomorrow’s train traffic systems requires new strategies and solutions for efficient traintraffic control and utilization of track capacity, especially in traffic systems with a highdegree of deregulated and mixed traffic. There are many different goals associated withthe traffic control tasks and the work of the traffic controllers (dispatchers). Examples aresafety, efficiency of the traffic with regard to timeliness and energy consumption, goodservice and information to passengers and customers etc. Today’s traffic controlsystems and user interfaces do not efficiently support such goals. In earlier research wehave analyzed important aspects of the traffic controller’s tasks, strategies, decisionmaking, use of information and support systems etc. Based on this research we,together with Banverket (Swedish Rail Administration), have designed prototypesystems and interfaces that better can meet future goals and contribute to more optimaluse of infrastructure capacity. These prototype systems have now been developed into afully operational system which has been tested during 6 months, for control of train trafficin a section of the Swedish rail system. The evaluation shows that the system efficientlysupports control tasks and is well accepted by the involved traffic controllers.

    Keywords
    train traffic control, dispatchers, operator interface, decision support, situation awareness
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-169138 (URN)978-0-415-64475-4 (ISBN)
    Conference
    Third International Conference on Rail Human Factors, March 3-5, 2009, Lille, France
    Available from: 2012-02-23 Created: 2012-02-23 Last updated: 2018-01-12Bibliographically approved
    3. Reducing unnecessary cognitive load in train traffic control
    Open this publication in new window or tab >>Reducing unnecessary cognitive load in train traffic control
    2011 (English)Conference paper, Published paper (Other academic)
    Abstract [en]

    Uppsala University has collaborated with Swedish National Railway Administration in research about train traffic control and how to improve traffic controllers’ work environment, so that they can better meet future demands. This has resulted in a new operational train traffic control system called STEG. The traffic controllers are today forced to develop and use very complex mental models which take a long time to learn. We have also found that their cognitive capacity is more used to indentify, understand and analyze the traffic situation and less to solve problems and find optimal solutions to disturbances. The objective for developing STEG was to change this situation and reduce unnecessary cognitive load. Interviews with traffic controllers show that STEG has reduced the complexity of their mental models and contributed to less unnecessary cognitive load in operation. Our conclusion is that by reducing the complexity of their mental model, they can be skilled much faster and they are now able to use their cognitive capacity and skills on the important parts of their work.

    Keywords
    mental models, cognitive load, learning, operator interface, decision making, situation awareness, perception, train traffic control
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-169142 (URN)
    Conference
    Conference for work environment research, June 15-17, 2011, Luleå, Sweden
    Available from: 2012-02-23 Created: 2012-02-23 Last updated: 2018-01-12Bibliographically approved
    4. All or nothing: Deployment must also be user-centred
    Open this publication in new window or tab >>All or nothing: Deployment must also be user-centred
    2012 (English)In: Ergonomics Open Journal, ISSN 1875-9343, E-ISSN 1875-9343Article in journal (Other academic) Submitted
    Abstract [en]

    This article describes the importance ofusing a user-centred deployment process.The article is based on a case study of twotrain traffic control centres where the samesystem, STEG, was deployed with differentcontexts.

    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-169144 (URN)
    Available from: 2012-02-23 Created: 2012-02-23 Last updated: 2018-01-12Bibliographically approved
  • 304.
    Isaksson-Lutteman, Gunnika
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sandblad, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Andersson, Arne W.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Tschirner, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    All or nothing: Deployment must also be user-centred2012In: Ergonomics Open Journal, ISSN 1875-9343, E-ISSN 1875-9343Article in journal (Other academic)
    Abstract [en]

    This article describes the importance ofusing a user-centred deployment process.The article is based on a case study of twotrain traffic control centres where the samesystem, STEG, was deployed with differentcontexts.

  • 305.
    Isaksson-Lutteman, Gunnika
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sandblad, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Andersson, Arne W.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Tschirner, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Reducing unnecessary cognitive load in train traffic control2011Conference paper (Other academic)
    Abstract [en]

    Uppsala University has collaborated with Swedish National Railway Administration in research about train traffic control and how to improve traffic controllers’ work environment, so that they can better meet future demands. This has resulted in a new operational train traffic control system called STEG. The traffic controllers are today forced to develop and use very complex mental models which take a long time to learn. We have also found that their cognitive capacity is more used to indentify, understand and analyze the traffic situation and less to solve problems and find optimal solutions to disturbances. The objective for developing STEG was to change this situation and reduce unnecessary cognitive load. Interviews with traffic controllers show that STEG has reduced the complexity of their mental models and contributed to less unnecessary cognitive load in operation. Our conclusion is that by reducing the complexity of their mental model, they can be skilled much faster and they are now able to use their cognitive capacity and skills on the important parts of their work.

  • 306.
    Ishaq, Omer
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Image Analysis and Deep Learning for Applications in Microscopy2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantitative microscopy deals with the extraction of quantitative measurements from samples observed under a microscope. Recent developments in microscopy systems, sample preparation and handling techniques have enabled high throughput biological experiments resulting in large amounts of image data, at biological scales ranging from subcellular structures such as fluorescently tagged nucleic acid sequences to whole organisms such as zebrafish embryos. Consequently, methods and algorithms for automated quantitative analysis of these images have become increasingly important. These methods range from traditional image analysis techniques to use of deep learning architectures.

    Many biomedical microscopy assays result in fluorescent spots. Robust detection and precise localization of these spots are two important, albeit sometimes overlapping, areas for application of quantitative image analysis. We demonstrate the use of popular deep learning architectures for spot detection and compare them against more traditional parametric model-based approaches. Moreover, we quantify the effect of pre-training and change in the size of training sets on detection performance. Thereafter, we determine the potential of training deep networks on synthetic and semi-synthetic datasets and their comparison with networks trained on manually annotated real data. In addition, we present a two-alternative forced-choice based tool for assisting in manual annotation of real image data. On a spot localization track, we parallelize a popular compressed sensing based localization method and evaluate its performance in conjunction with different optimizers, noise conditions and spot densities. We investigate its sensitivity to different point spread function estimates.

    Zebrafish is an important model organism, attractive for whole-organism image-based assays for drug discovery campaigns. The effect of drug-induced neuronal damage may be expressed in the form of zebrafish shape deformation. First, we present an automated method for accurate quantification of tail deformations in multi-fish micro-plate wells using image analysis techniques such as illumination correction, segmentation, generation of branch-free skeletons of partial tail-segments and their fusion to generate complete tails. Later, we demonstrate the use of a deep learning-based pipeline for classifying micro-plate wells as either drug-affected or negative controls, resulting in competitive performance, and compare the performance from deep learning against that from traditional image analysis approaches. 

