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Original Article: Artificial intelligence in cytopathology: A neural network to identify papillary carcinoma on thyroid fine-needle aspiration cytology smears
Parikshit Sanyal, Tanushri Mukherjee, Sanghita Barui, Avinash Das, Prabaha Gangopadhyay
J Pathol Inform 2018, 9:43 (3 December 2018)
Introduction: Fine-needle aspiration cytology (FNAC) for identification of papillary carcinoma thyroid is a moderately sensitive and specific modality. The present machine learning tools can correctly classify images into broad categories. Training software for recognition of papillary thyroid carcinoma on FNAC smears will be a decisive step toward automation of cytopathology. Aim: The aim of this study is to develop an artificial neural network (ANN) for the purpose of distinguishing papillary carcinoma thyroid and nonpapillary carcinoma thyroid on microphotographs from thyroid FNAC smears. Subjects and Methods: An ANN was developed in the Python programming language. In the training phase, 186 microphotographs from Romanowsky/Pap-stained smears of papillary carcinoma and 184 microphotographs from smears of other thyroid lesions (at ×10 and ×40 magnification) were used for training the ANN. After completion of training, performance was evaluated with a set of 174 microphotographs (66 – nonpapillary carcinoma and 21 – papillary carcinoma, each photographed at two magnifications ×10 and ×40). Results: The performance characteristics and limitations of the neural network were assessed, assuming FNAC diagnosis as gold standard. Combined results from two magnifications showed good sensitivity (90.48%), moderate specificity (83.33%), and a very high negative predictive value (96.49%) and 85.06% diagnostic accuracy. However, vague papillary formations by benign follicular cells identified wrongly as papillary carcinoma remain a drawback. Conclusion: With further training with a diverse dataset and in conjunction with automated microscopy, the ANN has the potential to develop into an accurate image classifier for thyroid FNACs.
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Research Article: Interactive digital microscopy at the center for a cross-continent undergraduate pathology course in Mozambique
Leonor David, Isabel Martins, Mamudo Rafik Ismail, Fabíola Fernandes, Mohsin Sidat, Mário Seixas, Elsa Fonseca, Carla Carrilho
J Pathol Inform 2018, 9:42 (3 December 2018)
Background: Recent medical education trends encourage the use of teaching strategies that emphasize student centeredness and self-learning. In this context, the use of new educative technologies is stimulated at the Faculty of Medicine of Eduardo Mondlane University (FMUEM) in Mozambique. The Faculty of Medicine of University of Porto (FMUP) and FMUEM have a long-lasting record of collaborative work. Within this framework, both institutions embarked in a partnership, aimed to develop a blended learning course of pathology for undergraduates, shared between the two faculties and incorporating interactive digital microscopy as a central learning tool. Methods: A core team of faculty members from both institutions identified the existing resources and previous experiences in the two faculties. The Moodle course for students from the University of Porto was the basis to implement the current project. The objective was to develop educational modules of mutual interest, designed for e-learning, followed by a voluntary student's survey conducted in FMUEM to get their perception about the process. Results: We selected contents from the pathology curricula of FMUP and FMUEM that were of mutual interest. We next identified and produced new contents for the shared curricula. The implementation involved joint collaboration and training to prepare the new contents, together with building quizzes for self-evaluation. All the practical sessions were based on the use of interactive digital microscopy. The students have reacted enthusiastically to the incorporation of the online component that increased their performance and motivation for pathology learning. For the students in Porto, the major acquisition was the access to slides from infectious diseases as well as autopsy videos. Conclusions: Our study indicates that students benefited from high-quality educational contents, with emphasis on digital microscopy, in a platform generated in a win-win situation for FMUP and FMUEM.
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Original Article: Parathyroid frozen section interpretation via desktop telepathology systems: A validation study
Edward Chandraratnam, Leonardo D Santos, Shaun Chou, Jun Dai, Juan Luo, Syeda Liza, Ronald Y Chin
J Pathol Inform 2018, 9:41 (3 December 2018)
Background: Telepathology can potentially be utilized as an alternative to having on-site pathology services for rural and regional hospitals. The goal of the study was to validate two small-footprint desktop telepathology systems for remote parathyroid frozen sections. Subjects and Methods: Three pathologists retrospectively diagnosed 76 parathyroidectomy frozen sections of 52 patients from three pathology services in Australia using the “live-view mode” of MikroScan D2 and Aperio LV1 and in-house direct microscopy. The final paraffin section diagnosis served as the “gold standard” for accuracy evaluation. Concordance rates of the telepathology systems with direct microscopy, inter-pathologist and intra-pathologist agreement, and the time taken to report each slide were analyzed. Results: Both telepathology systems showed high diagnostic accuracy (>99%) and high concordance (>99%) with direct microscopy. High inter-pathologist agreement for telepathology systems was demonstrated by overall kappa values of 0.92 for Aperio LV1 and 0.85 for MikroScan D2. High kappa values (from 0.85 to 1) for intra-pathologist agreement within the three systems were also observed. The time taken per slide by Aperio LV1 and MicroScan D2 within three pathologists was about 3.0 times (P < 0.001, 95% confidence interval [CI]: 2.8–3.2) and 7.7 times (P < 0.001, 95% CI: 7.1–8.3) as long as direct microscopy, respectively, while MikroScan D2 took about 2.6 times as long as Aperio LV1 (P < 0.001, 95% CI: 2.4–2.7). All pathologists evaluated Aperio LV1 as being more user-friendly. Conclusions: Telepathology diagnosis of parathyroidectomy frozen sections through small-footprint desktop systems is accurate, reliable, and comparable with in-house direct microscopy. Telepathology systems take longer than direct microscopy; however, the time taken is within clinically acceptable limits. Aperio LV1 takes shorter time than MikroScan D2 and is more user-friendly.
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Review Article: Twenty years of digital pathology: An overview of the road travelled, what is on the horizon, and the emergence of vendor-neutral archives
Liron Pantanowitz, Ashish Sharma, Alexis B Carter, Tahsin Kurc, Alan Sussman, Joel Saltz
J Pathol Inform 2018, 9:40 (21 November 2018)
Almost 20 years have passed since the commercial introduction of whole-slide imaging (WSI) scanners. During this time, the creation of various WSI devices with the ability to digitize an entire glass slide has transformed the field of pathology. Parallel advances in computational technology and storage have permitted rapid processing of large-scale WSI datasets. This article provides an overview of important past and present efforts related to WSI. An account of how the virtual microscope evolved from the need to visualize and manage satellite data for earth science applications is provided. The article also discusses important milestones beginning from the first WSI scanner designed by Bacus to the Food and Drug Administration approval of the first digital pathology system for primary diagnosis in surgical pathology. As pathology laboratories commit to going fully digitalize, the need has emerged to include WSIs into an enterprise-level vendor-neutral archive (VNA). The different types of VNAs available are reviewed as well as how best to implement them and how pathology can benefit from participating in this effort. Differences between traditional image algorithms that extract pixel-, object-, and semantic-level features versus deep learning methods are highlighted. The need for large-scale data management, analysis, and visualization in computational pathology is also addressed.
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Research Article: The use of screencasts with embedded whole-slide scans and hyperlinks to teach anatomic pathology in a supervised digital environment
Mary Wong, Joseph Frye, Stacey Kim, Alberto M Marchevsky
J Pathol Inform 2018, 9:39 (14 November 2018)
Background: There is an increasing interest in using digitized whole-slide imaging (WSI) for routine surgical pathology diagnoses. Screencasts are digital recordings of computer screen output with advanced interactive features that allow for the preparation of videos. Screencasts that include hyperlinks to WSIs could help teach pathology residents how to become familiar with technologies that they are likely to use in their future career. Materials and Methods: Twenty screencasts were prepared with Camtasia 2.0 software (TechSmith, Okemos, MI, USA). They included clinical history, videos of chest X-rays and/or chest computed tomography images, links to WSI digitized with an Aperio Turbo AT scanner (Leica Biosystems, Buffalo Grove, IL, USA), pre- and posttests, and faculty-narrated videos of the WSI in a manner closely resembling a slide seminar and other educational materials. Screencasts were saved in a hospital network,,, and The screencasts were viewed by 12 pathology residents and fellows who made diagnoses, answered the quizzes, and took a survey with questions designed to evaluate their perception of the quality of this technology. Quiz results were automatically e-mailed to faculty. Pre- and posttest results were compared using a paired t-test. Results: Screencasts can be viewed with Windows PC and Mac operating systems and mobile devices; only videos saved in our network and could be used to generate quizzes. Participants' feedback was very favorable with average scores ranging from 4.5 to 4.8 (on a scale of 5). Mean posttest scores (87.0% [±21.6%]) were significantly improved over those in the pretest quizzes (48.5% [±31.2%]) (P < 0.0001). Conclusion: Screencasts with WSI that allow residents and fellows to diagnose cases using digital microscopy may prove to be a useful technology to enhance the pathology education. Future studies with larger numbers of screencasts and participants are needed to optimize various teaching strategies.
