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  • 1.
    Asa, Sylvia
    et al.
    Department of Pathology, University Health Network, Toronto, Ontario, Canada.
    Bodén, Anna
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Clinical pathology.
    Treanor, Darren
    University of Leeds, and Leeds Teaching Hospitals NHS Trust Leeds, UK.
    Jarkman, Sofia
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Clinical pathology.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Pantatnowitz, Liron
    Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, USA.
    2020 vision of digital pathology in action2019In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 10, no 27Article in journal (Other academic)
  • 2.
    Cervin, Ida
    et al.
    Sectra AB, Chalmers University of Technology, Sectra AB, Gothenburg, Sweden.
    Molin, Jesper
    Center for Medical Image Science and Visualization, Chalmers University of Technology, Sectra AB, Gothenburg, Sweden.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Improving the creation and reporting of structured findings during digital pathology review2016In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 7, no 1, p. 32-32Article in journal (Refereed)
    Abstract [en]

    Background: Today, pathology reporting consists of many separate tasks, carried out by multiple people. Common tasks include dictation during case review, transcription, verification of the transcription, report distribution, and report the key findings to follow-up registries. Introduction of digital workstations makes it possible to remove some of these tasks and simplify others. This study describes the work presented at the Nordic Symposium on Digital Pathology 2015, in Linköping, Sweden. Methods: We explored the possibility to have a digital tool that simplifies image review by assisting note-taking, and with minimal extra effort, populates a structured report. Thus, our prototype sees reporting as an activity interleaved with image review rather than a separate final step. We created an interface to collect, sort, and display findings for the most common reporting needs, such as tumor size, grading, and scoring. Results: The interface was designed to reduce the need to retain partial findings in the head or on paper, while at the same time be structured enough to support automatic extraction of key findings for follow-up registry reporting. The final prototype was evaluated with two pathologists, diagnosing complicated partial mastectomy cases. The pathologists experienced that the prototype aided them during the review and that it created a better overall workflow. Conclusions: These results show that it is feasible to simplify the reporting tasks in a way that is not distracting, while at the same time being able to automatically extract the key findings. This simplification is possible due to the realization that the structured format needed for automatic extraction of data can be used to offload the pathologists' working memory during the diagnostic review.

  • 3.
    Chow, Joyce A
    et al.
    RISE Interactive Institute, Norrköping, Sweden.
    Törnros, Martin E
    Interaktiva Rum Sverige, Gothenburg, Sweden.
    Waltersson, Marie
    Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Richard, Helen
    Region Östergötland, Center for Diagnostics, Clinical pathology.
    Kusoffsky, Madeleine
    RISE Interactive Institute, Norrköping, Sweden.
    Lundström, Claes
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Sectra AB, Linköping, Sweden.
    Kurti, Arianit
    RISE Interactive Institute, Norrköping, Sweden.
    A Design Study Investigating Augmented Reality and Photograph Annotation in a Digitalized Grossing Workstation2017In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 8, no 31Article in journal (Refereed)
    Abstract [en]

    Context: Within digital pathology, digitalization of the grossing procedure has been relatively underexplored in comparison to digitalization of pathology slides. 

    Aims: Our investigation focuses on the interaction design of an augmented reality gross pathology workstation and refining the interface so that information and visualizations are easily recorded and displayed in a thoughtful view. 

    Settings and Design: The work in this project occurred in two phases: the first phase focused on implementation of an augmented reality grossing workstation prototype while the second phase focused on the implementation of an incremental prototype in parallel with a deeper design study. 

    Subjects and Methods: Our research institute focused on an experimental and “designerly” approach to create a digital gross pathology prototype as opposed to focusing on developing a system for immediate clinical deployment. 

    Statistical Analysis Used: Evaluation has not been limited to user tests and interviews, but rather key insights were uncovered through design methods such as “rapid ethnography” and “conversation with materials”. 

    Results: We developed an augmented reality enhanced digital grossing station prototype to assist pathology technicians in capturing data during examination. The prototype uses a magnetically tracked scalpel to annotate planned cuts and dimensions onto photographs taken of the work surface. This article focuses on the use of qualitative design methods to evaluate and refine the prototype. Our aims were to build on the strengths of the prototype's technology, improve the ergonomics of the digital/physical workstation by considering numerous alternative design directions, and to consider the effects of digitalization on personnel and the pathology diagnostics information flow from a wider perspective. A proposed interface design allows the pathology technician to place images in relation to its orientation, annotate directly on the image, and create linked information. 

    Conclusions: The augmented reality magnetically tracked scalpel reduces tool switching though limitations in today's augmented reality technology fall short of creating an ideal immersive workflow by requiring the use of a monitor. While this technology catches up, we recommend focusing efforts on enabling the easy creation of layered, complex reports, linking, and viewing information across systems. Reflecting upon our results, we argue for digitalization to focus not only on how to record increasing amounts of data but also how these data can be accessed in a more thoughtful way that draws upon the expertise and creativity of pathology professionals using the systems.

