Background: Determining the site of origin for metastatic well-differentiated neuroendocrine tumors (WDNETs) is challenging, and immunohistochemical (IHC) profiles do not always lead to a definitive diagnosis. We sought to determine if a deep-learning convolutional neural network (CNN) could improve upon established IHC profiles in predicting the site of origin in a cohort of WDNETs from the common primary sites. Materials and Methods: Hematoxylin and eosin (H&E)-stained tissue microarrays (TMAs) were created using 215 WDNETs arising from the known primary sites. A CNN trained and tested on 60% (n = 130) and 40% (n = 85) of these cases, respectively. One hundred and seventy-nine cases had TMA tissue remaining for the IHC analysis. These cases were stained with IHC markers pPAX8, CDX2, SATB2, and thyroid transcription factor-1 (markers of pancreas/duodenum, ileum/jejunum/duodenum, colorectum/appendix, and lung WDNET sites of origin, respectively). The CNN diagnosis was deemed correct if it designated a majority or plurality of the tumor area as the known site of origin. The IHC diagnosis was deemed correct if the most specific marker for a particular site of origin met an H-score threshold determined by two pathologists. Results: When all cases were considered, the CNN correctly identified the site of origin at a lower rate compared to IHC (72% vs. 82%, respectively). Of the 85 cases in the CNN test set, 66 had sufficient TMA material for IHC stains, thus 66 cases were available for a direct case-by-case comparison of IHC versus CNN. The CNN correctly identified 70% of these cases, while IHC correctly identified 76%, a finding that was not statistically significant (P = 0.56). Conclusion: A CNN can identify WDNET site of origin at an accuracy rate close to the current gold standard IHC methods.

Background: Gross imaging of surgical specimens is paramount for the accurate gross examination and diagnosis of disease. Optimized imaging workflow can facilitate consistently high-quality gross photographs, especially in high-volume, metropolitan hospitals such as ours. Most commercial medical gross imaging technology provides ergonomically well-designed hardware, remotely operated cameras, intuitive software interfaces, and automation of workflow. However, these solutions are usually cost-prohibitive and require a large sum of capital budget. Materials and Methods: We applied lean techniques such as value stream mapping (VSM) to design a streamlined and error-free workflow for gross imaging process. We implemented a cost-effective technology, UniTwain, combined with high-resolution webcam to achieve the ideal results. Results: We reduced the mean process time from 600 min to 4.0 min (99.3% decrease in duration); the median process time was reduced from 580 min to 3.0 min. The process efficiency increased from 20% to 100%. The implemented solution has a comparable durability, scalability, and archiving feasibility to commercial medical imaging systems and costs four times less. The only limitations are manual operation of the webcam and lower resolution. The webcam sensors have 8.2 megapixel (MP) resolution, approximately 12 MP less than medical imaging devices. However, we believe that this difference is not visually significant and the effect on gross diagnosis with the naked eye is minimal. Conclusions: To our knowledge, this is the first study that utilized UniTwain as a viable, low-cost solution to streamline the gross imaging workflow. The UniTwain combined with high-resolution webcam could be a suitable alternative for our institution that does not plan to heavily invest in medical imaging.

Background: Whole-slide images (WSI) are produced by a high-resolution scanning of pathology glass slides. There are a large number of whole-slide imaging scanners, and the resulting images are frequently larger than 100,000 × 100,000 pixels which typically image 100,000 to one million cells, ranging from several hundred megabytes to many gigabytes in size. Aims and Objectives: Provide HTTP access over the web to Whole Slide Image tiles that do not have localized tiling servers but only basic HTTP access. Move all image decode and tiling functions to calling agent (ImageBox). Methods: Current software systems require tiling image servers to be installed on systems providing local disk access to these images. ImageBox2 breaks this requirement by accessing tiles from remote HTTP source via byte-level HTTP range requests. This method does not require changing the client software as the operation is relegated to the ImageBox2 server which is local (or remote) to the client and can access tiles from remote images that have no server of their own such as Amazon S3 hosted images. That is, it provides a data service [on a server that does not need to be managed], the definition of serverless execution model increasingly favored by cloud computing infrastructure. Conclusions: The specific methodology described and assessed in this report preserves normal client connection semantics by enabling cloud-friendly tiling, promoting a web of http connected whole-slide images from a wide-ranging number of sources, and providing tiling where local tiling servers would have been otherwise unavailable.

Introduction: The initial point in the diagnostic workup of solid tumors remains manual, with the assessment of hematoxylin and eosin (H&E)-stained tissue sections by microscopy. This is a labor-intensive step that requires attention to detail. In addition, diagnoses are influenced by an individual pathologist's knowledge and experience and may not always be reproducible between pathologists. Methods: We introduce a deep learning-based method in colorectal cancer detection and segmentation from digitized H&E-stained histology slides. Results: In this study, we demonstrate that this neural network approach produces median accuracy of 99.9% for normal slides and 94.8% for cancer slides compared to pathologist-based diagnosis on H&E-stained slides digitized from clinical samples. Conclusion: Given that our approach has very high accuracy on normal slides, use of neural network algorithms may provide a screening approach to save pathologist time in identifying tumor regions. We suggest that this new method may be a powerful assistant for colorectal cancer diagnostics.