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Review Article: Artificial intelligence and digital pathology: Challenges and opportunities
Hamid Reza Tizhoosh, Liron Pantanowitz
J Pathol Inform 2018, 9:38 (14 November 2018)
In light of the recent success of artificial intelligence (AI) in computer vision applications, many researchers and physicians expect that AI would be able to assist in many tasks in digital pathology. Although opportunities are both manifest and tangible, there are clearly many challenges that need to be overcome in order to exploit the AI potentials in computational pathology. In this paper, we strive to provide a realistic account of all challenges and opportunities of adopting AI algorithms in digital pathology from both engineering and pathology perspectives.
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Original Article: Implementing the DICOM standard for digital pathology
Markus D Herrmann, David A Clunie, Andriy Fedorov, Sean W Doyle, Steven Pieper, Veronica Klepeis, Long P Le, George L Mutter, David S Milstone, Thomas J Schultz, Ron Kikinis, Gopal K Kotecha, David H Hwang, Katherine P Andriole, A John Iafrate, James A Brink, Giles W Boland, Keith J Dreyer, Mark Michalski, Jeffrey A Golden, David N Louis, Jochen K Lennerz
J Pathol Inform 2018, 9:37 (2 November 2018)
Background: Digital Imaging and Communications in Medicine (DICOM®) is the standard for the representation, storage, and communication of medical images and related information. A DICOM file format and communication protocol for pathology have been defined; however, adoption by vendors and in the field is pending. Here, we implemented the essential aspects of the standard and assessed its capabilities and limitations in a multisite, multivendor healthcare network. Methods: We selected relevant DICOM attributes, developed a program that extracts pixel data and pixel-related metadata, integrated patient and specimen-related metadata, populated and encoded DICOM attributes, and stored DICOM files. We generated the files using image data from four vendor-specific image file formats and clinical metadata from two departments with different laboratory information systems. We validated the generated DICOM files using recognized DICOM validation tools and measured encoding, storage, and access efficiency for three image compression methods. Finally, we evaluated storing, querying, and retrieving data over the web using existing DICOM archive software. Results: Whole slide image data can be encoded together with relevant patient and specimen-related metadata as DICOM objects. These objects can be accessed efficiently from files or through RESTful web services using existing software implementations. Performance measurements show that the choice of image compression method has a major impact on data access efficiency. For lossy compression, JPEG achieves the fastest compression/decompression rates. For lossless compression, JPEG-LS significantly outperforms JPEG 2000 with respect to data encoding and decoding speed. Conclusion: Implementation of DICOM allows efficient access to image data as well as associated metadata. By leveraging a wealth of existing infrastructure solutions, the use of DICOM facilitates enterprise integration and data exchange for digital pathology.
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Original Article: Complete routine remote digital pathology services
Aleksandar Vodovnik, Mohammad Reza F. Aghdam
J Pathol Inform 2018, 9:36 (29 October 2018)
Background: Validation studies in digital pathology addressed so far diverse aspects of the routine work. We aimed to establish a complete remote digital pathology service. Methods: Altogether 2295 routine cases (8640 slides) were reported in our studies on digital versus microscopic diagnostics, remote reporting, diagnostic time, fine-needle aspiration cytology (FNAC) clinics, frozen sections, and diagnostic sessions with residents. The same senior pathologist was involved in all studies. Slides were scanned by ScanScope AT Turbo (Aperio). Digital images were accessed through the laboratory system (LS) on either 14” laptops or desktop computers with double 23” displays for the remote and on-site digital reporting. Larger displays were used when available for remote reporting. First diagnosis was either microscopic, digital, or remote digital only (6 months washout period). Both diagnoses were recorded separately and compared. Turnaround was measured from the registration to sign off or scanning to diagnosis. A diagnostic time was measured from the point slides were made available to the point of diagnosis or additional investigations were necessary, recorded independently in minutes/session, and compared. Jabber Video (Cisco) and Lync (Microsoft) were interchangeably used for the secure, video supervision of activities. Mobile phone, broadband, broadband over Wi-Fi, and mobile broadband were tested for internet connections. Nine autopsies were performed remotely involving three staff pathologists, one autopsy technician, and one resident over the secure video link. Remote and on-site pathologists independently interpreted and compared gross findings. Diverse benefits and technical aspects were studied using logs or information recorded in LS. Satisfaction surveys on diverse technical and professional aspects of the studies were conducted. Results: The full concordance between digital and light microscopic diagnosis was 99% (594/600 cases). A minor discordance, without clinical implications, was 1% (6/600 cases). The instant upload of digital images was achieved at 20 Mbps. Deference to microscopic slides and rescanning were under 1%. Average turnaround was shorter and percentage of cases reported up to 3 days higher for remote digital reporting. Larger displays improved the most user experience at magnifications over ×20. A digital diagnostic time was shorter than microscopic in 13 sessions. Four sessions with shorter microscopic diagnostic time included more cases requiring extensive use of magnifications over ×20. Independent interpretations of gross findings between remote and on-site pathologists yielded full agreement in the remote autopsies. Delays in reporting of frozen sections and FNAC due to scanning were clinically insignificant. Satisfaction levels with diverse technical and/or professional aspects of all studies were high. Conclusions: Complete routine remote digital pathology services are found feasible in hands of experienced staff. The introduction of digital pathology has improved provisions and organizations of our pathology services in histology, cytology, and autopsy including teaching and interdepartmental collaboration.
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Original Article: Network analysis of autopsy diagnoses: Insights into the “cause of death” from unbiased disease clustering
Romulo Celli, Miguel Divo, Monica Colunga, Bartolome Celli, Kisha Anne Mitchell-Richards
J Pathol Inform 2018, 9:35 (9 October 2018)
Background: Autopsies usually serve to inform specific “causes of death” and associated mechanisms. However, multiple diseases can co-exist and interact leading to a final demise. We approached autopsy-produced data using network analysis in an unbiased fashion to inform about interaction among different diseases and identify possible targets of system-level health care. Methods: Reports of 261 full autopsies from one institution between 2011 and 2013 were reviewed. Comorbidities were recorded and their Spearman's association coefficients were calculated. Highly associated comorbidities (P < 0.01) were selected to construct a network in which each disease is represented by a node, and each link between the nodes represents significant co-occurrence. Results: The network comprised 140 diseases connected by 419 links. The mean number of connections per node was 6. The most highly connected nodes (“hubs”) represented infectious processes, whereas less connected nodes represented neoplasms and other chronic diseases. Eight clusters of biologically plausible associated diseases were identified. Conclusions: There is an unbiased relationship among autopsy-identified diseases. There were “hubs” (primarily infectious) with significantly more associations than others that could represent obligatory or important modulators of the final expression of other diseases. Clusters of co-occurring diseases, or “modules,” suggest the presence of clinically relevant presentations of pathobiologically related entities which are until now considered individual diseases. These modules may occur together prior to death and be amenable to interventions during life.