    List of papers
    1. An Evaluation of the Faster STORM Method for Super-resolution Microscopy
    Open this publication in new window or tab >>An Evaluation of the Faster STORM Method for Super-resolution Microscopy
    2014 (English)In: Proceedings of the 22nd International Conference on Pattern Recognition, 2014, p. 4435-4440Conference paper, Published paper (Refereed)
    Abstract [en]

    Development of new stochastic super-resolution methods together with fluorescence microscopy imaging enables visualization of biological processes at increasing spatial and temporal resolution. Quantitative evaluation of such imaging experiments call for computational analysis methods that localize the signals with high precision and recall. Furthermore, it is desirable that the methods are fast and possible to parallelize so that the ever increasing amounts of collected data can be handled in an efficient way. We here in address signal detection in super-resolution microscopy by approaches based on compressed sensing. We describe how a previously published approach can be parallelized, reducing processing time at least four times. We also evaluate the effect of a greedy optimization approach on signal recovery at high noise and molecule density. Furthermore, our evaluation reveals how previously published compressed sensing algorithms have a performance that degrades to that of a random signal detector at high molecule density. Finally, we show the approximation of the imaging system's point spread function affects recall and precision of signal detection, illustrating the importance of parameter optimization. We evaluate the methods on synthetic data with varying signal to noise ratio and increasing molecular density, and visualize performance on realsuper-resolution microscopy data from a time-lapse sequence of livingcells.

    Series
    International Conference on Pattern Recognition, ISSN 1051-4651
    National Category
    Signal Processing Medical Image Processing
    Research subject
    Computerized Image Processing
    Identifiers
    urn:nbn:se:uu:diva-238600 (URN)10.1109/ICPR.2014.759 (DOI)000359818004096 ()978-1-4799-5208-3 (ISBN)
    Conference
    22nd International Conference on Pattern Recognition, 24-28 August, 2014S, tockholm, Sweden
    Available from: 2014-12-14 Created: 2014-12-14 Last updated: 2016-05-20Bibliographically approved
    2. Evaluation of Deep Learning for Detection of Fluorescent Spots in Real Data
    Open this publication in new window or tab >>Evaluation of Deep Learning for Detection of Fluorescent Spots in Real Data
    (English)Manuscript (preprint) (Other academic)
    National Category
    Signal Processing
    Identifiers
    urn:nbn:se:uu:diva-283731 (URN)
    Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2016-05-20
    3. Training of Machine Learning Methods for Fluorescent Spot Detection
    Open this publication in new window or tab >>Training of Machine Learning Methods for Fluorescent Spot Detection
    (English)Article in journal (Refereed) Submitted
    National Category
    Signal Processing
    Identifiers
    urn:nbn:se:uu:diva-283736 (URN)
    Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2016-05-20
    4. Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio
    Open this publication in new window or tab >>Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio
    Show others...
    2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, p. 12317:1-10, article id 12317Article in journal (Refereed) Published
    National Category
    Medical Image Processing
    Research subject
    Computerized Image Processing
    Identifiers
    urn:nbn:se:uu:diva-260286 (URN)10.1038/srep12317 (DOI)000358358900001 ()26202090 (PubMedID)
    Funder
    EU, FP7, Seventh Framework Programme, 278568EU, FP7, Seventh Framework Programme, 259796Swedish Research Council
    Available from: 2015-07-23 Created: 2015-08-18 Last updated: 2018-02-27Bibliographically approved
    5. Bridging Histology and Bioinformatics: Computational analysis of spatially resolved transcriptomics
    Open this publication in new window or tab >>Bridging Histology and Bioinformatics: Computational analysis of spatially resolved transcriptomics
    2017 (English)In: Proceedings of the IEEE, ISSN 0018-9219, E-ISSN 1558-2256, Vol. 105, no 3, p. 530-541Article in journal (Refereed) Published
    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.

    Keywords
    Biomedical image processing, biomedical signal analysis, computer-aided analysis, genetics, image analysis, image processing
    National Category
    Medical Image Processing
    Research subject
    Computerized Image Processing
    Identifiers
    urn:nbn:se:uu:diva-283723 (URN)10.1109/JPROC.2016.2538562 (DOI)000395894900011 ()
    Funder
    Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceeSSENCE - An eScience CollaborationSwedish Research Council, 2012-4968 2014-00599
    Available from: 2016-04-06 Created: 2016-04-14 Last updated: 2017-04-27Bibliographically approved
    6. Automated quantification of Zebrafish tail deformation for high-throughput drug screening
    Open this publication in new window or tab >>Automated quantification of Zebrafish tail deformation for high-throughput drug screening
    Show others...
    2013 (English)In: Proc. 10th International Symposium on Biomedical Imaging: From Nano to Macro, Piscataway, NJ: IEEE , 2013, p. 902-905Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2013
    National Category
    Medical Image Processing
    Identifiers
    urn:nbn:se:uu:diva-215457 (URN)10.1109/ISBI.2013.6556621 (DOI)000326900100226 ()978-1-4673-6456-0 (ISBN)
    Conference
    ISBI 2013, April 7-11, San Francisco, CA
    Available from: 2013-04-11 Created: 2014-01-14 Last updated: 2016-05-20Bibliographically approved
    7. Deep Fish: Deep Learning-based Classification of Zebrafish Deformation for High-throughput Screening
    Open this publication in new window or tab >>Deep Fish: Deep Learning-based Classification of Zebrafish Deformation for High-throughput Screening
    (English)Manuscript (preprint) (Other academic)
    National Category
    Signal Processing
    Identifiers
    urn:nbn:se:uu:diva-283738 (URN)
    Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2016-05-20
  • 307.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Curic, Vladimir
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Evaluation of Deep Learning for Detection of Fluorescent Spots in Real DataManuscript (preprint) (Other academic)
  • 308.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Curic, Vladimir
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Training of Machine Learning Methods for Fluorescent Spot DetectionArticle in journal (Refereed)
  • 309.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Elf, Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    An Evaluation of the Faster STORM Method for Super-resolution Microscopy2014In: Proceedings of the 22nd International Conference on Pattern Recognition, 2014, p. 4435-4440Conference paper (Refereed)
    Abstract [en]

    Development of new stochastic super-resolution methods together with fluorescence microscopy imaging enables visualization of biological processes at increasing spatial and temporal resolution. Quantitative evaluation of such imaging experiments call for computational analysis methods that localize the signals with high precision and recall. Furthermore, it is desirable that the methods are fast and possible to parallelize so that the ever increasing amounts of collected data can be handled in an efficient way. We here in address signal detection in super-resolution microscopy by approaches based on compressed sensing. We describe how a previously published approach can be parallelized, reducing processing time at least four times. We also evaluate the effect of a greedy optimization approach on signal recovery at high noise and molecule density. Furthermore, our evaluation reveals how previously published compressed sensing algorithms have a performance that degrades to that of a random signal detector at high molecule density. Finally, we show the approximation of the imaging system's point spread function affects recall and precision of signal detection, illustrating the importance of parameter optimization. We evaluate the methods on synthetic data with varying signal to noise ratio and increasing molecular density, and visualize performance on realsuper-resolution microscopy data from a time-lapse sequence of livingcells.