Background: Whole-slide images (WSIs) as a kind of image data are rapidly growing in the digital pathology domain. With unusual high resolution, these images make them hard to be supported by conventional tools or file formats. Thus, it obstructs data sharing and automated analysis. Here, we propose a library, LibMI, along with its open and standardized image file format. They can be used together to efficiently read, write, modify, and annotate large images. Materials and Methods: LibMI utilizes the concept of pyramid image structure and lazy propagation from a segment tree algorithm to support reading and modifying and to guarantee that both operations have linear time complexity. Further, a cache mechanism was introduced to speed up the program. Results: LibMI is an open and efficient library for histopathological image processing. To demonstrate its functions, we applied it to several tasks including image thresholding, microscopic color correction, and storing pixel-wise information on WSIs. The result shows that libMI is particularly suitable for modifying large images. Furthermore, compared with congeneric libraries and file formats, libMI and modifiable multiscale image (MMSI) run 18.237 times faster on read-only tasks. Conclusions: The combination of libMI library and MMSI file format enables developers to efficiently read and modify WSIs, thus can assist in pixel-wise image processing on extremely large images to promote building image processing pipeline. The library together with the data schema is freely available on GitLab: https://gitlab.com/BioAI/libMI.

Unlocking the full potential of pathology data by gaining computational access to histological pixel data and metadata (digital pathology) is one of the key promises of computational pathology. Despite scientific progress and several regulatory approvals for primary diagnosis using whole-slide imaging, true clinical adoption at scale is slower than anticipated. In the U.S., advances in digital pathology are often siloed pursuits by individual stakeholders, and to our knowledge, there has not been a systematic approach to advance the field through a regulatory science initiative. The Alliance for Digital Pathology ( the Alliance) is a recently established, volunteer, collaborative, regulatory science initiative to standardize digital pathology processes to speed up innovation to patients. The purpose is: (1) to account for the patient perspective by including patient advocacy; (2) to investigate and develop methods and tools for the evaluation of effectiveness, safety, and quality to specify risks and benefits in the precompetitive phase; (3) to help strategize the sequence of clinically meaningful deliverables; (4) to encourage and streamline the development of ground-truth data sets for machine learning model development and validation; and (5) to clarify regulatory pathways by investigating relevant regulatory science questions. The Alliance accepts participation from all stakeholders, and we solicit clinically relevant proposals that will benefit the field at large. The initiative will dissolve once a clinical, interoperable, modularized, integrated solution (from tissue acquisition to diagnostic algorithm) has been implemented. In times of rapidly evolving discoveries, scientific input from subject-matter experts is one essential element to inform regulatory guidance and decision-making. The Alliance aims to establish and promote synergistic regulatory science efforts that will leverage diverse inputs to move digital pathology forward and ultimately improve patient care.

Background: To improve communication between clinical providers and the laboratory, we recently implemented secure text messaging for our critical value notifications. This was done to communicate laboratory critical values (CV) to providers faster so changes to patient care could be done faster. Our previous method of communicating CV to providers was paging and relied on a call back to receive the critical value. Methods: We implemented delivery of CV through a secure texting application in which the CV was directly communicated to the provider on their smart phone device. Results: The mean pre-implementation turnaround time (TAT) was 11.3 minutes (median: 7 minutes, range: 0 - 210 minutes). The mean post- secure text messaging implementation TAT was 3.03 minutes (median: 0.89 minutes, range: < 1 - 95 minutes).When comparing pre- and post-implementation, there was a significant reduction in the TAT from using secure text messaging (p < 0.001). Of the 234 surveys sent out, 81 providers responded (35%). Of these responses, 85% reported that critical value notification by secure text messaging has increased their efficiency and 95% reported that critical value notification is more effective than a pager-phone-call based system. 83% of providers reported that they were able to provide better, faster care to their patients. Conclusions: Using secure text messaging (STM) to deliver critical values significantly reduces the CV TAT. Furthermore, providers noted they preferred to receive CV notifications through STM and reported that they were able to provide more effective care to their patients.