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Original Article: Validation of remote digital frozen sections for cancer and transplant intraoperative services
Luca Cima, Matteo Brunelli, Anil Parwani, Ilaria Girolami, Andrea Ciangherotti, Giulio Riva, Luca Novelli, Francesca Vanzo, Alessandro Sorio, Vito Cirielli, Mattia Barbareschi, Antonietta D'Errico, Aldo Scarpa, Chiara Bovo, Filippo Fraggetta, Liron Pantanowitz, Albino Eccher
J Pathol Inform 2018, 9:34 (9 October 2018)
Introduction: Whole-slide imaging (WSI) technology can be used for primary diagnosis and consultation, including intraoperative (IO) frozen section (FS). We aimed to implement and validate a digital system for the FS evaluation of cancer and transplant specimens following recommendations of the College of American Pathologists. Materials and Methods: FS cases were routinely scanned at ×20 employing the “Navigo” scanner system. IO diagnoses using glass versus digital slides after a 3-week washout period were recorded. Intraobserver concordance was evaluated using accuracy rate and kappa statistics. Feasibility of WSI diagnoses was assessed by the way of sensitivity, specificity, as well as positive and negative predictive values. Participants also completed a survey denoting scan time, time spent viewing cases, preference for glass versus WSI, image quality, interface experience, and any problems encountered. Results: Of the 125 cases submitted, 121 (436 slides) were successfully scanned including 93 oncological and 28 donor-organ FS biopsies. Four cases were excluded because of failed digitalization due to scanning problems or sample preparation artifacts. Full agreement between glass and digital-slide diagnosis was obtained in 90 of 93 (97%, κ = 0.96) oncology and in 24 of 28 (86%, κ = 0.91) transplant cases. There were two major and one minor discrepancy for cancer cases (sensitivity 100%, specificity 96%) and two major and two minor disagreements for transplant cases (sensitivity 96%, specificity 75%). Average scan and viewing/reporting time were 12 and 3 min for cancer cases, compared to 18 and 5 min for transplant cases. A high diagnostic comfort level among pathologists emerged from the survey. Conclusions: These data demonstrate that the “Navigo” digital WSI system can reliably support an IO FS service involving complicated cancer and transplant cases.
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Symposium: Innovation in transplantation: The digital era
Albino Eccher, Matteo Brunelli, Liron Pantanowitz, Anil Parwani, Ilaria Girolami, Aldo Scarpa
J Pathol Inform 2018, 9:33 (27 September 2018)
DOI:10.4103/jpi.jpi_55_18  PMID:30294502
The international symposium entitled “Innovation in Transplantation: The Digital Era” took place on June 7 and 8, 2018 in Verona, Italy. This meeting was borne out of the productive collaboration between the Universities and Hospital Trusts of Verona and Padua in Italy, in the context of a vast regional project called Research and innovation project within the Health Technology Assessment. The project aimed to create an innovative digital platform for teleconsultation and delivering diagnostic second opinions in the field of organ transplantation within the Veneto region. This conference brought together pathologists, health informatics leaders, clinicians, researchers, vendors, and health-care planners from all around the globe. The symposium was conceived to promote the exchange of knowledge and kindle fertile discussion among the 130 attendees from 15 different countries. This article conveys the highlights of this symposium.
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Original Article: Diagnostic performance of deep learning algorithms applied to three common diagnoses in dermatopathology
Thomas George Olsen, B Hunter Jackson, Theresa Ann Feeser, Michael N Kent, John C Moad, Smita Krishnamurthy, Denise D Lunsford, Rajath E Soans
J Pathol Inform 2018, 9:32 (27 September 2018)
DOI:10.4103/jpi.jpi_31_18  PMID:30294501
Background: Artificial intelligence is advancing at an accelerated pace into clinical applications, providing opportunities for increased efficiency, improved accuracy, and cost savings through computer-aided diagnostics. Dermatopathology, with emphasis on pattern recognition, offers a unique opportunity for testing deep learning algorithms. Aims: This study aims to determine the accuracy of deep learning algorithms to diagnose three common dermatopathology diagnoses. Methods: Whole slide images (WSI) of previously diagnosed nodular basal cell carcinomas (BCCs), dermal nevi, and seborrheic keratoses were annotated for areas of distinct morphology. Unannotated WSIs, consisting of five distractor diagnoses of common neoplastic and inflammatory diagnoses, were included in each training set. A proprietary fully convolutional neural network was developed to train algorithms to classify test images as positive or negative relative to ground truth diagnosis. Results: Artificial intelligence system accurately classified 123/124 (99.45%) BCCs (nodular), 113/114 (99.4%) dermal nevi, and 123/123 (100%) seborrheic keratoses. Conclusions: Artificial intelligence using deep learning algorithms is a potential adjunct to diagnosis and may result in improved workflow efficiencies for dermatopathologists and laboratories.
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Technical Note: Using heatmaps to identify opportunities for optimization of test utilization and care delivery
Yonah C Ziemba, Liya Lomsadze, Yehuda Jacobs, Tylis Y Chang, Nina Haghi
J Pathol Inform 2018, 9:31 (27 September 2018)
DOI:10.4103/jpi.jpi_7_18  PMID:30294500
Background: When a provider orders a test in a pattern that is substantially different than their peers, it may indicate confusion in the test name or inappropriate use of the test, which can be elucidated by initiating dialog between clinicians and the laboratory. However, the analysis of ordering patterns can be challenging. We propose a utilization index (UI) as a means to quantify utilization patterns for individual providers and demonstrate the use of heatmaps to identify opportunities for improvement. Materials and Methods: Laboratory test orders by all providers were extracted from the laboratory information system. Providers were grouped into cohorts based on the specialty and patient population. A UI was calculated for each provider's use of each test using the following formula: (UI = [provider volume of specific test/provider volume of all tests]/[cohort volume of specific test/cohort volume of all tests]). A heatmap was generated to compare each provider to their cohort. Results: This method identified several hot spots and was helpful in reducing confusion and overutilization. Conclusion: The UI is a useful measure of test ordering behavior, and heatmaps provide a clear visual illustration of the utilization indices. This information can be used to identify areas for improvement and initiate meaningful dialog with providers, which will ultimately bring improvement and reduction in costs. Our method is simple and uses resources that are widely available, making this method effective convenient for many other laboratories.
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Review Article: The human interface of biomedical informatics
Edward C Klatt
J Pathol Inform 2018, 9:30 (6 September 2018)
DOI:10.4103/jpi.jpi_39_18  PMID:30237909
Biomedical informatics is the science of information, where information is defined as data with meaning. This definition identifies a fundamental challenge for informaticians: connecting with the healthcare team by enabling the acquisition, retrieval, and processing of information within the cognitive capabilities of the human brain. Informaticians can become aware of the constraints involved with cognitive processing and with workplace factors that impact how information is acquired and used to facilitate an improved user interface providing information to healthcare teams. Constraints affecting persons in the work environment include as follows: (1) cognitive processing of information; (2) cognitive load and memory capacity; (3) stress-affecting cognition; (4) cognitive distraction, attention, and multitasking; (5) cognitive bias and flexibility; (6) communication barriers; and (7) workplace environment. The human brain has a finite cognitive load capacity for processing new information. Short-term memory has limited throughput for processing of new informational items, while long-term memory supplies immediate simultaneous access to multiple informational items. Visual long-term memories can be extensive and detailed. Attention may be task dependent and highly variable among persons and requires maintaining control over distracting information. Multitasking reduces the effectiveness of working memory applied to each task. Transfer of information from person to person, or machine to person, is subject to cognitive bias and environmental stressors. High-stress levels increase emotional arousal to reduce memory formation and retrieval. The workplace environment can impact cognitive processes and stress, so maintaining civility augments cognitive abilities. Examples of human-computer interfaces employing principles of cognitive informatics inform design of systems to enhance the user interface.
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Research Article: Conventional microscopical versus digital whole-slide imaging-based diagnosis of thin-layer cervical specimens: A validation study
Odille Bongaerts, Carla Clevers, Marij Debets, Daniëlle Paffen, Lisanne Senden, Kim Rijks, Linda Ruiten, Daisy Sie-Go, Paul J van Diest, Marius Nap
J Pathol Inform 2018, 9:29 (27 August 2018)
DOI:10.4103/jpi.jpi_28_18  PMID:30197818
Background: Whole-slide imaging (WSI) has been implemented in many areas of pathology, but primary diagnostics of cytological specimens are lagging behind. One of the objectives of viewing scanned whole-slide images from histological or cytological specimens is remote exchange of knowledge and expertise of professionals to increase diagnostic accuracy. We compared the scoring results of our team obtained in double readings of two different data sets: conventional light microscopy (CLM) versus CLM and CLM versus WSI. We hypothesized that WSI is noninferior to CLM for primary diagnostics of thin-layer cervical slides. Materials and Methods: First, we determined the concordance rate at different thresholds of the participating cytotechnicians by double reading with CLM of 500 thin-layer cervical slides (Cohort 1). Next, CLM was compared with WSI examination of another 505 thin-layer cervical slides (Cohort 2) scanned at ×20 in single focus plane. Finally, all major discordant cases of Cohort 1 were evaluated by an external expert in the field of gynecological cytology and of Cohort 2 in the weekly case meetings. Results: The overall concordance rate of Cohort 1 (CLM vs. CLM) was 97.8% (95% confidence interval [CI]: 96.0%–98.7%) and of Cohort 2 was 95.3% (95% CI: 93.0%–96.9%). Conclusion: Concordance rates of WSI versus CLM were comparable with those of CLM versus CLM. We have made a step forward paving the road to implementation of WSI also in routine diagnostic cytology.