  • 310.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kecheril Sadanandan, Sajith
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Deep Fish: Deep Learning-based Classification of Zebrafish Deformation for High-throughput ScreeningManuscript (preprint) (Other academic)
  • 311.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Negri, Joseph
    Anthony, Mark-Bray
    Pacureanu, Alexandra
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Peterson, Randall
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Image-based screening of zebrafish2013Conference paper (Other academic)
  • 312.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Negri, Joseph
    Bray, Mark-Anthony
    Pacureanu, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Peterson, Randall T.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Automated quantification of Zebrafish tail deformation for high-throughput drug screening2013In: Proc. 10th International Symposium on Biomedical Imaging: From Nano to Macro, Piscataway, NJ: IEEE , 2013, p. 902-905Conference paper (Refereed)
  • 313.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Negri, Joseph
    Broad Institute of Harvard and MIT.
    Bray, Mark-Anthony
    Broad Institute of Harvard and MIT.
    Pacureanu, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    An image based high-throughput assay for chemical screening using zebrafish.2012Conference paper (Refereed)
  • 314.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pacureanu, Alexandra
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Light Tomography2013Conference paper (Other academic)
  • 315.
    Ishaq, Omer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sadanandan, Sajith Kecheril
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Deep Fish: Deep Learning-Based Classification of Zebrafish Deformation for High-Throughput Screening2017In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 22, no 1, p. 102-107Article in journal (Refereed)
    Abstract [en]

    Zebrafish (Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.

  • 316. Isomöttönen, Ville
    et al.
    Daniels, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Cajander, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Pears, Arnold
    McDermott, Roger
    Searching for global employability: Can students capitalize on enabling learning environments?2019In: ACM Transactions on Computing Education, ISSN 1946-6226, E-ISSN 1946-6226, Vol. 19, no 2, p. 11:1-29, article id 11Article in journal (Refereed)
  • 317.
    Issac Niwas, Swamidoss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Kårsnäs, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Uhlmann, Virginie
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts MA, USA and Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.
    Palanisamy, P.
    Dept. of Electronics and Communication Engineering (ECE), National Institute of Technology (NIT), Tiruchirappalli, India.
    Kampf, Caroline
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Simonsson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Strand, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Automated classification of immunostaining patterns in breast tissue from the Human Protein Atlas2012In: Histopathology Image Analysis (HIMA): a MICCAI 2012 workshop, 2012Conference paper (Refereed)
    Abstract [en]

    Background:

    The Human Protein Atlas (HPA) is an effort to map the location of all human proteins (http://www.proteinatlas.org/ ). It contains a large number of histological images of sections from human tissue. Tissue micro arrays are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples.

    Methods and Material:

    The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM) features, complex wavelet co-occurrence matrix (CWCM) features and WND-CHARM-inspired features. The extracted features are used into two different multivariate classifiers (SVM and LDA classifier). Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue.

    Results:

    Good results have been obtained by using the combinations of GLCM and wavelets and texture features, edge features, histograms, transforms, etc. (WND-CHARM). The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert.

    Conclusions:

    Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for quantification of staining patterns in histopathology have many applications, ranging from antibody quality control to tumour grading.

  • 318.
    Issac Niwas, Swamidoss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Kårsnäs, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Uhlmann, Virginie
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts MA, USA and Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.
    Ponnusamy, Palanisamy
    Dept. of Electronics and Communication Engineering (ECE), National Institute of Technology (NIT), Tiruchirappalli, India.
    Kampf, Caroline
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Molecular and Morphological Pathology.
    Simonsson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Institute of Harvard and Massachusetts Institute Technology (MIT), Cambridge, Massachusetts, MA, USA, .
    Strand, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Automated classification of immunostaining patterns in breast tissue from the Human Protein Atlas2013In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 4, no 14Article in journal (Refereed)
    Abstract [en]

    Background:

    The Human Protein Atlas (HPA) is an effort to map the location of all human proteins (http://www.proteinatlas.org/). It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA) are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples.

    Materials and Methods:

    The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM) features, complex wavelet co-occurrence matrix (CWCM) features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM)-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM) and linear discriminant analysis (LDA) classifier). Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue.

    Results:

    We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert.

    Conclusions:

    Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for quantification of staining patterns in histopathology have many applications, ranging from antibody quality control to tumor grading.

  • 319.
    Issac Niwas, Swamidoss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Palanisamy, P
    National Institute of Technology (NIT), Tiruchirappalli, India.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    An Investigation on Nuclei of Histopathological Images using Curvelet Statistical Features2012Conference paper (Other academic)
  • 320.
    Issac Niwas, Swamidoss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Palanisamy, P
    National Institute of Technology (NIT), Tiruchirappalli, India.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Color deconvolution method for breast tissue core biopsy images cell nuclei detection and analysis using multiresolution techniques2013In: International Journal of Imaging and Robotics, ISSN 2231-525X, Vol. 9, no 1, p. 61-72Article in journal (Refereed)
  • 321.
    Issac Niwas, Swamidoss
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Palanisamy, P
    National Institute of Technology (NIT), Tiruchirappalli, India.
    Sujathan, K
    Regional Cancer Centre, Thiruvanathapuram, India.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Analysis of nuclei textures of fine needle aspirated cytology images for breast cancer diagnosis using complex Daubechies wavelets2013In: Signal Processing, ISSN 0165-1684, E-ISSN 1872-7557, Vol. 93, no 10, p. 2828-2837Article in journal (Refereed)
    Abstract [en]

    Breast cancer is the most frequent cause of cancer induced death among women in the world. Diagnosis of this cancer can be done through radiological, surgical, and pathological assessments of breast tissue samples. A common test for detection of this cancer involves visual microscopic inspection of Fine Needle Aspiration Cytology (FNAC) samples of breast tissue. The result of analysis on this sample by a cytopathologist is crucial for the breast cancer patient. For the assessment of malignancy, the chromatin texture patterns of the cell nuclei are essential. Wavelet transforms have been shown to be good tools for extracting information about texture. In this paper, it has been investigated whether complex wavelets can provide better performance than the more common real valued wavelet transform. The features extracted through the wavelets are used as input to a k-nn classifier. The correct classification results are obtained as 93.9% for the complex wavelets and 70.3% for the real wavelets.