Introduction: In this study, we report on our experience using digital pathology to overcome the severe limitations imposed on health care by the Covid-19 outbreak in Northern Italy. Social distancing had a major impact on public transportation, causing it to run with reduced timetables. This resulted in a major challenge for hospital commuters. To limit the presence in our hospital of no more than two pathologists at a time out of four, a web-based digital pathology system (DPS) was employed to work remotely. Subjects and Methods: We used a DPS in which a scanner, a laboratory information system, a storage device, and a web server were interfaced so that tissue slides could be viewed over the Internet by whole-slide imaging (WSI). After a brief internal verification test, the activity on the DPS was recorded, taking track of a set of performance and efficiency indicators. At the end of the study, 405 cases were signed out remotely. Results: Of 693 cases, 58.4% were signed out remotely by WSI, while 8.4% needed to be kept on hold to return to the original microscope slide. In three cases, at least one slide had to be rescanned. In eight cases, one slide was recut. Panel discussion by WSI was necessary in 34 cases, a condition in which all pathologists were asked for their opinion. A consultation with a more experienced colleague was necessary in 17 cases. Conclusions: We show that WSI easily allows pathologists to overcome the problems caused by the severe social distancing measures imposed by the Covid-19 pandemic. Our experience shows that soon there will not be alternatives to digital pathology, given that there is no assurance that other similar outbreaks will not occur.

Introduction: Teleneuropathology at our institution evolved over the last 17 years from using static to dynamic robotic microscopy. Historically (2003–2007), using older technology, the deferral rate was 19.7%, and the concordance was 81% with the final diagnosis. Two years ago, we switched to use hybrid robotic devices to perform these intraoperative (IO) consultations because our older devices were obsolete. The aim of this study was to evaluate the impact this change had on our deferral and concordance rates with teleneuropathology using this newer instrument. Materials and Methods: Aperio LV1 4-slide capacity hybrid robotic scanners with an attached desktop console (Leica Biosystems, Vista, CA, USA) and GoToAssist (v4.5.0.1620, Boston, MA, USA) were used for IO telepathology cases. A cross-sectional comparative study was conducted comparing teleneuropathology from three remote hospitals (193 cases) to IO neuropathology consultation performed by conventional glass slide examination at a light microscope (310 cases) from the host hospital. Deferral and concordance rates were compared to final histopathological diagnoses. Results: The deferral rate for IO teleneuropathology was 26% and conventional glass slide 24.24% (P = 0.58). The concordance rate for teleneuropathology was 93.94%, which was slightly higher than 89.09% for conventional glass slides (P = 0.047). Conclusion: The new hybrid robotic device for performing IO teleneuropathology interpretations at our institution was as effective as conventional glass slide interpretation. While we did observe a noticeable change in the deferral rate compared to prior years, we did appreciate the marked improvement of the concordance rate using this new hybrid scanner.

Background: Cervical screening could potentially be improved by better stratifying individual risk for the development of cervical cancer or precancer, possibly even allowing follow-up of individual patients differently than proposed under current guidelines that focus primarily on recent screening test results. We explore the use of a Bayesian decision science model to quantitatively stratify individual risk for the development of cervical squamous neoplasia. Materials and Methods: We previously developed a dynamic multivariate Bayesian network model that uses cervical screening and histopathologic data collected over 13 years in our system to quantitatively estimate the risk of individuals for the development of cervical precancer or invasive cervical cancer. The database includes 1,126,048 liquid-based cytology test results belonging to 389,929 women. From-the-vial, high risk human papilloma virus (HPV) test results and follow-up gynecological surgical procedures were available on 33.6% and 12% of these results (378,896 and 134,727), respectively. Results: Historical data impacted 5-year cumulative risk for both histopathologic cervical intraepithelial neoplasia 3 (CIN3) and squamous cell carcinoma (SCC) diagnoses. The risk was highest in patients with prior high grade squamous intraepithelial lesion cytology results. Persistent abnormal cervical screening test results, either cytologic or HPV results, were associated with variable increasing risk for squamous neoplasia. Risk also increased with prior histopathologic diagnoses of precancer, including CIN2, CIN3, and adenocarcinoma in situ. Conclusions: Bayesian modeling allows for individualized quantitative risk assessments of system patients for histopathologic diagnoses of significant cervical squamous neoplasia, including very rare outcomes such as SCC.

Health care is undergoing a profound transformation driven by an increase in new types of diagnostic data, increased data sharing enabled by interoperability, and improvements in our ability to interpret data through the application of artificial intelligence and machine learning. Paradoxically, we are also discovering that our current paradigms for implementing electronic health-care records and our ability to create new models for reforming the health-care system have fallen short of expectations. This article traces these shortcomings to two basic issues. The first is a reliance on highly centralized quality improvement and measurement strategies that fail to account for the high level of variation and complexity found in human disease. The second is a reliance on legacy payment systems that fail to reward the sharing of data and knowledge across the health-care system. To address these issues, and to better harness the advances in health care noted above, the health-care system must undertake a phased set of reforms. First, efforts must focus on improving both the diagnostic process and data sharing at the local level. These efforts should include the formation of diagnostic management teams and increased collaboration between pathologists and radiologists. Next, building off current efforts to develop national federated research databases, providers must be able to query national databases when information is needed to inform the care of a specific complex patient. In addition, providers, when treating a specific complex patient, should be enabled to consult nationally with other providers who have experience with similar patient issues. The goal of these efforts is to build a health-care system that is funded in part by a novel fee-for-knowledge-sharing paradigm that fosters a collaborative decentralized approach to patient care and financially incentivizes large-scale data and knowledge sharing.

