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Treanor, Darren
Publications (6 of 6) Show all publications
Asa, S., Bodén, A., Treanor, D., Jarkman, S., Lundström, C. & Pantatnowitz, L. (2019). 2020 vision of digital pathology in action. Journal of Pathology Informatics, 10(27)
Open this publication in new window or tab >>2020 vision of digital pathology in action
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2019 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 10, no 27Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
Medknow Publications, 2019
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:liu:diva-160147 (URN)10.4103/jpi.jpi_31_19 (DOI)31516758 (PubMedID)
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2019-11-27Bibliographically approved
Skoglund, K., Rose, J., Lindvall, M., Lundström, C. & Treanor, D. (2019). Annotations, ontologies, and whole slide images: Development of an annotated ontology-driven whole slide image library of normal and abnormal human tissue. Journal of Pathology Informatics, 10(22)
Open this publication in new window or tab >>Annotations, ontologies, and whole slide images: Development of an annotated ontology-driven whole slide image library of normal and abnormal human tissue
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2019 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 10, no 22Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Medknow Publications, 2019
Keywords
Annotation, digital pathology, image database, ontology, whole slide images
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:liu:diva-160146 (URN)10.4103/jpi.jpi_81_18 (DOI)
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2019-11-27Bibliographically approved
Falk, M., Ynnerman, A., Treanor, D. & Lundström, C. (2019). Interactive Visualization of 3D Histopathology in Native Resolution. IEEE Transactions on Visualization and Computer Graphics, 25(1), 1008-1017
Open this publication in new window or tab >>Interactive Visualization of 3D Histopathology in Native Resolution
2019 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 25, no 1, p. 1008-1017Article in journal (Refereed) Published
Abstract [en]

We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue. Clinical work flows and research based on pathology have, until now, largely been dominated by 2D imaging. As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice. Our starting point is the current lack of appropriate visualization tools in histopathology, which has been a limiting factor in the uptake of digital pathology. Visualization of 3D histology data does pose difficult challenges in several aspects. The full-color datasets are dense and large in scale, on the order of 100,000 x 100,000 x 100 voxels. This entails serious demands on both rendering performance and user experience design. Despite this, our developed application supports interactive study of 3D histology datasets at native resolution. Our application is based on tailoring and tuning of existing methods, system integration work, as well as a careful study of domain specific demands emanating from a close participatory design process with domain experts as team members. Results from a user evaluation employing the tool demonstrate a strong agreement among the 14 participating pathologists that 3D histopathology will be a valuable and enabling tool for their work.

Keywords
Histology, Pathology, Volume Rendering, Expert Evaluation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-150420 (URN)10.1109/tvcg.2018.2864816 (DOI)000452640000096 ()
Funder
VINNOVA, 2014-04257
Note

Funding agencies: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC); DigiPat project by VINNOVA grant [2014-04257]

Available from: 2018-08-22 Created: 2018-08-22 Last updated: 2019-01-07
Capitanio, A., Dina, R. E. & Treanor, D. (2018). Digital cytology: A short review of technical and methodological approaches and applications. Cytopathology, 29(4), 317-325
Open this publication in new window or tab >>Digital cytology: A short review of technical and methodological approaches and applications
2018 (English)In: Cytopathology, ISSN 0956-5507, E-ISSN 1365-2303, Vol. 29, no 4, p. 317-325Article, review/survey (Refereed) Published
Abstract [en]

The recent years have been characterised by a rapid development of whole slide imaging (WSI) especially in its applications to histology. The application of WSI technology to cytology is less common because of technological problems related to the three-dimensional nature of cytology preparations (which requires capturing of z-stack information, with an increase in file size and usability issues in viewing cytological preparations). The aim of this study is to provide a review of the literature on the use of digital cytology and provide an overview of cytological applications of WSI in current practice as well as identifying areas for future development.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
cytology; digital cytology; review; whole slide imaging
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:liu:diva-150228 (URN)10.1111/cyt.12554 (DOI)000439927300001 ()29665178 (PubMedID)
Available from: 2018-08-22 Created: 2018-08-22 Last updated: 2019-05-01
Lundström, C., Waltersson, M., Persson, A. & Treanor, D. (2016). Summary of third Nordic symposium on digital pathology. Journal of Pathology Informatics, 7(12)
Open this publication in new window or tab >>Summary of third Nordic symposium on digital pathology
2016 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 7, no 12Article in journal, Editorial material (Other academic) Published
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.

Place, publisher, year, edition, pages
Medknow Publications, 2016
Keywords
Implementation; pathology informatics; validation
National Category
Other Medical Engineering Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-130542 (URN)10.4103/2153-3539.179902 (DOI)27141318 (PubMedID)2-s2.0-85009253042 (Scopus ID)
Funder
VINNOVA, 2012-01121
Available from: 2016-08-15 Created: 2016-08-15 Last updated: 2018-01-10Bibliographically approved
Lundström, C., Thorstenson, S., Waltersson, M., Persson, A. & Treanor, D. (2015). Summary of 2nd Nordic symposium on digital pathology. Journal of Pathology Informatics, 6
Open this publication in new window or tab >>Summary of 2nd Nordic symposium on digital pathology
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2015 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 6Article in journal, Editorial material (Refereed) Published
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.

Place, publisher, year, edition, pages
Medknow Publications, 2015
National Category
Other Medical Engineering
Identifiers
urn:nbn:se:liu:diva-118879 (URN)10.4103/2153-3539.151889 (DOI)25774316 (PubMedID)
Funder
VINNOVA
Available from: 2015-06-04 Created: 2015-06-04 Last updated: 2017-12-04
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