  • 322.
    Janols, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Evolving Systems – Engaged Users: Key Principles for Improving Region-wide Health IT Adoption2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many countries have formulated their eHealth visions and billions of dollars have been spent on supporting the eHealth development throughout the world. An important part of the development is the electronic patient record (EPR). To enable sharing and increase cooperation between care providers, most Swedish county councils have decided to use a region-wide EPR. The health professionals often experience numerous problems and consider the region-wide EPR to be too generic and require them to tailor their practices instead of the system evolving towards supporting their needs.

    The aim of the PhD research is to gain knowledge of adoption when deploying and using region-wide health IT systems. This is accomplished by studying, analysing and reflecting upon what region-wide health IT systems are and how professionals use them in their practice. In the research a grounded theory method has been used, which means that the empirical data, not theories and hypotheses, have driven the research process. The data-gathering methods have been interviews, observations, participating in meetings, questionnaires, seminars and conducting literature reviews.

    In order to be able to improve the adoption, a set of four key principles has been identified: (1) Evolving systems-Engaged users, (2) Treat IT deployment and usage as part of organisational development, (3) Identify, respect and support differences, and (4) Identify what must be customised and what can be centralised.

    These four principles challenge the traditional way of developing enterprise-wide IT and emphasise the importance that users must engage in the development, procurement and deployment process to identify their similar and unique needs and procedures. It is crucial that both the similarities and uniqueness are respected and supported. The similarities can be supported by a centralised, standardised solution, while uniqueness requires a customised solution. In order to accomplish that, the IT deployment and usage needs to be treated as an important part of the on-going organisational development, and the IT systems must evolve, i.e., be continuously developed in order to engage the users to participate. 

    List of papers
    1. Physicians' concept of time usage: A key concern in EPR deployment
    Open this publication in new window or tab >>Physicians' concept of time usage: A key concern in EPR deployment
    2010 (English)Conference paper, Published paper (Refereed)
    Abstract [en]

    This paper is based on an interview study with 19 resident, specialist and senior physicians. The study was initiated by a Swedish Hospital management to investigate physicians’ attitude towards their EPR (Electronic Patient Records) and give recommendations for improvement in organization, development, deployment and training. The management had experienced that the physicians were unwilling to take part in the EPR deployment process and simultaneously complained about the low usability and potential safety risks of the systems. The study shows that the EPR must be considered a shared responsibility within the whole organization and not just a property of the IT department. The physicians must consider, and really experience, EPR as efficient support in their daily work rather than something they are forced to use. This includes considering work with the EPR as an important part of their work with patients.

    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2010
    Series
    IFIP Advances in Information and Communication Technology ; 335
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-134219 (URN)10.1007/978-3-642-15515-4_8 (DOI)978-3-642-15514-7 (ISBN)
    Conference
    World Computer Congress 2010
    Available from: 2010-11-22 Created: 2010-11-22 Last updated: 2018-01-12
    2. Same System – Different Experiences: Physicians' and Nurses' Experiences in Using IT Systems
    Open this publication in new window or tab >>Same System – Different Experiences: Physicians' and Nurses' Experiences in Using IT Systems
    2011 (English)Conference paper, Published paper (Refereed)
    Abstract [en]

    In this paper we use a sociotechnical approach and theories about group processes to analyse how two main clinician groups, nurses and physicians, are influenced by their main IT tool, the Electronic Patient Record (EPR), in their clinical practice. The paper is based on interviews with 19 physicians and 17 nurses that work at a Swedish university hospital. The clinicians considered the use of an EPR system necessary, but experienced the need to change their clinical practice to less efficient work routines in order for the EPR system to support them. The main result of the paper is that the EPR system affected nurses and physicians differently. The physicians were more frustrated and experienced that the EPR system worsened their clinical practice and a decreased status among the other clinical professions. The nurses on the other hand experienced that their work became more visible than before and found it easier to claim the importance of their work towards the physicians.

    Place, publisher, year, edition, pages
    New York: ACM Press, 2011
    Keywords
    electronic patient records, group and organization interfaces, group processes, health care, sociotechnical system, studies of organisations, technology and work, usability
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-163527 (URN)10.1145/2071536.2071562 (DOI)978-1-4503-1090-1 (ISBN)
    Conference
    23rd Australian Computer-Human Interaction Conference
    Available from: 2011-12-13 Created: 2011-12-13 Last updated: 2018-01-12
    3. Three Key Concerns for a Successful EPR Deployment and Usage
    Open this publication in new window or tab >>Three Key Concerns for a Successful EPR Deployment and Usage
    2011 (English)In: User Centred Networked Health Care: Proceedings of MIE 2011 / [ed] Anne Moen, Stig Kjær Andersen, Jos Aarts, Petter Hurlen, 2011, p. 260-264Conference paper, Published paper (Refereed)
    Abstract [en]

    The health care environment is unique because of the large and complex organisation with a traditional hierarchic structure that is governed by laws and regulations. This paper examines how a large Swedish health care organisation work with usability issues regarding Electronic Patient Record (EPR) deployment and usage. EPR systems have great impact on work environment and clinical work routines will not be performed in the same way as before. This paper analyse how the EPR management and core business understand their EPR responsibilities and work with usability aspects at different levels in the organisations. The paper reveals that there is a conflict about responsibility between EPR management and core business management. The reasons for the confusion are contradictive understanding of what an EPR system is, an IT system or a tool for the core business to perform better health care work. This leads to that care staff's experience regarding the EPR system's usability, is not being listened to within the organisation. Three key concerns for a successful EPR deployment and usage are identified and further analysed; education, evaluation and support & improvement ideas.

    Series
    Studies in Health Technology and Informatics, ISSN 0926-9630 ; 169
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-163528 (URN)10.3233/978-1-60750-806-9-260 (DOI)978-1-60750-806-9 (ISBN)978-1-60750-805-2 (ISBN)
    Conference
    MIE 2011 - XXIII International Conference of the European Federation for Medical Informatics, August 28-31, 2011, Oslo, Norway
    Available from: 2011-12-15 Created: 2011-12-13 Last updated: 2018-01-12Bibliographically approved
    4. Time Does Not Heal Usability Issues!: Results from a Longitudinal Evaluation of a Health IT Deployment Performed at Three Swedish Hospital Units
    Open this publication in new window or tab >>Time Does Not Heal Usability Issues!: Results from a Longitudinal Evaluation of a Health IT Deployment Performed at Three Swedish Hospital Units
    2012 (English)In: OzCHI '12 Proceedings of the 24th Australian Computer-Human Interaction Conference, New York, NY, USA: ACM Press, 2012, p. 273-280Conference paper, Published paper (Refereed)
    Abstract [en]

    This paper presents a longitudinal evaluation of user adoption during a Patient Administrative System (PAS) deployment. The research was performed at three units within a Swedish university hospital. Both qualitative and quantitative methods have been used to gather data before, during and up to two years after the deployment. The results show that all users experienced usability problems. After two years of usage the system was still not considered to be as supportive as the old system. The users that were required to use the system felt unsure and stressed about whether all information was consulted or not. The users that were less dependent on the system solved the problems by not doing the tasks; instead they let the clerks continue to do the PAS tasks as they did before the deployment. The results indicate that time will not heal usability problems; instead they need to be addressed in other ways.