Background: Little is known about the effect of a minimum number of slides required in generating image datasets used to build generalizable machine-learning (ML) models. In addition, the assumption within deep learning is that the increased number of training images will always enhance accuracy and that the initial validation accuracy of the models correlates well with their generalizability. In this pilot study, we have been able to test the above assumptions to gain a better understanding of such platforms, especially when data resources are limited. Methods: Using 10 colon histology slides (5 carcinoma and 5 benign), we were able to acquire 1000 partially overlapping images (Dataset A) that were then trained and tested on three convolutional neural networks (CNNs), ResNet50, AlexNet, and SqueezeNet, to build a large number of unique models for a simple task of classifying colon histopathology into benign and malignant. Different quantities of images (10–1000) from Dataset A were used to construct >200 unique CNN models whose performances were individually assessed. The performance of these models was initially assessed using 20% of Dataset A's images (not included in the training phase) to acquire their initial validation accuracy (internal accuracy) followed by their generalization accuracy on Dataset B (a very distinct secondary test set acquired from public domain online sources).Results: All CNNs showed similar peak internal accuracies (>97%) from the Dataset A test set. Peak accuracies for the external novel test set (Dataset B), an assessment of the ability to generalize, showed marked variation (ResNet50: 98%; AlexNet: 92%; and SqueezeNet: 80%). The models with the highest accuracy were not generated using the largest training sets. Further, a model's internal accuracy did not always correlate with its generalization accuracy. The results were obtained using an optimized number of cases and controls. Conclusions: Increasing the number of images in a training set does not always improve model accuracy, and significant numbers of cases may not always be needed for generalization, especially for simple tasks. Different CNNs reach peak accuracy with different training set sizes. Further studies are required to evaluate the above findings in more complex ML models prior to using such ancillary tools in clinical settings.

Background: Free-text sections of pathology reports contain the most important information from a diagnostic standpoint. However, this information is largely underutilized for computer-based analytics. The vast majority of NLP-based methods lack a capacity to accurately extract complex diagnostic entities and relationships among them as well as to provide an adequate knowledge representation for downstream data-mining applications. Methods: In this paper, we introduce a novel informatics pipeline that extends open information extraction (openIE) techniques with artificial intelligence (AI) based modeling to extract and transform complex diagnostic entities and relationships among them into Knowledge Graphs (KGs) of relational triples (RTs). Results: Evaluation studies have demonstrated that the pipeline's output significantly differs from a random process. The semantic similarity with original reports is high (Mean Weighted Overlap of 0.83). The precision and recall of extracted RTs based on experts' assessment were 0.925 and 0.841 respectively (P <0.0001). Inter-rater agreement was significant at 93.6% and inter-rated reliability was 81.8%. Conclusion: The results demonstrated important properties of the pipeline such as high accuracy, minimality and adequate knowledge representation. Therefore, we conclude that the pipeline can be used in various downstream data-mining applications to assist diagnostic medicine.

Background: Previous studies have demonstrated the noninferiority of pathologists' interpretation of whole slide images (WSIs) compared to microscopic slides in diagnostic surgical pathology; however, to our knowledge, no published studies have tested analytical precision of an entire WSI system. Methods: In this study, five pathologists at three locations tested intra-system, inter-system/site, and intra- and inter-pathologist precision of the Aperio AT2 DX System (Leica Biosystems, Vista, CA, USA). Sixty-nine microscopic slides containing 23 different morphologic features suggested by the Digital Pathology Association as important to diagnostic pathology were identified and scanned. Each of 202 unique fields of view (FOVs) had 1–3 defined morphologic features, and each feature was represented in three different tissues. For intra-system precision, each site scanned 23 slides at three different times and one pathologist interpreted all FOVs. For inter-system/site precision, all 69 slides were scanned once at each of three sites, and FOVs from each site were read by one pathologist. To test intra- and inter-pathologist precision, all 69 slides were scanned at one site, FOVs were saved in three different orientations, and the FOVs were transferred to a different site. Three different pathologists then interpreted FOVs from all 69 slides. Wildcard (unscored) slides and washout intervals were included in each study. Agreement estimates with 95% confidence intervals were calculated. Results: Combined precision from all three studies, representing 606 FOVs in each of the three studies, showed overall intra-system agreement of 97.9%; inter-system/site agreement was 96%, intra-pathologist agreement was 95%, and inter-pathologist agreement was 94.2%. Conclusions: Pathologists using the Aperio AT2 DX System identified histopathological features with high precision, providing increased confidence in using WSI for primary diagnosis in surgical pathology.