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Original Article: Virtual autopsy as a screening test before traditional autopsy: The verona experience on 25 Cases
Vito Cirielli, Luca Cima, Federica Bortolotti, Murali Narayanasamy, Maria Pia Scarpelli, Olivia Danzi, Matteo Brunelli, Albino Eccher, Francesca Vanzo, Maria Chiara Ambrosetti, Ghassan El-Dalati, Peter Vanezis, Domenico De Leo, Franco Tagliaro
J Pathol Inform 2018, 9:28 (19 July 2018)
DOI:10.4103/jpi.jpi_23_18  PMID:30167343
Background: Interest has grown into the use of multidetector computed tomography (CT) and magnetic resonance imaging as an adjunct or alternative to the invasive autopsy. We sought to investigate these possibilities in postmortem CT scan using an innovative virtual autopsy approach. Methods: Twenty-five postmortem cases were scanned with the Philips Brilliance CT-64 and then underwent traditional autopsy. The images were interpreted by two blinded forensic pathologists assisted by a radiologist with the INFOPSY® Digital Autopsy Software System which provides three-dimensional images in Digital Imaging and Communications in Medicine format. Diagnostic validity of virtual autopsy (accuracy rate, sensitivity, specificity, and predictive values) and concordance between the two forensic pathologists (kappa intraobserver coefficients) were determined. Results: The causes of death at traditional autopsies were hemorrhage due to traumatic injuries (n = 8), respiratory failure (5), asphyxia due to drowning (4), asphyxia due to hanging or strangulation (2), heart failure (2), nontraumatic hemorrhage (1), and severe burns (1). In two cases, the cause of death could not be ascertained. In 15/23 (65%) cases, the cause of death diagnosed after virtual autopsy matched the diagnosis reported after traditional autopsy. In 8/23 cases (35%), traditional autopsy was necessary to establish the cause of death. Digital data provided relevant information for inferring both cause and manner of death in nine traumatic cases. The validity of virtual autopsy as a diagnostic tool was higher for traumatic deaths than other causes of death (accuracy 84%, sensitivity 82%, and specificity 86%). The concordance between the two forensic pathologists was almost perfect (>0.80). Conclusions: Our experience supports the use of virtual autopsy in postmortem investigations as an alternative diagnostic practice and does suggest a potential role as a screening test among traumatic deaths.
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Commentary: Will digital pathology be as disruptive as genomics?
Steven N Hart
J Pathol Inform 2018, 9:27 (19 July 2018)
DOI:10.4103/jpi.jpi_25_18  PMID:30167342
Digital pathology is the science of performing traditional pathological assessment in a digital environment. A digital transition is long overdue since histochemical analysis such as hematoxylin and eosin staining has remained unchanged in over 100 years. Importantly, the digitization of whole slide images further lends itself to advances in computational pathology and artificial intelligence to transform qualitative assessment into quantitative assessment. The impact of this transition from a computational infrastructure perspective is reminiscent of a similar transition in the field of genomics. In this article, I describe some of the similarities between genomics and digital pathology as well as highlight some key lessons learned to prevent the same mistakes and delays that slowed the genomics revolution.
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Research Article: A new software platform to improve multidisciplinary tumor board workflows and user satisfaction: A pilot study
Elizabeth A Krupinski, Merce Comas, Leia Garrote Gallego, on behalf of the GISMAR Group
J Pathol Inform 2018, 9:26 (19 July 2018)
DOI:10.4103/jpi.jpi_16_18  PMID:30167341
Background: Workflow and preparation for holding multidisciplinary cancer case reviews (i.e., Tumor Boards) is time-consuming and cumbersome. Use of a software platform might improve this process. This pilot study assessed the impact of a new software platform on tumor board preparation workflow and user satisfaction compared to current methods. Materials and Methods: Using current methods and the NAVIFY Tumor Board Solution, this study assessed the number of tasks and time to prepare tumor board cases. Participants completed online surveys assessing ease of use and satisfaction with current and new platforms. Results: A total of 41 sessions included two surgeons, two oncologists, two pathologists, and two radiologists preparing tumor board cases with 734 tasks were recorded. Overall, there was no difference in the number of tasks using either preparation method (341 current, 393 NAVIFY Tumor Board solution). There was a significant difference in overall preparation time as a function of specialty (F = 71.74, P < 0.0001), with oncologists, radiologists, and surgeons having reduced times with NAVIFY Tumor Board solution compared to the current platform and pathologists having equivalent times. There was a significant difference (F = 38.98, P < 0.0001) for times as a function of task category. Review of clinical course data and other preparation tasks decreased significantly, but pathology and radiology review did not differ significantly. The new platform received higher ratings than the current methods on all survey questions regarding the ease of use and satisfaction. Conclusions: The study supported the hypothesis that the new software platform can improve Tumor Board preparation. Further study is needed to assess the impact of this platform in different hospitals, different data storage systems, with different observers, and different types of Tumor board cases as well as its impact on the quality of the tumor board discussion.
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Book Review: Deep learning for medical image analysis
Caglar Senaras, Metin Nafi Gurcan
J Pathol Inform 2018, 9:25 (25 June 2018)
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Technical Note: Interfacing complex laboratory instruments during a change to epic beaker
Gregory David Scott, Cary Schrandt, Chandler C Ho, Michael C Chung, Daniel Zhou, Run Zhang Shi
J Pathol Inform 2018, 9:24 (25 June 2018)
DOI:10.4103/jpi.jpi_21_18  PMID:30034922
Background: Implementing a laboratory-developed test sometimes requires incorporating an unconventional device into the laboratory information system (LIS) and customizing an interface to reduce transcription error and improve turnaround time. Such a custom interface is a necessity for complicated high-volume tests such as 25-OH Vitamin D by liquid chromatography-tandem mass spectrometry (LC-MS/MS) when there is no vendor-or LIS-supplied interface available. Here, we describe our work and experience interfacing a API 5000 LC-MS/MS instrument with our newly implemented LIS, Epic Beaker, using a combination of in-house scripting software and a middleware vendor, Data Innovations. Materials and Methods: For input interfacing, custom scripting software was developed to transcribe batched order lists generated by Epic into files usable by the instrument software, Analyst®. For output interfacing, results from the LC-MS/MS system were fed to a unidirectional instrument driver made by Data Innovations and selected data were transferred to the LIS. Results: Creation and validation of a new driver by Data Innovations took approximately 6 months. The interface was adopted for 25-OH Vitamin D and testosterone testing during periods of increasing test volume (4.5-fold over 8 years and 1.25-fold over 5 years). The amount of time spent reporting 25-OH Vitamin D results decreased 82% per order resulting in a savings of 1370 technician work hours and the amount of time spent reporting testosterone results decreased 75% per order resulting in a savings of 400 technician work hours. Conclusions: A mixed model using custom scripting and curated commercial middleware serve as a durable interface solution for laboratory instrumentation such as an LC-MS/MS and are flexible to future changes in instrument software, networking protocols, and the scope of LISs and work area managers.
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Commentary: Next-generation sequencing bioinformatics: Guidance between the sequencing and sign out
Jeffrey Szymanski, Eric Duncavage, John Pfeifer
J Pathol Inform 2018, 9:23 (25 June 2018)
DOI:10.4103/jpi.jpi_19_18  PMID:30034921
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Commentary: Commentary: What can augmented reality do for you?