    Place, publisher, year, edition, pages
    New York, NY, USA: ACM Press, 2012
    Keywords
    EPR, deployment, ehealth, evaluation, implementation, organisational change, sociotechnical systems, usability, user adoption
    National Category
    Human Computer Interaction
    Research subject
    Medical Informatics; Human-Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-188363 (URN)10.1145/2414536.2414582 (DOI)978-1-4503-1438-1 (ISBN)
    Conference
    24rd Australian Computer-Human Interaction Conference
    Available from: 2013-01-17 Created: 2012-12-16 Last updated: 2018-01-11Bibliographically approved
    5. Evaluation of User Adoption during Three Module Deployments of Region-wide Electronic Patient Record Systems
    Open this publication in new window or tab >>Evaluation of User Adoption during Three Module Deployments of Region-wide Electronic Patient Record Systems
    2014 (English)In: International Journal of Medical Informatics, ISSN 1386-5056, E-ISSN 1872-8243, Vol. 83, no 6, p. 438-449Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND:

    In Sweden there are modular region-wide EPR systems that are implemented at various health organisations in the region. The market is dominated by four IT systems that have been procured and deployed in 18 out of 21 regions.

    METHODS:

    In a 2.5-year research study, deployments of three region-wide EPR modules: a patient administration system, eReferral module and eMedication module were followed and evaluated. Health professionals, EPR maintenance organisation, IT and health care managers were observed, interviewed and responded to questionnaires.

    RESULTS:

    Although the same deployment process was used during the three deployments, large variations in the units' adoptions were observed. The variations were due to: (1) expectation and attitude, (2) management and steering, (3) end-user involvement, (4) EPR learning, and (5) usability and the possibility of changing and improving the EPR.

    CONCLUSIONS:

    If changes in work processes are not considered in development and deployment, the potential benefits will not be achieved. It is therefore crucial that EPR deployment is conceived as organisational development. Users must be supported not just before and during the go-live phase, but also in the post-period. A problem often encountered is that it is difficult to make late changes in a region-wide EPR, and it is an open question whether it is possible to talk about a successful deployment if the usability of the introduced system is low.

    National Category
    Human Computer Interaction
    Research subject
    Human-Computer Interaction; Medical Informatics
    Identifiers
    urn:nbn:se:uu:diva-196508 (URN)10.1016/j.ijmedinf.2014.02.003 (DOI)000335903400005 ()24630924 (PubMedID)
    Available from: 2013-03-11 Created: 2013-03-11 Last updated: 2018-01-11Bibliographically approved
    6. Secondary Users Interpretations on Key Concerns for Achieving an Effective and Efficient Region-wide Electronic Patient Record Usage
    Open this publication in new window or tab >>Secondary Users Interpretations on Key Concerns for Achieving an Effective and Efficient Region-wide Electronic Patient Record Usage
    2013 (English)In: The 21st European Conference on Information Systems (ECIS 2013), AIS Electronic Library , 2013Conference paper, Published paper (Refereed)
    Abstract [en]

    The paper presents secondary users interpretation of key concerns (KC) for achieving an efficient and effective electronic patient record (EPR) usage. The evaluation is based on twelve interviews with Clinical Directors and IT Directors that are responsible for delivering high quality care, procuring and implementing IT. The participants represented five Swedish county councils who all use a region-wide EPR for all primary and hospital services. The analysis indicated that there were an unresolved conflict regarding what influence the IT should have on how the health professionals performed practice. Either the systems’ usability or the health professionals unwillingness to change, were blamed for the problems. We argue that the conflict is based on the idea that one EPR is going to support all user groups. Using a region-wide EPR must not be a problem. In the studied organisations, however, it became a problem because to achieve “one system that fits all” the fact that different user groups had different needs, roles and responsibilities were neglected. Neglecting the users’ needs is not solving the problems; instead it will increase the conflict. Using the KC will shed light on differences between primary and secondary users interpretations of the aim of the region-wide EPR. 

    Place, publisher, year, edition, pages
    AIS Electronic Library, 2013
    National Category
    Human Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-196509 (URN)
    Conference
    The 21st European Conference on Information Systems (ECIS 2013)
    Available from: 2013-03-20 Created: 2013-03-11 Last updated: 2018-01-11Bibliographically approved
    7. Interpretation of the Concepts of Enterprise-wide and Best of Breed IT within the New Zealand eHealth Community
    Open this publication in new window or tab >>Interpretation of the Concepts of Enterprise-wide and Best of Breed IT within the New Zealand eHealth Community
    2013 (English)In: Health Care and Informatics Review Online, ISSN 1176-4201, Vol. 17, no 1, p. 11-17Article in journal (Refereed) Published
    Abstract [en]

    Purpose The New Zealand eHealth landscape is diverse with hundreds of systems ‘wired together’ in a complex puzzle. The purpose of this paper is to explore the current debate about selecting and using Best of Breed (BoB) or Enterprise-wide (EW) eHealth systems.

    Method Strategic eHealth documents were analysed and 14 senior IS executives from health and IT organisations were interviewed.

    Findings There appears to be agreement about: (1) what the concepts mean; (2) the problems caused by the mix of BoB and EW, e.g., the strong influence of clinicians on IT decision making; and (3) a possible solution to the complex puzzle lies in changing the mix to emphasise patient-centric eHealth. However, when discussing to what degree IT systems should be customised and/or centralised disagreements become visible.

    Discussion and conclusions There is a trend among decision-makers towards patients’ needs rather than the physical context in deciding system use and design, with an emphasis on what is considered to be ‘best practice’. In this process the preferred systems are EW, however it is important to remember that it is not the only option. There is a risk that if the IT system is too generic (centralised) it might be an unsupportive tool for clinicians and undermine its purpose. 

    Keywords
    eHealth, enterprise-wide systems, Best of Breed systems, procurement, development, system usage
    National Category
    Human Computer Interaction
    Research subject
    Medical Informatics; Human-Computer Interaction
    Identifiers
    urn:nbn:se:uu:diva-196505 (URN)
    Available from: 2013-04-01 Created: 2013-03-10 Last updated: 2018-01-11Bibliographically approved
  • 323.
    Janols, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Tailor the system or tailor the user?: How to make better use of electronic patient record systems2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Health care organisations are extremely complex because they consist of heterogeneous groups of people (clinical professions, patients, managers), use advanced technology (medical devices and patient record systems), and apply many organisational and clinical routines. When introducing Electronic Patient Record systems (EPR) in health care organisations, all these aspects get affected. Using a sociotechnical perspective is necessary in order to get a "successful" EPR usage.