Introduction: Digital pathology has the potential to revolutionize the way clinical diagnoses are made while improving safety and quality. With a few notable exceptions in the UK, few National Health Service (NHS) departments have deployed digital pathology platforms. Thus, in the next few years, many departments are anticipated to undergo the transition to digital pathology. In this period of transition, capturing attitudes and experiences can elucidate issues to be addressed and foster collaboration between NHS Trusts. This study aims to qualitatively ascertain the benefits and challenges of transitioning to digital pathology from the perspectives of pathologists and biomedical scientists in a department about to undergo the transition from diagnostic reporting via traditional microscopy to digital pathology. Methods:A focus group discussion was held in the setting of a large NHS teaching hospital's cellular pathology department which was on the brink of transitioning to digital pathology. A set of open questions were developed and posed to a group of pathologists and biomedical scientists in a focus group setting. Notes of the discussion were made along with an audio recording with permission. The discussion was subsequently turned into a series of topic headings and analyzed using content analysis. Results:Identified benefits of digital pathology included enhanced collaboration, teaching, cost savings, research, growth of specialty, multidisciplinary teams, and patient-centered care. Barriers to transitioning to digital pathology included standardization, validation, national implementation, storage and backups, training, logistical implementation, cost-effectiveness, privacy, and legality. Conclusion:Many benefits of digital pathology were identified, but key barriers need to be addressed in order to fully implement digital pathology on a trust and national level.

Background:A common challenge in the development of laboratory clinical decision support (CDS) and laboratory utilization management (UM) initiatives stems from the fact that many laboratory tests have multiple potential indications, limiting the ability to develop context-specific alerts. As a potential solution, we designed a CDS alert that asks the ordering clinician to provide the indication for testing, using D-dimer as an exemplar. Using data collected over a nearly 3-year period, we sought to determine whether the indication capture was a useful feature within the CDS alert and whether it provided actionable intelligence to guide the development of an UM strategy. Methods: We extracted results and ordering data for D-dimer testing performed in our laboratory over a 35-month period. We analyzed order patterns by clinical indication, hospital service, and length of hospitalization. Results: Our final data set included 13,971 result-order combinations and indeed provided actionable intelligence regarding test utilization patterns. For example, pulmonary embolism was the most common emergency department indication (86%), while disseminated intravascular coagulation was the most common inpatient indication (56%). D-dimer positivity rates increased with the duration of hospitalization and our data suggested limited utility for ordering this test in the setting of suspected venous thromboembolic disease in admitted patients. In addition, we found that D-dimer was ordered for unexpected indications including the assessment of stroke, dissection, and extracorporeal membrane oxygenation. Conclusions: Indication capture within a CDS alert and correlation with result data can provide insight into order patterns which can be used to develop future CDS strategies to guide appropriate test use by clinical indication.

Background: The need for extending pathology diagnostic expertise to more areas is now being met by the maturation of technology that can effectively deliver this level of care. The experience and lessons learned from our successfully deployed International Telepathology Service (ITS) to a hospital system in China guided us in starting a domestic telepathology network, the California Telepathology Service (CTS). Many of the lessons learned from the ITS project informed our decision-making for the CTS. New challenges were recognized and overcome, such as addressing the complexity and cost–benefit tradeoffs involved in setting up a digital consultation system that competes with an established conventional glass slide delivery system. Methods: The CTS is based on a hub-and-spoke telepathology network using Leica Biosystems whole-slide image scanners and the eSlide Manager (eSM Version 12.3.3.7055, Leica Biosystems) digital image management software solution. The service currently comprises six spoke sites (UC San Diego [UCSD], UC Irvine [UCI], UC Davis, Northridge Hospital Medical Center [NHMC], Olive View Medical Center [OVMC], and Children's Hospital Los Angeles) and one central hub site (UCLA Medical Center). So far, five sites have been validated for telepathology case consultations following established practice guidelines, and four sites (UCI, UCSD, NHMC, and OVMC) have activated the service. Results: For the active spoke sites, we reviewed the volume, turnaround time (TAT), and case types and evaluated for utility and value. From May 2017 to July 2018, a total of 165 cases were submitted. Of note, digital consultations were particularly advantageous for preliminary kidney biopsy diagnoses (avg TAT 0.7 day). Conclusion: For spoke sites, telepathology provided shortened TAT and significant financial savings over hiring faculty with expertise to support a potentially low-volume service. For the hub site, the value includes exposure to educationally valuable cases, additional caseload volume to support specialized services, and improved communication with referring facilities over traditional carrier mail. The creation of a hub-and-spoke telepathology network is an expensive undertaking, and careful consideration needs to be given to support the needs of the clinical services, acquisition and effective deployment of the appropriate equipment, network requirements, and laboratory workflows to ensure a successful and cost-effective system.