Emilio Madrigal
J Pathol Inform 2018, 9:22 (13 June 2018)
DOI:10.4103/jpi.jpi_22_18  PMID:30034920
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Brief Report: Machine learning provides an accurate classification of diffuse large b-cell lymphoma from immunohistochemical Data
Carlos Bruno Tavares Da Costa
J Pathol Inform 2018, 9:21 (13 June 2018)
DOI:10.4103/jpi.jpi_14_18  PMID:30034919
Background: The classification of diffuse large B-cell lymphomas into Germinal Center (GCB) and non-GC subtypes defines disease subgroups which are different both in terms of gene expression and prognosis. Given their clinical significance, several classification algorithms have been designed, some by making use of widely availability immunohistochemical techniques. Despite their high concordance with gene expression profiles (GEP) and prognostic value, these algorithms were based on technical and biological assumptions that could be improved in terms of performance for classification. Methods: In order to overcome this limitation, a new algorithm was obtained by analyzing a previously published dataset of 475 patients by using an automatic classification tree method. Results: The resulting algorithm classifies correctly 91.6% of the cases when compared to GEP, displaying a Receiver-Operator Characteristic (ROC) area under the curve of 0.934. Noteworthy features of this algorithm include the capability to classify GEP-unclassifiable cases and a significant prognostic value, both in terms of overall survival (60 months for non-GC vs not reached for GCB, P = 0.007) and progression-free survival (61.9 months vs not reached, P = 0.017). Conclusion: By using a machine learning classification method that avoids most pre-assumptions, the novel algorithm obtained is accurate and maintains relevant features for clinical implementation.
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Technical Note: Optimized JPEG 2000 compression for efficient storage of histopathological whole-Slide images
Henrik Helin, Teemu Tolonen, Onni Ylinen, Petteri Tolonen, Juha Näpänkangas, Jorma Isola
J Pathol Inform 2018, 9:20 (25 May 2018)
DOI:10.4103/jpi.jpi_69_17  PMID:29910969
Background: Whole slide images (WSIs, digitized histopathology glass slides) are large data files whose long-term storage remains a significant cost for pathology departments. Currently used WSI formats are based on lossy image compression alogrithms, either using JPEG or its more efficient successor JPEG 2000. While the advantages of the JPEG 2000 algorithm (JP2) are commonly recognized, its compression parameters have not been fully optimized for pathology WSIs. Methods: We defined an optimized parametrization for JPEG 2000 image compression, designated JP2-WSI, to be used specifically with histopathological WSIs. Our parametrization is based on allowing a very high degree of compression on the background part of the WSI while using a conventional amount of compression on the tissue-containing part of the image, resulting in high overall compression ratios. Results: When comparing the compression power of JP2-WSI to the commonly used fixed 35:1 compression ratio JPEG 2000 and the default image formats of proprietary Aperio, Hamamatsu, and 3DHISTECH scanners, JP2-WSI produced the smallest file sizes and highest overall compression ratios for all 17 slides tested. The image quality, as judged by visual inspection and peak signal-to-noise ratio (PSNR) measurements, was equal to or better than the compared image formats. The average file size by JP2-WSI amounted to 15, 9, and 16 percent, respectively, of the file sizes of the three commercial scanner vendors' proprietary file formats (3DHISTECH MRXS, Aperio SVS, and Hamamatsu NDPI). In comparison to the commonly used 35:1 compressed JPEG 2000, JP2-WSI was three times more efficient. Conclusions: JP2-WSI allows very efficient and cost-effective data compression for whole slide images without loss of image information required for histopathological diagnosis.
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Technical Note: Utilization of open source technology to create cost-effective microscope camera systems for teaching
Anil Reddy Konduru, Balasaheb R Yelikar, KV Sathyashree, Ankur Kumar
J Pathol Inform 2018, 9:19 (25 May 2018)
DOI:10.4103/jpi.jpi_15_18  PMID:29910968
Background: Open source technologies and mobile innovations have radically changed the way people interact with technology. These innovations and advancements have been used across various disciplines and already have a significant impact. Microscopy, with focus on visually appealing contrasting colors for better appreciation of morphology, forms the core of the disciplines such as Pathology, microbiology, and anatomy. Here, learning happens with the aid of multi-head microscopes and digital camera systems for teaching larger groups and in organizing interactive sessions for students or faculty of other departments. Methods: The cost of the original equipment manufacturer (OEM) camera systems in bringing this useful technology at all the locations is a limiting factor. To avoid this, we have used the low-cost technologies like Raspberry Pi, Mobile high definition link and 3D printing for adapters to create portable camera systems. Results: Adopting these open source technologies enabled us to convert any binocular or trinocular microscope be connected to a projector or HD television at a fraction of the cost of the OEM camera systems with comparable quality. Conclusion: These systems, in addition to being cost-effective, have also provided the added advantage of portability, thus providing the much-needed flexibility at various teaching locations.
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Original Article: Can text-search methods of pathology reports accurately identify patients with rectal cancer in large administrative databases? Highly accessed article
Reilly P Musselman, Deanna Rothwell, Rebecca C Auer, Husein Moloo, Robin P Boushey, Carl van Walraven
J Pathol Inform 2018, 9:18 (2 May 2018)
DOI:10.4103/jpi.jpi_71_17  PMID:29862128
Background: The aim of this study is to derive and to validate a cohort of rectal cancer surgical patients within administrative datasets using text-search analysis of pathology reports. Materials and Methods: A text-search algorithm was developed and validated on pathology reports from 694 known rectal cancers, 1000 known colon cancers, and 1000 noncolorectal specimens. The algorithm was applied to all pathology reports available within the Ottawa Hospital Data Warehouse from 1996 to 2010. Identified pathology reports were validated as rectal cancer specimens through manual chart review. Sensitivity, specificity, and positive predictive value (PPV) of the text-search methodology were calculated. Results: In the derivation cohort of pathology reports (n = 2694), the text-search algorithm had a sensitivity and specificity of 100% and 98.6%, respectively. When this algorithm was applied to all pathology reports from 1996 to 2010 (n = 284,032), 5588 pathology reports were identified as consistent with rectal cancer. Medical record review determined that 4550 patients did not have rectal cancer, leaving a final cohort of 1038 rectal cancer patients. Sensitivity and specificity of the text-search algorithm were 100% and 98.4%, respectively. PPV of the algorithm was 18.6%. Conclusions: Text-search methodology is a feasible way to identify all rectal cancer surgery patients through administrative datasets with high sensitivity and specificity. However, in the presence of a low pretest probability, text-search methods must be combined with a validation method, such as manual chart review, to be a viable approach.
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Research Article: Convolutional deep belief network with feature encoding for classification of neuroblastoma histological images Highly accessed article
Soheila Gheisari, Daniel R Catchpoole, Amanda Charlton, Paul J Kennedy
J Pathol Inform 2018, 9:17 (2 May 2018)
DOI:10.4103/jpi.jpi_73_17  PMID:29862127
Background: Neuroblastoma is the most common extracranial solid tumor in children younger than 5 years old. Optimal management of neuroblastic tumors depends on many factors including histopathological classification. The gold standard for classification of neuroblastoma histological images is visual microscopic assessment. In this study, we propose and evaluate a deep learning approach to classify high-resolution digital images of neuroblastoma histology into five different classes determined by the Shimada classification. Subjects and Methods: We apply a combination of convolutional deep belief network (CDBN) with feature encoding algorithm that automatically classifies digital images of neuroblastoma histology into five different classes. We design a three-layer CDBN to extract high-level features from neuroblastoma histological images and combine with a feature encoding model to extract features that are highly discriminative in the classification task. The extracted features are classified into five different classes using a support vector machine classifier. Data: We constructed a dataset of 1043 neuroblastoma histological images derived from Aperio scanner from 125 patients representing different classes of neuroblastoma tumors. Results: The weighted average F-measure of 86.01% was obtained from the selected high-level features, outperforming state-of-the-art methods. Conclusion: The proposed computer-aided classification system, which uses the combination of deep architecture and feature encoding to learn high-level features, is highly effective in the classification of neuroblastoma histological images.