    The aim of my PhD studies is to provide health care organisations with knowledge and insights into how they can improve their organisation and practice in relation to usage of EPR systems. In my research I have used a grounded theory methodology for studying, analysing and reflecting on how electronic patient record systems are used by professionals in their practice. Studies have been conducted during a 2.5 years collaborative research project. Within the studied health care organisation there are differing opinions if an EPR system is mainly a technical system or a tool to support the clinical organisation. This conceptual division leads to an uncertainty in who is responsible for the proper function of the EPR system and have a major effect for the clinicians in their clinical practice. During the research seven potential problems areas, mandate, usability, education, participation, improvements, support and evaluation have been identified as crucial for the health care organisation to manage to achieve an effective EPR usage.

    The main results are 1) The health care organisation needs to establish a problem-solving strategy that questions the reasons behind the problems occurred, 2) The different stakeholder groups need to interact, create a better understanding for each other's perspective and agree on the same goal for the EPR system, 3) The clinical organisation needs help to improve their clinical practice in relation to the EPR system, 4) The EPR deployment and usage affect the clinicians in different ways. Their attitude towards the EPR system is dependent on the usability of the EPR system, the deployment process, their experience of participation, education, support and possibilities to improve the system.

  • 324.
    Janols, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Time Does Not Heal Usability Issues!: Results from a Longitudinal Evaluation of a Health IT Deployment Performed at Three Swedish Hospital Units2012In: OzCHI '12 Proceedings of the 24th Australian Computer-Human Interaction Conference, New York, NY, USA: ACM Press, 2012, p. 273-280Conference paper (Refereed)
    Abstract [en]

    This paper presents a longitudinal evaluation of user adoption during a Patient Administrative System (PAS) deployment. The research was performed at three units within a Swedish university hospital. Both qualitative and quantitative methods have been used to gather data before, during and up to two years after the deployment. The results show that all users experienced usability problems. After two years of usage the system was still not considered to be as supportive as the old system. The users that were required to use the system felt unsure and stressed about whether all information was consulted or not. The users that were less dependent on the system solved the problems by not doing the tasks; instead they let the clerks continue to do the PAS tasks as they did before the deployment. The results indicate that time will not heal usability problems; instead they need to be addressed in other ways.

  • 325.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Day, Karen
    University of Auckland.
    Orr, Martin
    University of Auckland.
    Interpretation and Adoption of the Concept of Enterprise-wide and Best of Breed Health IT within the New Zealand eHealth Community2012In: Health Informatics New Zeeland, 2012Conference paper (Refereed)
    Abstract [en]

    The purpose of this research was to explore the current debate about ‘Best of Breed’ (BoB) vs. Enterprise-wide (EW) Information Systems (IS) in New Zealand healthcare. The ehealth landscape is diverse with hundreds of systems ‘wired together’ in a complex puzzle. Method Strategic ehealth documents were analysed and 14 senior IS executives from different organisations were interviewed. Findings There appears to be agreement about (1) what the concepts mean, (2) the problems caused by the mix of BoB and EW, e.g. the strong influence of clinicians on IS decision making, and (3) a possible solution to the complex puzzle lies in changing the mix to emphasise patient-centric ehealth. However, when discussing to what degree information systems should be customised and/or centralised disagreements become visible. Discussion and conclusions There is a trend towards patients’ needs rather than the physical context in deciding system use and design, with an emphasis on what is considered to be best practice. In the process towards patient-centred care it is important to remember that a generic solution might become an unsupportive tool for clinicians and undermine the purpose. The next step is to conduct a comparative analysis of ehealth development in Sweden and New Zealand.

  • 326.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Day, Karen
    Orr, Martin
    Interpretation of the Concepts of Enterprise-wide and Best of Breed IT within the New Zealand eHealth Community2013In: Health Care and Informatics Review Online, ISSN 1176-4201, Vol. 17, no 1, p. 11-17Article in journal (Refereed)
    Abstract [en]

    Purpose The New Zealand eHealth landscape is diverse with hundreds of systems ‘wired together’ in a complex puzzle. The purpose of this paper is to explore the current debate about selecting and using Best of Breed (BoB) or Enterprise-wide (EW) eHealth systems.

    Method Strategic eHealth documents were analysed and 14 senior IS executives from health and IT organisations were interviewed.

    Findings There appears to be agreement about: (1) what the concepts mean; (2) the problems caused by the mix of BoB and EW, e.g., the strong influence of clinicians on IT decision making; and (3) a possible solution to the complex puzzle lies in changing the mix to emphasise patient-centric eHealth. However, when discussing to what degree IT systems should be customised and/or centralised disagreements become visible.

    Discussion and conclusions There is a trend among decision-makers towards patients’ needs rather than the physical context in deciding system use and design, with an emphasis on what is considered to be ‘best practice’. In this process the preferred systems are EW, however it is important to remember that it is not the only option. There is a risk that if the IT system is too generic (centralised) it might be an unsupportive tool for clinicians and undermine its purpose. 

  • 327.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Göransson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Same System – Different Experiences: Physicians' and Nurses' Experiences in Using IT Systems2011Conference paper (Refereed)
    Abstract [en]

    In this paper we use a sociotechnical approach and theories about group processes to analyse how two main clinician groups, nurses and physicians, are influenced by their main IT tool, the Electronic Patient Record (EPR), in their clinical practice. The paper is based on interviews with 19 physicians and 17 nurses that work at a Swedish university hospital. The clinicians considered the use of an EPR system necessary, but experienced the need to change their clinical practice to less efficient work routines in order for the EPR system to support them. The main result of the paper is that the EPR system affected nurses and physicians differently. The physicians were more frustrated and experienced that the EPR system worsened their clinical practice and a decreased status among the other clinical professions. The nurses on the other hand experienced that their work became more visible than before and found it easier to claim the importance of their work towards the physicians.