Background: Recent studies show various cytomorphologic features that can assist in the differentiation of classic papillary thyroid carcinoma (cPTC) from noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP). Differentiating these two entities changes the clinical management significantly. We evaluated the performance of support vector machine (SVM), a machine learning algorithm, in differentiating cases of NIFTP and encapsulated follicular variant of papillary thyroid carcinoma with no capsular or lymphovascular invasion (EFVPTC) from cases of cPTC with the use of microscopic descriptions. SVM is a supervised learning algorithm used in classification problems. It assigns the input data to one of two categories by building a model based on a set of training examples (learning) and then using that learned model to classify new examples. Methods: Surgical pathology cases with the diagnosis of cPTC, NIFTP, and EFVPTC, were obtained from the laboratory information system. Only cases with existing fine-needle aspiration matching the tumor and available microscopic description were included. NIFTP cases with ipsilateral micro-PTC were excluded. The final cohort consisted of 59 cases (29 cPTCs and 30 NIFTP/EFVPTCs). Results: SVM successfully differentiated cPTC from NIFTP/EFVPTC 76.05 ± 0.96% of times (above chance,P < 0.05) with the sensitivity of 72.6% and specificity of 81.6% in detecting cPTC. Conclusions: This machine learning algorithm was successful in distinguishing NIFTP/EFVPTC from cPTC. Our results are compatible with the prior studies, which show cytologic features are helpful in differentiating these two entities. Furthermore, this study shows the power and potential of this approach for clinical use and in developing data-driven scoring systems, which can guide cytopathology and surgical pathology diagnosis.

Background: Pathology report defects refer to errors in the pathology reports, such as transcription/voice recognition errors and incorrect nondiagnostic information. Examples of the latter include incorrect gender, incorrect submitting physician, incorrect description of tissue blocks submitted, report formatting issues, and so on. Over the past 5 years, we have implemented computational algorithms to identify and correct these report defects. Materials and Methods: Report texts, tissue blocks submitted, and other relevant information are retrieved from the pathology information system database. Two complementary algorithms are used to identify the voice recognition errors by parsing the gross description texts to either (i) identify previously encountered error patterns or (ii) flag sentences containing previously-unused two-word sequences (bigrams). A third algorithm based on identifying conflicting information from two different sources is used to identify tissue block designation errors in the gross description; the information on actual block submission is compared with the block designation information parsed from the gross description text. Results: The computational algorithms identify voice recognition errors in approximately 8%–10% of the cases and block designation errors in approximately 0.5%–1% of all the cases. Conclusions: The algorithms described here have been effective in reducing pathology report defects. In addition to detecting voice recognition and block designation errors, these algorithms have also be used to detect other report defects, such as wrong gender, wrong provider, special stains or immunostains performed but not reported, and so on.

Background: The introduction of digital pathology into clinical practice has led to the development of clinical workflows with digital images, in connection with pathology reports. Still, most of the current work is time-consuming manual analysis of image areas at different scales. Links with data in the biomedical literature are rare, and a need for search based on visual similarity within whole slide images (WSIs) exists. Objectives: The main objective of the work presented is to integrate content-based visual retrieval with a WSI viewer in a prototype. Another objective is to connect cases analyzed in the viewer with cases or images from the biomedical literature, including the search through visual similarity and text. Methods: An innovative retrieval system for digital pathology is integrated with a WSI viewer, allowing to define regions of interest (ROIs) in images as queries for finding visually similar areas in the same or other images and to zoom in/out to find structures at varying magnification levels. The algorithms are based on a multimodal approach, exploiting both text information and content-based image features. Results: The retrieval system allows viewing WSIs and searching for regions that are visually similar to manually defined ROIs in various data sources (proprietary and public datasets, e.g., scientific literature). The system was tested by pathologists, highlighting its capabilities and suggesting ways to improve it and make it more usable in clinical practice. Conclusions: The developed system can enhance the practice of pathologists by enabling them to use their experience and knowledge to control artificial intelligence tools for navigating repositories of images for clinical decision support and teaching, where the comparison with visually similar cases can help to avoid misinterpretations. The system is available as open source, allowing the scientific community to test, ideate and develop similar systems for research and clinical practice.