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Technical Note: A method for the interpretation of flow cytometry data using genetic algorithms
Cesar Angeletti
J Pathol Inform 2018, 9:16 (20 April 2018)
DOI:10.4103/jpi.jpi_76_17  PMID:29770255
Background: Flow cytometry analysis is the method of choice for the differential diagnosis of hematologic disorders. It is typically performed by a trained hematopathologist through visual examination of bidimensional plots, making the analysis time-consuming and sometimes too subjective. Here, a pilot study applying genetic algorithms to flow cytometry data from normal and acute myeloid leukemia subjects is described. Subjects and Methods: Initially, Flow Cytometry Standard files from 316 normal and 43 acute myeloid leukemia subjects were transformed into multidimensional FITS image metafiles. Training was performed through introduction of FITS metafiles from 4 normal and 4 acute myeloid leukemia in the artificial intelligence system. Results: Two mathematical algorithms termed 018330 and 025886 were generated. When tested against a cohort of 312 normal and 39 acute myeloid leukemia subjects, both algorithms combined showed high discriminatory power with a receiver operating characteristic (ROC) curve of 0.912. Conclusions: The present results suggest that machine learning systems hold a great promise in the interpretation of hematological flow cytometry data.
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Letter: Patient portal access to diagnostic test results
Beuy Joob, Viroj Wiwanitkit
J Pathol Inform 2018, 9:15 (20 April 2018)
DOI:10.4103/jpi.jpi_13_18  PMID:29770254
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Original Article: Career paths of pathology informatics fellowship alumni
Joseph W Rudolf, Christopher A Garcia, Matthew G Hanna, Christopher L Williams, Ulysses G Balis, Liron Pantanowitz, J Mark Tuthill, John R Gilbertson
J Pathol Inform 2018, 9:14 (9 April 2018)
DOI:10.4103/jpi.jpi_66_17  PMID:29721362
Background: The alumni of today's Pathology Informatics and Clinical Informatics fellowships fill diverse roles in academia, large health systems, and industry. The evolving training tracks and curriculum of Pathology Informatics fellowships have been well documented. However, less attention has been given to the posttraining experiences of graduates from informatics training programs. Here, we examine the career paths of subspecialty fellowship-trained pathology informaticians. Methods: Alumni from four Pathology Informatics fellowship training programs were contacted for their voluntary participation in the study. We analyzed various components of training, and the subsequent career paths of Pathology Informatics fellowship alumni using data extracted from alumni provided curriculum vitae. Results: Twenty-three out of twenty-seven alumni contacted contributed to the study. A majority had completed undergraduate study in science, technology, engineering, and math fields and combined track training in anatomic and clinical pathology. Approximately 30% (7/23) completed residency in a program with an in-house Pathology Informatics fellowship. Most completed additional fellowships (15/23) and many also completed advanced degrees (10/23). Common primary posttraining appointments included chief medical informatics officer (3/23), director of Pathology Informatics (10/23), informatics program director (2/23), and various roles in industry (3/23). Many alumni also provide clinical care in addition to their informatics roles (14/23). Pathology Informatics alumni serve on a variety of institutional committees, participate in national informatics organizations, contribute widely to scientific literature, and more than half (13/23) have obtained subspecialty certification in Clinical Informatics to date. Conclusions: Our analysis highlights several interesting phenomena related to the training and career trajectory of Pathology Informatics fellowship alumni. We note the long training track alumni complete in preparation for their careers. We believe flexible training pathways combining informatics and clinical training may help to alleviate the burden. We highlight the importance of in-house Pathology Informatics fellowships in promoting interest in informatics among residents. We also observe the many important leadership roles in academia, large community health systems, and industry available to early career alumni and believe this reflects a strong market for formally trained informaticians. We hope this analysis will be useful as we continue to develop the informatics fellowships to meet the future needs of our trainees and discipline.
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Technical Note: Constant quest for quality: Digital cytopathology
Simone L Van Es, Janelle Greaves, Stephanie Gay, Jennifer Ross, Derek Holzhauser, Tony Badrick
J Pathol Inform 2018, 9:13 (9 April 2018)
DOI:10.4103/jpi.jpi_6_18  PMID:29721361
Background: Special consideration should be given when creating and selecting cytopathology specimens for digitization to maximize quality. Advances in scanning and viewing technology can also improve whole-slide imaging (WSI) output quality. Methods: Accumulated laboratory experience with digitization of glass cytopathology slides was collected. Results: This paper describes characteristics of a cytopathology glass slide that can reduce quality on resulting WSI. Important points in the glass cytopathology slide selection process, preparation, scanning, and WSI-editing process that will maximize the quality of the resulting acquired digital image are covered. The paper outlines scanning solutions which have potential to predict issues with a glass cytopathology slide before image acquisition, allowing for adjustment of the scanning approach. WSI viewing solutions that better simulate the traditional microscope experience are also discussed. Conclusion: In addition to taking advantage of technical advances, practical steps can taken to maximize quality of cytopathology WSI.
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View Point: Psychological aspects of utilizing telecytology for rapid on-site adequacy assessments
Aparna Mahajan, Suzanne Selvaggi, Liron Pantanowitz
J Pathol Inform 2018, 9:12 (9 April 2018)
DOI:10.4103/jpi.jpi_2_18  PMID:29721360
Rapid On-Site Evaluation (ROSE) has been well documented in its ability to improve the diagnostic yield and accuracy of fine needle aspirations across many sites, resulting in better quality of patient management and a simultaneous reduction in treatment costs. Telecytology makes it possible for cytology laboratories to offer ROSE in a cost effective manner, whilst employing only a small number of trained cytopathologists to cover many sites from a single connected location. However, the adoption of telecytology for ROSE has been lackluster. We believe that this reluctance is not only due to barriers such as technology limitations and financial obstacles, but also due to overlooked psychological factors. This article discusses the unaddressed psychological considerations of telecytology for ROSE.
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Erratum: Erratum: Preconceived stakeholders' attitude toward telepathology: Implications for successful implementation

J Pathol Inform 2018, 9:11 (2 April 2018)
DOI:10.4103/2153-3539.228968  PMID:29692429
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Technical Note: Implementation of a mobile clinical decision support application to augment local antimicrobial stewardship
Brian M Hoff, Diana C Ford, Dilek Ince, Erika J Ernst, Daniel J Livorsi, Brett H Heintz, Vincent Masse, Michael J Brownlee, Bradley A Ford
J Pathol Inform 2018, 9:10 (2 April 2018)
DOI:10.4103/jpi.jpi_77_17  PMID:29692947
Background: Medical applications for mobile devices allow clinicians to leverage microbiological data and standardized guidelines to treat patients with infectious diseases. We report the implementation of a mobile clinical decision support (CDS) application to augment local antimicrobial stewardship. Methods: We detail the implementation of our mobile CDS application over 20 months. Application utilization data were collected and evaluated using descriptive statistics to quantify the impact of our implementation. Results: Project initiation focused on engaging key stakeholders, developing a business case, and selecting a mobile platform. The preimplementation phase included content development, creation of a pathway for content approval within the hospital committee structure, engaging clinical leaders, and formatting the first version of the guide. Implementation involved a media campaign, staff education, and integration within the electronic medical record and hospital mobile devices. The postimplementation phase required ongoing quality improvement, revision of outdated content, and repeated staff education. The evaluation phase included a guide utilization analysis, reporting to hospital leadership, and sustainability and innovation planning. The mobile application was downloaded 3056 times and accessed 9259 times during the study period. The companion web viewer was accessed 8214 times. Conclusions: Successful implementation of a customizable mobile CDS tool enabled our team to expand beyond microbiological data to clinical diagnosis, treatment, and antimicrobial stewardship, broadening our influence on antimicrobial prescribing and incorporating utilization data to inspire new quality and safety initiatives. Further studies are needed to assess the impact on antimicrobial utilization, infection control measures, and patient care outcomes.