  • 328.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Göransson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Secondary Users Interpretations on Key Concerns for Achieving an Effective and Efficient Region-wide Electronic Patient Record Usage2013In: The 21st European Conference on Information Systems (ECIS 2013), AIS Electronic Library , 2013Conference paper (Refereed)
    Abstract [en]

    The paper presents secondary users interpretation of key concerns (KC) for achieving an efficient and effective electronic patient record (EPR) usage. The evaluation is based on twelve interviews with Clinical Directors and IT Directors that are responsible for delivering high quality care, procuring and implementing IT. The participants represented five Swedish county councils who all use a region-wide EPR for all primary and hospital services. The analysis indicated that there were an unresolved conflict regarding what influence the IT should have on how the health professionals performed practice. Either the systems’ usability or the health professionals unwillingness to change, were blamed for the problems. We argue that the conflict is based on the idea that one EPR is going to support all user groups. Using a region-wide EPR must not be a problem. In the studied organisations, however, it became a problem because to achieve “one system that fits all” the fact that different user groups had different needs, roles and responsibilities were neglected. Neglecting the users’ needs is not solving the problems; instead it will increase the conflict. Using the KC will shed light on differences between primary and secondary users interpretations of the aim of the region-wide EPR. 

  • 329.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Göransson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sandblad, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Three Key Concerns for a Successful EPR Deployment and Usage2011In: User Centred Networked Health Care: Proceedings of MIE 2011 / [ed] Anne Moen, Stig Kjær Andersen, Jos Aarts, Petter Hurlen, 2011, p. 260-264Conference paper (Refereed)
    Abstract [en]

    The health care environment is unique because of the large and complex organisation with a traditional hierarchic structure that is governed by laws and regulations. This paper examines how a large Swedish health care organisation work with usability issues regarding Electronic Patient Record (EPR) deployment and usage. EPR systems have great impact on work environment and clinical work routines will not be performed in the same way as before. This paper analyse how the EPR management and core business understand their EPR responsibilities and work with usability aspects at different levels in the organisations. The paper reveals that there is a conflict about responsibility between EPR management and core business management. The reasons for the confusion are contradictive understanding of what an EPR system is, an IT system or a tool for the core business to perform better health care work. This leads to that care staff's experience regarding the EPR system's usability, is not being listened to within the organisation. Three key concerns for a successful EPR deployment and usage are identified and further analysed; education, evaluation and support & improvement ideas.

  • 330.
    Janols, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Lind, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Göransson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sandblad, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Evaluation of User Adoption during Three Module Deployments of Region-wide Electronic Patient Record Systems2014In: International Journal of Medical Informatics, ISSN 1386-5056, E-ISSN 1872-8243, Vol. 83, no 6, p. 438-449Article in journal (Refereed)
    Abstract [en]

    BACKGROUND:

    In Sweden there are modular region-wide EPR systems that are implemented at various health organisations in the region. The market is dominated by four IT systems that have been procured and deployed in 18 out of 21 regions.

    METHODS:

    In a 2.5-year research study, deployments of three region-wide EPR modules: a patient administration system, eReferral module and eMedication module were followed and evaluated. Health professionals, EPR maintenance organisation, IT and health care managers were observed, interviewed and responded to questionnaires.

    RESULTS:

    Although the same deployment process was used during the three deployments, large variations in the units' adoptions were observed. The variations were due to: (1) expectation and attitude, (2) management and steering, (3) end-user involvement, (4) EPR learning, and (5) usability and the possibility of changing and improving the EPR.

    CONCLUSIONS:

    If changes in work processes are not considered in development and deployment, the potential benefits will not be achieved. It is therefore crucial that EPR deployment is conceived as organisational development. Users must be supported not just before and during the go-live phase, but also in the post-period. A problem often encountered is that it is difficult to make late changes in a region-wide EPR, and it is an open question whether it is possible to talk about a successful deployment if the usability of the introduced system is low.

  • 331.
    Jansson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    En resa genom tänkandets labyrinter2013In: Uppsala Nya Tidning, Vol. 02/04Article, book review (Other (popular science, discussion, etc.))
  • 332.
    Jansson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Utvärdering av förändringar i trafikledarnas beslutsfattande: Delrapport I: Den svenska ansatsen till kontrollstrategier i ett nutidshistoriskt och vetenskapligt internationellt perspektiv2014Report (Other academic)
  • 333.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Axelsson, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Knowledge Elicitation in Naturalistic Decision Making: Collegial Verbalisation with "Conspective Protocols"2017In: Naturalistic Decision Making and Uncertainty: Proceedings of the 13th Bi-annual International Conference on Naturalistic Decision Making / [ed] Julie Gore & Paul Ward, 2017, p. 87-93Conference paper (Refereed)
  • 334.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Erlandsson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Collegial verbalisation: The value of verbal reports from colleagues as subjectsManuscript (preprint) (Other academic)
  • 335.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Erlandsson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Recognizing complexity: A prerequisite for skilled intuitive judgments and dynamic decisions2013In: SPUDM24: Subjective Probability, Utility, and Decision Making, 2013, p. 194-Conference paper (Refereed)
  • 336.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Erlandsson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Axelsson, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Collegial verbalisation — the value of an independent observer: an ecological approach2015In: Theoretical Issues in Ergonomics Science, ISSN 1463-922X, E-ISSN 1464-536X, Vol. 16, no 5, p. 474-494Article in journal (Refereed)
  • 337.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Erlandsson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Fröjd, Camilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Anaesthesiology and Intensive Care.
    Arvidsson, Marcus
    Collegial collaboration for safety: Assessing situation awareness by exploring cognitive strategies2013In: Past History and Future Challenges of Human Work Interaction Design (HWID): Generating Cross-domain Knowledge about Connecting Work Analysis and Interaction Design / [ed] Torkil Clemmensen, Bengt Sandblad, Arminda Lopes and Jose Abdelnour- Nocera, 2013, p. 35-40Conference paper (Refereed)
  • 338.
    Jansson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Stensson, Patrik
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
    Bodin, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Axelsson, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Tschirner, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Authority and level of automation: Lessons to be learned in design of in-vehicle assistance systems2014In: Human-Computer Interaction: Applications and Services, Part III, Springer Berlin/Heidelberg, 2014, p. 413-424Conference paper (Refereed)
  • 339. Jia, Yuan
    et al.
    Lárusdóttir, Marta Kristín
    Cajander, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    The usage of usability techniques in Scrum projects2012In: Human-Centered Software Engineering, Springer Berlin/Heidelberg, 2012, p. 331-341Conference paper (Refereed)
  • 340.
    Joffre, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Miettinen, Arttu
    Wernersson, Erik L. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Gamstedt, E. Kristofer
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Effects of defects on the tensile strength of short-fibre composite materials2014In: Mechanics of materials (Print), ISSN 0167-6636, E-ISSN 1872-7743, Vol. 75, p. 125-134Article in journal (Refereed)
  • 341.
    Joffre, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Segerholm, Kristoffer
    SP Technical Research Institute of Sweden, Sustainable Built Environment & KTH, Div. of Building Materials.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Bardage, Stig L.
    SP Technical Research Institute of Sweden, Sustainable Built Environment.
    Luengo Hendriks, Cris L.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Characterization of interfacial stress transfer ability in acetylation-treated wood fibre composites using X-ray microtomography2017In: Industrial crops and products (Print), ISSN 0926-6690, E-ISSN 1872-633X, Vol. 95, p. 43-49Article in journal (Refereed)
    Abstract [en]