Background: At our department, each specimen was assigned a tentative current procedural terminology (CPT) code at accessioning. The codes were subject to subsequent changes by pathologist assistants and pathologists. After the cases had been finalized, their CPT codes went through a final verification step by coding staff, with the aid of a keyword-based CPT code-checking web application. Greater than 97% of the initial assignments were correct. This article describes the construction of a CPT code-predicting neural network model and its incorporation into the CPT code-checking application. Materials and Methods: R programming language was used. Pathology report texts and CPT codes for the cases finalized during January 1–November 30, 2018, were retrieved from the database. The order of the specimens was randomized before the data were partitioned into training and validation set. R Keras package was used for both model training and prediction. The chosen neural network had a three-layer architecture consisting of a word-embedding layer, a bidirectional long short-term memory (LSTM) layer, and a densely connected layer. It used concatenated header-diagnosis texts as the input. Results: The model predicted CPT codes in both the validation data set and the test data set with an accuracy of 97.5% and 97.6%, respectively. Closer examination of the test data set (cases from December 1 to 27, 2018) revealed two interesting observations. First, among the specimens that had incorrect initial CPT code assignments, the model disagreed with the initial assignments in 73.6% (117/159) and agreed in 26.4% (42/159). Second, the model identified nine additional specimens with incorrect CPT codes that had evaded all steps of checking. Conclusions: A neural network model using report texts to predict CPT codes can achieve high accuracy in prediction and moderate sensitivity in error detection. Neural networks may play increasing roles in CPT coding in surgical pathology.

Background: Determining mitotic index by counting mitotic figures (MFs) microscopically from tumor areas with most abundant MF (hotspots [HS]) produces a prognostically useful tumor grading biomarker. However, interobserver concordance identifying MF and HS can be poorly reproducible. Immunolabeling MF, coupled with computer-automated counting by image analysis, can improve reproducibility. A computational system for obtaining MF values across digitized whole-slide images (WSIs) was sought that would minimize impact of artifacts, generate values clinically relatable to counting ten high-power microscopic fields of view typical in conventional microscopy, and that would reproducibly map HS topography. Materials and Methods: Relatively low-resolution WSI scans (0.50 μm/pixel) were imported in grid-tile format for feature-based MF segmentation, from naturally occurring canine melanomas providing a wide range of proliferative activity. MF feature extraction conformed to anti-phospho-histone H3-immunolabeled mitotic (M) phase cells. Computer vision image processing was established to subtract key artifacts, obtain MF counts, and employ rotationally invariant feature extraction to map MF topography. Results: The automated topometric HS (TMHS) algorithm identified mitotic HS and mapped select tissue tiles with greatest MF counts back onto WSI thumbnail images to plot HS topographically. Influence of dye, pigment, and extraneous structure artifacts was minimized. TMHS diagnostic decision support included image overlay graphics of HS topography, as well as a spreadsheet and plot of tile-based MF count values. TMHS performance was validated examining both mitotic HS counting and mapping functions. Significantly correlated TMHS MF mapping and metrics were demonstrated using repeat analysis with WSI in different orientation (R² = 0.9916) and by agreement with a pathologist (R² = 0.8605) as well as through assessment of counting function using an independently tuned object counting algorithm (OCA) (R² = 0.9482). Limits of agreement analysis support method interchangeability. MF counts obtained led to accurate patient survival prediction in all (n = 30) except one case. By contrast, more variable performance was documented when several pathologists examined similar cases using microscopy (pair-wise correlations, rho range = 0.7597–0.9286). Conclusions: Automated TMHS MF segmentation and feature engineering performance were interchangeable with both observer and OCA in digital mode. Moreover, enhanced HS location accuracy and superior method reproducibility were achieved using the automated TMHS algorithm compared to the current practice employing clinical microscopy.

Introduction: A whole slide image (WSI) is typically comprised of a macro image (low-power snapshot of the entire glass slide) and stacked tiles in a pyramid structure (with the lowest resolution thumbnail at the top). The macro image shows the label and all pieces of tissue on the slide. Many whole slide scanner vendors do not readily show the macro overview to pathologists. We demonstrate that failure to do so may result in a serious misdiagnosis. Materials and Methods: Various examples of errors were accumulated that occurred during the digitization of glass slides where the virtual slide differed from the macro image of the original glass slide. Such examples were retrieved from pathology laboratories using different types of scanners in the USA, Canada, Europe, and Asia. Results: The reasons for image errors were categorized into technical problems (e.g., automatic tissue finder failure, image mismatches, and poor scan coverage) and human operator mistakes (e.g., improper manual region of interest selection). These errors were all detected because they were highlighted in the macro image. Conclusion: Our experience indicates that WSI can be subject to inadvertent errors related to glitches in scanning slides, corrupt images, or mistakes made by humans when scanning slides. Displaying the macro image that accompanies WSIs is critical from a quality control perspective in digital pathology practice as this can help detect these serious image-related problems and avoid compromised diagnoses.