  • 4.
    Kost, Henning
    et al.
    Fraunhofer Mevis.
    Homeyer, André
    Fraunhofer Mevis.
    Molin, Jesper
    Sectra AB.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Science & Engineering.
    Hahn, Horst
    Fraunhofer Mevis.
    Training Nuclei Detection Algorithms with Simple Annotations2017In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 8Article in journal (Refereed)
    Abstract [en]

    Background:

    Generating good training datasets is essential for machine learning-based nuclei detection methods. However, creating exhaustive nuclei contour annotations, to derive optimal training data from, is often infeasible.

    Methods:

    We compared different approaches for training nuclei detection methods solely based on nucleus center markers. Such markers contain less accurate information, especially with regard to nuclear boundaries, but can be produced much easier and in greater quantities. The approaches use different automated sample extraction methods to derive image positions and class labels from nucleus center markers. In addition, the approaches use different automated sample selection methods to improve the detection quality of the classification algorithm and reduce the run time of the training process. We evaluated the approaches based on a previously published generic nuclei detection algorithm and a set of Ki-67-stained breast cancer images.

    Results:

    A Voronoi tessellation-based sample extraction method produced the best performing training sets. However, subsampling of the extracted training samples was crucial. Even simple class balancing improved the detection quality considerably. The incorporation of active learning led to a further increase in detection quality.

    Conclusions:

    With appropriate sample extraction and selection methods, nuclei detection algorithms trained on the basis of simple center marker annotations can produce comparable quality to algorithms trained on conventionally created training sets.

  • 5.
    Lundström, Claes
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Science & Engineering. Sectra AB.
    Thorstenson, Sten
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Waltersson, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Persson, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Radiology in Linköping.
    Treanor, Darren
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. St. James University Hospital, Leeds, England.
    Summary of 2nd Nordic symposium on digital pathology2015In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 6Article in journal (Refereed)
    Abstract [en]

    Techniques for digital pathology are envisioned to provide great benefits in clinical practice, but experiences also show that solutions must be carefully crafted. The Nordic countries are far along the path toward the use of whole-slide imaging in clinical routine. The Nordic Symposium on Digital Pathology (NDP) was created to promote knowledge exchange in this area, between stakeholders in health care, industry, and academia. This article is a summary of the NDP 2014 symposium, including conclusions from a workshop on clinical adoption of digital pathology among the 144 attendees.

  • 6.
    Lundström, Claes
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra AB, Sweden.
    Waltersson, Marie
    Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Persson, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Treanor, Darren
    Linköping University, Center for Medical Image Science and Visualization (CMIV). University of Leeds, UK; St. James University Hospital, Leeds, UK.
    Summary of the 4th Nordic Symposium on Digital Pathology2017In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 8Article in journal (Other academic)
    Abstract [en]

    The Nordic symposium on digital pathology (NDP) was created to promote knowledge exchange across stakeholders in health care, industry, and academia. In 2016, the 4th NDP installment took place in Linköping, Sweden, promoting development and collaboration in digital pathology for the benefit of routine care advances. This article summarizes the symposium, gathering 170 attendees from 13 countries. This summary also contains results from a survey on integrated diagnostics aspects, in particular radiology-pathology collaboration.

  • 7.
    Lundström, Claes
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Waltersson, Marie
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Persson, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Department of Radiology in Linköping.
    Treanor, Darren
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Department of Cellular Pathology, St. James University Hospital, Leeds, UK.
    Summary of third Nordic symposium on digital pathology2016In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 7, no 12Article in journal (Other academic)
    Abstract [en]

    Cross-disciplinary and cross-sectorial collaboration is a key success factor for turning the promise of digital pathology into actual clinical benefits. The Nordic symposium on digital pathology (NDP) was created to promote knowledge exchange in this area, among stakeholders in health care, industry, and academia. This article is a summary of the third NDP symposium in Linkφping, Sweden. The Nordic experiences, including several hospitals using whole-slide imaging for substantial parts of their primary reviews, formed a fertile base for discussions among the 190 NDP attendees originating from 15 different countries. This summary also contains results from a survey on adoption and validation aspects of clinical digital pathology use.