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Original Article: Electronic p-Chip-based system for identification of glass slides and tissue cassettes in histopathology laboratories
Wlodek Mandecki, Jay Qian, Katie Gedzberg, Maryanne Gruda, Efrain Frank Rodriguez, Leslie Nesbitt, Michael Riben
J Pathol Inform 2018, 9:9 (2 April 2018)
DOI:10.4103/jpi.jpi_64_17  PMID:29692946
Background: The tagging system is based on a small, electronic, wireless, laser-light-activated microtransponder named “p-Chip.” The p-Chip is a silicon integrated circuit, the size of which is 600 μm × 600 μm × 100 μm. Each p-Chip contains a unique identification code stored within its electronic memory that can be retrieved with a custom reader. These features allow the p-Chip to be used as an unobtrusive and scarcely noticeable ID tag on glass slides and tissue cassettes. Methods: The system is comprised of p-Chip-tagged sample carriers, a dedicated benchtop p-Chip ID reader that can accommodate both objects, and an additional reader (the Wand), with an adapter for reading IDs of glass slides stored vertically in drawers. On slides, p-Chips are attached with adhesive to the center of the short edge, and on cassettes – embedded directly into the plastic. ID readout is performed by bringing the reader to the proximity of the chip. Standard histopathology laboratory protocols were used for testing. Results: Very good ID reading efficiency was observed for both glass slides and cassettes. When processed slides are stored in vertical filing drawers, p-Chips remain readable without the need to remove them from the storage location, thereby improving the speed of searches in collections. On the cassettes, the ID continues to be readable through a thin layer of paraffin. Both slides and tissue cassettes can be read with the same reader, reducing the need for redundant equipment. Conclusions: The p-Chip is stable to all chemical challenges commonly used in the histopathology laboratory, tolerates temperature extremes, and remains durable in long-term storage. The technology is compatible with laboratory information management systems software systems. The p-Chip system is very well suited for identification of glass slides and cassettes in the histopathology laboratory.
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Brief Report: Challenges in communication from referring clinicians to pathologists in the electronic health record era
Andrea Lynne Barbieri, Oluwole Fadare, Linda Fan, Hardeep Singh, Vinita Parkash
J Pathol Inform 2018, 9:8 (2 April 2018)
DOI:10.4103/jpi.jpi_70_17  PMID:29692945
We report on the role played by electronic health record inbox messages (EHRmsg) in a safety event involving pathology. Evolving socio-cultural norms led to the coopting of EHRmsg for alternate use and oversight of a clinician to pathologist request. We retrospectively examined EHR inbox messages to pathologists over a 3 month block. 36 messages from 22 pathologists were assessed. 26 pertained to patient care including requests for report corrections and additional testing. 88% of requests had gone unaddressed. Clinicians assumed that pathologists used EHRmsg as clinical care team members, however, pathologists rarely did. Communication gaps exist between primary clinicians and pathologists in the EHR era and they have potential to result in patient harm. Different sociocultural norms and practice patterns between specialties underlie some of the breakdowns. Health information technology implementation needs to proactively look for new sociotechnical failure modes to avoid patient harm from communication lapses.
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Letter: The case for an entropic simian in your laboratory: The case for laboratory information system failure scenario testing in the live production environment
Christopher L Williams, David S McClintock, Ulysses G J Balis
J Pathol Inform 2018, 9:7 (2 April 2018)
DOI:10.4103/jpi.jpi_96_16  PMID:29692944
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Editorial: Digital Imaging and Communications in Medicine Whole Slide Imaging Connectathon at Digital Pathology Association Pathology Visions 2017
David Clunie, Dan Hosseinzadeh, Mikael Wintell, David De Mena, Nieves Lajara, Marcial Garcia-Rojo, Gloria Bueno, Kiran Saligrama, Aaron Stearrett, David Toomey, Esther Abels, Frank Van Apeldoorn, Stephane Langevin, Sean Nichols, Joachim Schmid, Uwe Horchner, Bruce Beckwith, Anil Parwani, Liron Pantanowitz
J Pathol Inform 2018, 9:6 (5 March 2018)
DOI:10.4103/jpi.jpi_1_18  PMID:29619278
As digital pathology systems for clinical diagnostic work applications become mainstream, interoperability between these systems from different vendors becomes critical. For the first time, multiple digital pathology vendors have publicly revealed the use of the digital imaging and communications in medicine (DICOM) standard file format and network protocol to communicate between separate whole slide acquisition, storage, and viewing components. Note the use of DICOM for clinical diagnostic applications is still to be validated in the United States. The successful demonstration shows that the DICOM standard is fundamentally sound, though many lessons were learned. These lessons will be incorporated as incremental improvements in the standard, provide more detailed profiles to constrain variation for specific use cases, and offer educational material for implementers. Future Connectathon events will expand the scope to include more devices and vendors, as well as more ambitious use cases including laboratory information system integration and annotation for image analysis, as well as more geographic diversity. Users should request DICOM features in all purchases and contracts. It is anticipated that the growth of DICOM-compliant manufacturers will likely also ease DICOM for pathology becoming a recognized standard and as such the regulatory pathway for digital pathology products.
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Original Article: Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels
Sudhir Sornapudi, Ronald Joe Stanley, William V Stoecker, Haidar Almubarak, Rodney Long, Sameer Antani, George Thoma, Rosemary Zuna, Shelliane R Frazier
J Pathol Inform 2018, 9:5 (5 March 2018)
DOI:10.4103/jpi.jpi_74_17  PMID:29619277
Background: Advances in image analysis and computational techniques have facilitated automatic detection of critical features in histopathology images. Detection of nuclei is critical for squamous epithelium cervical intraepithelial neoplasia (CIN) classification into normal, CIN1, CIN2, and CIN3 grades. Methods: In this study, a deep learning (DL)-based nuclei segmentation approach is investigated based on gathering localized information through the generation of superpixels using a simple linear iterative clustering algorithm and training with a convolutional neural network. Results: The proposed approach was evaluated on a dataset of 133 digitized histology images and achieved an overall nuclei detection (object-based) accuracy of 95.97%, with demonstrated improvement over imaging-based and clustering-based benchmark techniques. Conclusions: The proposed DL-based nuclei segmentation Method with superpixel analysis has shown improved segmentation results in comparison to state-of-the-art methods.
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Original Article: Initial Assessments of E-learning modules in cytotechnology education
Maheswari S Mukherjee, Amber D Donnelly
J Pathol Inform 2018, 9:4 (14 February 2018)
DOI:10.4103/jpi.jpi_62_17  PMID:29531849
Background: Nine E-learning modules (ELMs) were developed in our program using Articulate software. This study assessed our cytotechnology (CT) students' perceptions on the content of the ELMs, and the perceived influence of the ELMs on students' performance during clinical rotations. Subjects and Methods: All CT students watched nine ELMs before the related classroom lecture and group discussion. Following that, students completed nine preclinical rotation surveys. After their clinical rotations, students completed nine postclinical rotation surveys. Results: Statements on the content of the ELMs regarding the quality of the video and audio, duration, navigation, and the materials presented, received positive responses from the majority of the students. While there were a few disagreements and neutral responses, most of the students responded positively saying that the ELMs better prepared them for their role, as well as helped them to better perform their roles during the clinical rotation. The majority of the students recommended developing more EMLs for cytology courses in the future Conclusions: This study has given hope that the ELMs have potential to enhance our online curriculum and benefit students, within the United States and internationally, who have no easy access to cytology clinical laboratories for hands-on training.
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Commentary: Commentary: Whole-slide Images – Good enough for primary diagnosis?
Thomas W Bauer
J Pathol Inform 2018, 9:3 (14 February 2018)
DOI:10.4103/jpi.jpi_72_17  PMID:29531848
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Review Article: A review on the applications of crowdsourcing in human pathology
Roshanak Alialy, Sasan Tavakkol, Elham Tavakkol, Amir Ghorbani-Aghbologhi, Alireza Ghaffarieh, Seon Ho Kim, Cyrus Shahabi
J Pathol Inform 2018, 9:2 (14 February 2018)
DOI:10.4103/jpi.jpi_65_17  PMID:29531847
The advent of the digital pathology has introduced new avenues of diagnostic medicine. Among them, crowdsourcing has attracted researchers' attention in the recent years, allowing them to engage thousands of untrained individuals in research and diagnosis. While there exist several articles in this regard, prior works have not collectively documented them. We, therefore, aim to review the applications of crowdsourcing in human pathology in a semi-systematic manner. We first, introduce a novel method to do a systematic search of the literature. Utilizing this method, we, then, collect hundreds of articles and screen them against a predefined set of criteria. Furthermore, we crowdsource part of the screening process, to examine another potential application of crowdsourcing. Finally, we review the selected articles and characterize the prior uses of crowdsourcing in pathology.
