| 1. |
- Cervin, Ida, et al.
(författare)
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Improving the creation and reporting of structured findings during digital pathology review
- 2016
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Ingår i: Journal of Pathology Informatics. - : Medknow Publications. - 2229-5089 .- 2153-3539. ; 7:1, s. 32-32
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Issac Niwas, Swamidoss, et al.
(författare)
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Automated classification of immunostaining patterns in breast tissue from the Human Protein Atlas
- 2013
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Ingår i: Journal of Pathology Informatics. - : Elsevier BV. - 2229-5089 .- 2153-3539. ; 4:14
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Kårsnäs, Andreas, et al.
(författare)
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Learning histopathological patterns
- 2012
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Ingår i: Journal of Pathology Informatics. - : Elsevier BV. - 2229-5089 .- 2153-3539. ; 2, s. 12-
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Tidskriftsartikel (refereegranskat)abstract
- Aims: The aim was to demonstrate a method for automated image analysis of immunohistochemically stained tissue samples for extracting features that correlate with patient disease. We address the problem of quantifying tumor tissue and segmenting and counting cell nuclei. Materials and Methods: Our method utilizes a flexible segmentation method based on sparse coding trained from representative image samples. Nuclei counting is based on a nucleus model that takes size, shape, and nucleus probability into account. Nuclei clustering and overlays are resolved using a gray-weighted distance transform. We obtain a probability measure for pixels belonging to a nucleus from our segmentation procedure. Experiments are carried out on two sets of immunohistochemically stained images - one set based on the estrogen receptor (ER) and the other on antigen KI-67. For the nuclei separation we have selected 207 ER image samples from 58 tissue micro array-cores corresponding to 58 patients and 136 KI-67 image samples also from 58 cores. The images are hand-annotated by marking the center position of each nucleus. For the ER data we have a total of 1006 nuclei and for the KI-67 we have 796 nuclei. Segmentation performance was evaluated in terms of missing nuclei, falsely detected nuclei, and multiple detections. The proposed method is compared to state-of-the-art Bayesian classification. Statistical analysis used: The performance of the proposed method and a state-of-the-art algorithm including variations thereof is compared using the Wilcoxon rank sum test. Results: For both the ER experiment and the KI-67 experiment the proposed method exhibits lower error rates than the state-of-the-art method. Total error rates were 4.8 % and 7.7 % in the two experiments, corresponding to an average of 0.23 and 0.45 errors per image, respectively. The Wilcoxon rank sum tests show statistically significant improvements over the state-of-the-art method. Conclusions: We have demonstrated a method and obtained good performance compared to state-of-the-art nuclei separation. The segmentation procedure is simple, highly flexible, and we demonstrate how it, in addition to the nuclei separation, can perform precise segmentation of cancerous tissue. The complexity of the segmentation procedure is linear in the image size and the nuclei separation is linear in the number of nuclei. Additionally the method can be parallelized to obtain high-speed computations.
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| 4. |
- Lundström, Claes, 1973-, et al.
(författare)
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Summary of 2nd Nordic symposium on digital pathology
- 2015
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Ingår i: Journal of Pathology Informatics. - : Medknow Publications. - 2229-5089 .- 2153-3539. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Lundström, Claes, 1973-, et al.
(författare)
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Summary of third Nordic symposium on digital pathology
- 2016
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Ingår i: Journal of Pathology Informatics. - : Medknow Publications. - 2229-5089 .- 2153-3539. ; 7:12
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 6. |
- Molin, Jesper, 1987, et al.
(författare)
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A comparative study of input devices for digital slide navigation
- 2015
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Ingår i: Journal of Pathology Informatics. - : Elsevier BV. - 2229-5089 .- 2153-3539. ; 6:7
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Tidskriftsartikel (refereegranskat)abstract
- 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
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| 7. |
- Thorstenson, Sten, et al.
(författare)
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Implementation of large‑scale routine diagnostics using whole slide imaging in Sweden: Digital pathology experiences 2006-2013
- 2014
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Ingår i: Journal of Pathology Informatics. - : Elsevier BV. - 2229-5089 .- 2153-3539. ; 5:14
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Tidskriftsartikel (refereegranskat)abstract
- 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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| 8. |
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| 9. |
- Sintorn, Ida-Maria, 1976-, et al.
(författare)
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Facilitating Ultrastructural Pathology through Automated Imaging and Analysis
- 2019
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Ingår i: Journal of Pathology Informatics. - : Elsevier. - 2229-5089 .- 2153-3539. ; 10:1, s. 38-39
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Transmission electron microscopy (TEM) is an important diagnostic tool for analyzing human tissue at the nm scale. It is the only option, or gold standard, for diagnosing several disorders e.g. cilia and renal diseases, rare cancers etc. However, conventional TEM microscopes are highly manual, technically complex and a special environment is required to house the bulky and sensitive machines. Interpretation of information is subjective, time consuming, and relies on a high level of expertise which, unfortunately, is rare for this specialty within pathology. Here, we present methods and results from an ongoing project with the goal to develop a smart and easy to use platform for ultrastructural pathologic diagnoses. The platform is based on the recently developed MiniTEM instrument, a highly automated table-top TEM. In the project we develop image analysis methods for guided as well as fully automated search and analysis of structures of interest. In addition we enrich MiniTEM with an integrated database for convenient image handling and traceability. These points are identified by user representatives as crucial for creating a cost-effective diagnostic platform. We will show strategies and results for using image analysis and machine learning for automated search for objects/regions of interest at low magnification as well as combining multiple object instances acquired at high magnification to enhance nm details necessary for correct diagnosis. This will be exemplified for diagnosing primary cilia dyskinesia and renal disorders. The automation in imaging and analysis within the platform is a big step towards digital ultrapathology.
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| 10. |
- Asa, Sylvia, et al.
(författare)
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2020 vision of digital pathology in action
- 2019
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Ingår i: Journal of Pathology Informatics. - : Medknow Publications. - 2229-5089 .- 2153-3539. ; 10:27
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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