  • 8.
    Molin, Jesper
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Chalmers University of Technology, Gothenburg, Sweden.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Science & Engineering. Sectra AB.
    Fjeld, Morten
    Chalmers University of Technology, Gothenburg, Sweden.
    A comparative study of input devices for digital slide navigation2015In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 6Article in journal (Refereed)
    Abstract [en]

    This paper describes work presented at the Nordic Symposium on Digital Pathology 2014, Linköping, Sweden. Quick and seamless integration between input devices and the navigation of digital slides remains a key barrier for many pathologists to “go digital.” To better understand this integration, three different input device implementations were compared in terms of time to diagnose, perceived workload and users’ preferences. Six pathologists reviewed in total nine cases with a computer mouse, a 6 degrees-of-freedom (6DOF) navigator and a touchpad. The participants perceived significantly less workload (P < 0.05) with the computer mouse and the 6DOF navigator, than with the touchpad, while no effect of the input device used on the time to diagnose was observed. Five out of six pathologists preferred the 6DOF navigator, while the touchpad was the least preferred device. While digital slide navigation is often designed to mimic microscope interaction, the results of this study demonstrate that in order to minimize workload there is reason to let the digital interaction move beyond the familiar microscope tradition.

  • 9.
    Skoglund, Karin
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Diagnostics, Clinical pathology.
    Rose, Jeronimo
    Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Lindvall, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra AB, Linköping, Sweden.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra AB, Linköping, Sweden.
    Treanor, Darren
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Region Östergötland, Center for Diagnostics, Clinical pathology. St. James University Hospital, Leeds, UK.
    Annotations, ontologies, and whole slide images: Development of an annotated ontology-driven whole slide image library of normal and abnormal human tissue2019In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 10, no 22Article in journal (Refereed)
    Abstract [en]

    Objective: Digital pathology is today a widely used technology, and the digitalization of microscopic slides into whole slide images (WSIs) allows the use of machine learning algorithms as a tool in the diagnostic process. In recent years, “deep learning” algorithms for image analysis have been applied to digital pathology with great success. The training of these algorithms requires a large volume of high-quality images and image annotations. These large image collections are a potent source of information, and to use and share the information, standardization of the content through a consistent terminology is essential. The aim of this project was to develop a pilot dataset of exhaustive annotated WSI of normal and abnormal human tissue and link the annotations to appropriate ontological information. 

    Materials and Methods: Several biomedical ontologies and controlled vocabularies were investigated with the aim of selecting the most suitable ontology for this project. The selection criteria required an ontology that covered anatomical locations, histological subcompartments, histopathologic diagnoses, histopathologic terms, and generic terms such as normal, abnormal, and artifact. WSIs of normal and abnormal tissue from 50 colon resections and 69 skin excisions, diagnosed 2015-2016 at the Department of Clinical Pathology in Linköping, were randomly collected. These images were manually and exhaustively annotated at the level of major subcompartments, including normal or abnormal findings and artifacts. 

    Results: Systemized nomenclature of medicine clinical terms (SNOMED CT) was chosen, and the annotations were linked to its codes and terms. Two hundred WSI were collected and annotated, resulting in 17,497 annotations, covering a total area of 302.19 cm2, equivalent to 107,7 gigapixels. Ninety-five unique SNOMED CT codes were used. The time taken to annotate a WSI varied from 45 s to over 360 min, a total time of approximately 360 h. 

    Conclusion: This work resulted in a dataset of 200 exhaustive annotated WSIs of normal and abnormal tissue from the colon and skin, and it has informed plans to build a comprehensive library of annotated WSIs. SNOMED CT was found to be the best ontology for annotation labeling. This project also demonstrates the need for future development of annotation tools in order to make the annotation process more efficient.

  • 10.
    Thorstenson, Sten
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Molin, Jesper
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology. Chalmers University of Technology, Göteborg.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Implementation of large‑scale routine diagnostics using whole slideimaging in Sweden: Digital pathology experiences 2006-20132014In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 5, no 14Article in journal (Refereed)
    Abstract [en]

    Recent technological advances have improved the whole slide imaging (WSI) scanner quality and reduced the cost of storage, thereby enabling the deployment of digital pathology for routine diagnostics. In this paper we present the experiences from two Swedish sites having deployed routine large-scale WSI for primary review. At Kalmar County Hospital, the digitization process started in 2006 to reduce the time spent at the microscope in order to improve the ergonomics. Since 2008, more than 500,000 glass slides have been scanned in the routine operations of Kalmar and the neighboring Linköping University Hospital. All glass slides are digitally scanned yet they are also physically delivered to the consulting pathologist who can choose to review the slides on screen, in the microscope, or both. The digital operations include regular remote case reporting by a few hospital pathologists, as well as around 150 cases per week where primary review is outsourced to a private clinic. To investigate how the pathologists choose to use the digital slides, a web-based questionnaire was designed and sent out to the pathologists in Kalmar and Linköping. The responses showed that almost all pathologists think that ergonomics have improved and that image quality was sufficient for most histopathologic diagnostic work. 38 ± 28% of the cases were diagnosed digitally, but the survey also revealed that the pathologists commonly switch back and forth between digital and conventional microscopy within the same case. The fact that two full-scale digital systems have been implemented and that a large portion of the primary reporting is voluntarily performed digitally shows that large-scale digitization is possible today.

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