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Original Article: Enabling histopathological annotations on immunofluorescent images through virtualization of hematoxylin and eosin
Amal Lahiani, Eldad Klaiman, Oliver Grimm
J Pathol Inform 2018, 9:1 (14 February 2018)
DOI:10.4103/jpi.jpi_61_17  PMID:29531846
Context: Medical diagnosis and clinical decisions rely heavily on the histopathological evaluation of tissue samples, especially in oncology. Historically, classical histopathology has been the gold standard for tissue evaluation and assessment by pathologists. The most widely and commonly used dyes in histopathology are hematoxylin and eosin (H&E) as most malignancies diagnosis is largely based on this protocol. H&E staining has been used for more than a century to identify tissue characteristics and structures morphologies that are needed for tumor diagnosis. In many cases, as tissue is scarce in clinical studies, fluorescence imaging is necessary to allow staining of the same specimen with multiple biomarkers simultaneously. Since fluorescence imaging is a relatively new technology in the pathology landscape, histopathologists are not used to or trained in annotating or interpreting these images. Aims, Settings and Design: To allow pathologists to annotate these images without the need for additional training, we designed an algorithm for the conversion of fluorescence images to brightfield H&E images. Subjects and Methods: In this algorithm, we use fluorescent nuclei staining to reproduce the hematoxylin information and natural tissue autofluorescence to reproduce the eosin information avoiding the necessity to specifically stain the proteins or intracellular structures with an additional fluorescence stain. Statistical Analysis Used: Our method is based on optimizing a transform function from fluorescence to H&E images using least mean square optimization. Results: It results in high quality virtual H&E digital images that can easily and efficiently be analyzed by pathologists. We validated our results with pathologists by making them annotate tumor in real and virtual H&E whole slide images and we obtained promising results. Conclusions: Hence, we provide a solution that enables pathologists to assess tissue and annotate specific structures based on multiplexed fluorescence images.
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Original Article: Routine digital pathology workflow: The Catania experience
Filippo Fraggetta, Salvatore Garozzo, Gian Franco Zannoni, Liron Pantanowitz, Esther Diana Rossi
J Pathol Inform 2017, 8:51 (19 December 2017)
DOI:10.4103/jpi.jpi_58_17  PMID:29416914
Introduction: Successful implementation of whole slide imaging (WSI) for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. Methods: All (100%) permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D) barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Results: Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Conclusion: Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory.
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Original Article: Preconceived stakeholders' attitude toward telepathology: Implications for successful implementation
Elahe Gozali, Reza Safdari, Malihe Sadeghi, Marjan Ghazi Saeidi, Sharareh R Niakan Kalhori, Farahnaz Noroozinia, Zahra Zare Fazlollahi, Bahlol Rahimi
J Pathol Inform 2017, 8:50 (19 December 2017)
DOI:10.4103/jpi.jpi_59_17  PMID:29416913
Introduction: Telepathology is a subdiscipline of telemedicine. It has opened new horizons to pathology, especially to the field of organizing consultations. This study aims to determine the capabilities and equipment required for the implementation of telepathology from the viewpoints of managers, IT professionals, and pathologists of the hospitals of West Azerbaijan, Iran. Methods: This is a descriptive-analytical study conducted as a cross-sectional study in 2015. All public and private hospitals of West Azerbaijan were selected as the study sites. The population of the study was the managers, directors, pathologists, and IT professionals of the hospitals. The study population was considered as the study sample. Data were collected using questionnaires. The validity and reliability of the questionnaires were assessed, and data were analyzed using SPSS (Statistical Product and Services Solutions, version 16.0, SPSS Inc, Chicago, IL, USA). Results: The mean awareness of the study population of telepathology in the studied hospitals was 2.43 with a standard deviation of 0.89. According to analysis results (F = 7.211 and P = 0.001), in the studied hospitals, the mean awareness of pathologists, managers, directors, and IT professionals' of telepathology is significant. In addition, the mean awareness of pathologists is higher than that of managers, directors, and IT professionals, and this relation is significant (P = 0.001). According to IT professionals, among the influential dimensions of the implementation of telepathology in the studied hospitals, the effect of all dimensions, except hardware capabilities, was above moderate level. Conclusion: According to our findings, stakeholders believe that the implementation of telepathology promotes the quality of health-care services and caring patients on the one hand and decreases health-care costs on the other hand. Therefore, it crucial and important to consider users' viewpoints into the process of implementing such systems as they play a vital role in the success or failure, and the accurate estimation of required sources, of the systems.
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Commentary: Commentary: Improving the efficiency of the ova and parasite examination using cloud-based image analysis
Daniel D Rhoads
J Pathol Inform 2017, 8:49 (14 December 2017)
DOI:10.4103/jpi.jpi_63_17  PMID:29416912
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Original Article: Application of text information extraction system for real-time cancer case identification in an integrated healthcare organization
Fagen Xie, Janet Lee, Corrine E Munoz-Plaza, Erin E Hahn, Wansu Chen
J Pathol Inform 2017, 8:48 (14 December 2017)
DOI:10.4103/jpi.jpi_55_17  PMID:29416911
Background: Surgical pathology reports (SPR) contain rich clinical diagnosis information. The text information extraction system (TIES) is an end-to-end application leveraging natural language processing technologies and focused on the processing of pathology and/or radiology reports. Methods: We deployed the TIES system and integrated SPRs into the TIES system on a daily basis at Kaiser Permanente Southern California. The breast cancer cases diagnosed in December 2013 from the Cancer Registry (CANREG) were used to validate the performance of the TIES system. The National Cancer Institute Metathesaurus (NCIM) concept terms and codes to describe breast cancer were identified through the Unified Medical Language System Terminology Service (UTS) application. The identified NCIM codes were used to search for the coded SPRs in the back-end datastore directly. The identified cases were then compared with the breast cancer patients pulled from CANREG. Results: A total of 437 breast cancer concept terms and 14 combinations of “breast” and “cancer” terms were identified from the UTS application. A total of 249 breast cancer cases diagnosed in December 2013 was pulled from CANREG. Out of these 249 cases, 241 were successfully identified by the TIES system from a total of 457 reports. The TIES system also identified an additional 277 cases that were not part of the validation sample. Out of the 277 cases, 11% were determined as highly likely to be cases after manual examinations, and 86% were in CANREG but were diagnosed in months other than December of 2013. Conclusions: The study demonstrated that the TIES system can effectively identify potential breast cancer cases in our care setting. Identified potential cases can be easily confirmed by reviewing the corresponding annotated reports through the front-end visualization interface. The TIES system is a great tool for identifying potential various cancer cases in a timely manner and on a regular basis in support of clinical research studies.
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Technical Note: Implementation of epic beaker anatomic pathology at an academic medical center
John Larry Blau, Joseph D Wilford, Susan K Dane, Nitin J Karandikar, Emily S Fuller, Debbie J Jacobsmeier, Melissa A Jans, Elisabeth A Horning, Matthew D Krasowski, Bradley A Ford, Kent R Becker, Jeanine M Beranek, Robert A Robinson
J Pathol Inform 2017, 8:47 (14 December 2017)
DOI:10.4103/jpi.jpi_31_17  PMID:29387505
Background: Beaker is a relatively new laboratory information system (LIS) offered by Epic Systems Corporation as part of its suite of health-care software and bundled with its electronic medical record, EpicCare. It is divided into two modules, Beaker anatomic pathology (Beaker AP) and Beaker Clinical Pathology. In this report, we describe our experience implementing Beaker AP version 2014 at an academic medical center with a go-live date of October 2015. Methods: This report covers preimplementation preparations and challenges beginning in September 2014, issues discovered soon after go-live in October 2015, and some post go-live optimizations using data from meetings, debriefings, and the project closure document. Results: We share specific issues that we encountered during implementation, including difficulties with the proposed frozen section workflow, developing a shared specimen source dictionary, and implementation of the standard Beaker workflow in large institution with trainees. We share specific strategies that we used to overcome these issues for a successful Beaker AP implementation. Several areas of the laboratory-required adaptation of the default Beaker build parameters to meet the needs of the workflow in a busy academic medical center. In a few areas, our laboratory was unable to use the Beaker functionality to support our workflow, and we have continued to use paper or have altered our workflow. In spite of several difficulties that required creative solutions before go-live, the implementation has been successful based on satisfaction surveys completed by pathologists and others who use the software. However, optimization of Beaker workflows has continued to be an ongoing process after go-live to the present time. Conclusions: The Beaker AP LIS can be successfully implemented at an academic medical center but requires significant forethought, creative adaptation, and continued shared management of the ongoing product by institutional and departmental information technology staff as well as laboratory managers to meet the needs of the laboratory.
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