    The properties of the fibre/matrix interface contribute to stiffness, strength and fracture behaviour of fibre-reinforced composites. In cellulosic composites, the limited affinity between the hydrophilic fibres and the hydrophobic thermoplastic matrix remains a challenge, and the reinforcing capability ofthe fibres is hence not fully utilized. A direct characterisation of the stress transfer ability through pull-out tests on single fibres is extremely cumbersome due to the small dimension of the wood fibres. Here a novel approach is proposed:the length distribution ofthe fibres sticking out ofthe matrix atthe fracture surface is approximated using X-ray microtomography and is used as an estimate of the adhesion between the fibres and the matrix. When a crack grows in the material, the fibres will either break or be pulled-out of the matrix depending on their adhesion to the matrix: good adhesion between the fibres and the matrix should result in more fibre breakage and less pull-out of the fibres than poor adhesion. The effect of acetylation on the adhesion between the wood fibres and the PLA matrix was evaluated at different moisture contents using the proposed method. By using an acetylation treatment of the fibres it was possible to improve the strength of the composite samples soaked in the water by more than 30%.

  • 342.
    Joffre, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Segerholm, Kristoffer
    SP Technical Research Institute of Sweden, Sustainable Built Environment & KTH, Div. of Building Materials.
    Persson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Luengo Hendriks, Chris
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Bardage, Stig L.
    SP Technical Research Institute of Sweden, Sustainable Built Environment.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    A combined computational and experimental X-ray CT multiscale study of stable, slowly growing cracks in wood-fibre based composite materials2016Conference paper (Other academic)
  • 343.
    Joffre, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Wernersson, Erik L. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Miettinen, Arttu
    Luengo Hendriks, Cris L.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Gamstedt, E. Kristofer
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Swelling of cellulose fibres in composite materials: Constraint effects of the surrounding matrix2013In: Composites Science And Technology, ISSN 0266-3538, E-ISSN 1879-1050, Vol. 74, p. 52-59Article in journal (Refereed)
  • 344. Johal, Wafa
    et al.
    Castellano, Ginevra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Tanaka, Fumihide
    Okita, Sandra
    Robots for Learning2018In: International Journal of Social Robotics, ISSN 1875-4791, E-ISSN 1875-4805, Vol. 10, no 3, p. 293-294Article in journal (Other academic)
  • 345. Jones, Aidan
    et al.
    Bull, Susan
    Castellano, Ginevra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    "I know that now, I'm going to learn this next": Promoting self-regulated learning with a robotic tutor2018In: International Journal of Social Robotics, ISSN 1875-4791, E-ISSN 1875-4805, Vol. 10, no 4, p. 439-454Article in journal (Refereed)
  • 346.
    Jones, Aidan
    et al.
    University Of Birmingham, Birmingham, United Kingdom.
    Castellano, Ginevra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Adaptive robotic tutors that support self-regulated learning: A longer-term investigation with primary school children2018In: International Journal of Social Robotics, ISSN 1875-4791, E-ISSN 1875-4805, Vol. 10, no 3, p. 357-370Article in journal (Refereed)
    Abstract [en]

    Robots are increasingly being used to provide motivating, engaging and personalised support to learners. These robotic tutors have been able to increase student learning gain by providing personalised hints or problem selection. However, they have never been used to assist children in developing self regulated learning (SRL) skills. SRL skills allow a learner to more effectively self-assess and guide their own learning; learners that engage these skills have been shown to perform better academically. This paper explores how personalised tutoring by a robot achieved using an open learner model (OLM) promotes SRL processes and how this can impact learning and SRL skills compared to personalised domain support alone. An OLM allows the learner to view the model that the system holds about them. We present a longer-term study where participants take part in a geography-based task on a touch screen with adaptive feedback provided by the robot. In addition to domain support the robotic tutor uses an OLM to prompt the learner to monitor their developing skills, set goals, and use appropriate tools. Results show that, when a robotic tutor personalises and adaptively scaffolds SRL behaviour based upon an OLM, greater indication of SRL behaviour can be observed over the control condition where the robotic tutor only provides domain support and not SRL scaffolding.

  • 347. Jones, Aidan
    et al.
    Küster, Dennis
    Basedow, Christina Anne
    Alves-Oliveira, Patrícia
    Serholt, Sofia
    Hastie, Helen
    Corrigan, Lee J.
    Barendregt, Wolmet
    Kappas, Arvid
    Paiva, Ana
    Castellano, Ginevra
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Empathic robotic tutors for personalised learning: A multidisciplinary approach2015In: Social Robotics, Springer, 2015, p. 285-295Conference paper (Refereed)
  • 348. Jordan, Philipp
    et al.
    Mubin, Omar
    Obaid, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Silva, Paula Alexandra
    Exploring the referral and usage of science fiction in HCI literature2018In: Design, User Experience, and Usability: Part II, Springer, 2018, p. 19-38Conference paper (Refereed)
  • 349.
    Karjalainen, Kari Daniel
    et al.
    Chalmers Univ Technol, Dept CSE, Gothenburg, Sweden.
    Romell, Anna Elisabeth Sofia
    Chalmers Univ Technol, Dept CSE, Gothenburg, Sweden.
    Ratsamee, Photchara
    Osaka Univ, Cybermedia Ctr, Osaka, Japan.
    Yantaç, Asım Evren
    Koc Univ, Dept Media & Visual Arts, KUAR, Istanbul, Turkey.
    Fjeld, Morten
    Chalmers Univ Technol, Dept CSE, Gothenburg, Sweden.
    Obaid, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Social drone companion for the home environment: a user-centric exploration2017In: Proc. 5th International Conference on Human Agent Interaction, New York: ACM Press, 2017, p. 89-96Conference paper (Refereed)
    Abstract [en]

    Recent research has focused on how to facilitate interaction between humans and robots, giving rise to the field of human robot interaction. A related research area is human-drone interaction (HDI), investigating how interaction between humans and drones can be expanded in novel and meaningful ways. In this work, we explore the use of drones as companions in a home environment. We present three consecutive studies addressing user requirements and design space of companion drones. Following a user-centered approach, the three stages include online questionnaire, design workshops, and simulated virtual reality (VR) home environment. Our results show that participants preferred the idea of a drone companion at home, particularly for tasks such as fetching items and cleaning. The participants were also positive towards a drone companion that featured anthropomorphic features.

  • 350.
    Kavathatzopoulos, Iordanis
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    AI and philosophizing2018Conference paper (Other academic)
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