Background: In an effort to provide improved user experience and system reliability at a moderate cost, our department embarked on targeted upgrades of a total of 87 computers over a period of 3 years. Upgrades came in three forms: (i) replacement of the computer with newer architecture, (ii) replacement of the computer's hard drive with a solid-state drive (SSD), or (iii) replacement of the computer with newer architecture and a SSD. Methods: We measured the impact of each form of upgrade on a set of pathology-relevant tasks that fell into three categories: standard use, whole-slide navigation, and whole-slide analysis. We used time to completion of a task as the primary variable of interest. Results: We found that for most tasks, the SSD upgrade had a greater impact than the upgrade in architecture. This effect was especially prominent for whole-slide viewing, likely due to the way in which most whole-slide viewers cached image tiles. However, other tasks, such as whole-slide image analysis, often relied less on disk input or output and were instead more sensitive to the computer architecture. Conclusions: Based on our experience, we suggest that SSD upgrades are viewed in some settings as a viable alternative to complete computer replacement and recommend that computer replacements in a digital pathology setting are accompanied by an upgrade to SSDs.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Context: The College of American Pathologists (CAP) requires synoptic reporting of all tumor excisions. Objective: To compare the performance of different methods of generating synoptic reports. Methods: Completeness, amendment rates, rate of timely ordering of ancillary studies (KRAS in T4/N1 colon carcinoma), and structured data file extraction were compared for four different synoptic report generating methods. Results: Use of the printed tumor protocols directly from the CAP website had the lowest completeness (84%) and highest amendment (1.8%) rates. Reformatting these protocols was associated with higher completeness (94%, P < 0.001) and reduced amendment (1%, P = 0.20) rates. Extraction into a structured data file was successful 93% of the time. Word-based macros improved completeness (98% vs. 94%, P < 0.001) but not amendment rates (1.5%). KRAS was ordered before sign out 89% of the time. In contrast, a web-based product with a reminder flag when items were missing, an embedded flag for data extraction, and a reminder to order KRAS when appropriate resulted in improved completeness (100%, P = 0.005), amendment rates (0.3%, P = 0.03), KRAS ordering before sign out (100%, P = 0.23), and structured data extraction (100%, P < 0.001) without reducing the speed (P = 0.34) or accuracy (P = 1.00) of data extraction by the reader. Conclusion: Completeness, amendment rates, ancillary test ordering rates, and data extraction rates vary significantly with the method used to construct the synoptic report. A web-based method compares favorably with all other methods examined and does not reduce reader usability.

Background: Our institution's pathology unknown conferences provide educational cases for our residents. However, the cases have not been previously available digitally, have not been collated for postconference review, and were not accessible to a wider audience. Our objective was to create an inexpensive whole slide image (WSI) education suite to address these limitations and improve the education of pathology trainees. Materials and Methods: We surveyed residents regarding their preference between four unique WSI systems. We then scanned weekly unknown conference cases and study set cases and uploaded them to our custom built WSI viewer located at RecutClub.com. We measured site utilization and conference participation. Results: Residents preferred our OpenLayers WSI implementation to Ventana Virtuoso, Google Maps API, and OpenSlide. Over 16 months, we uploaded 1366 cases from 77 conferences and ten study sets, occupying 793.5 GB of cloud storage. Based on resident evaluations, the interface was easy to use and demonstrated minimal latency. Residents are able to review cases from home and from their mobile devices. Worldwide, 955 unique IP addresses from 52 countries have viewed cases in our site. Conclusions: We implemented a low-cost, publicly available repository of WSI slides for resident education. Our trainees are very satisfied with the freedom to preview either the glass slides or WSI and review the WSI postconference. Both local users and worldwide users actively and repeatedly view cases in our study set.

Background: Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO), which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs) (WHO Grade II–III) have fewer malignant characteristics than high-grade gliomas (WHO Grade IV), and a better clinical prognosis, however, accurate discrimination of overall survival (OS) remains a challenge. In this study, we aimed to identify tissue-derived image features using a machine learning approach to predict OS in a mixed histology and grade cohort of lower grade glioma patients. To achieve this aim, we used H and E stained slides from the public LGG cohort of The Cancer Genome Atlas (TCGA) to create a machine learned dictionary of “image-derived visual words” associated with OS. We then evaluated the combined efficacy of using these visual words in predicting short versus long OS by training a generalized machine learning model. Finally, we mapped these predictive visual words back to molecular signaling cascades to infer potential drivers of the machine learned survival-associated phenotypes. Methods: We analyzed digitized histological sections downloaded from the LGG cohort of TCGA using a bag-of-words approach. This method identified a diverse set of histological patterns that were further correlated with OS, histology, and molecular signaling activity using Cox regression, analysis of variance, and Spearman correlation, respectively. A support vector machine (SVM) model was constructed to discriminate patients into short and long OS groups dichotomized at 24-month. Results: This method identified disease-relevant phenotypes associated with OS, some of which are correlated with disease-associated molecular pathways. From these image-derived phenotypes, a generalized SVM model which could discriminate 24-month OS (area under the curve, 0.76) was obtained. Conclusion: Here, we demonstrated one potential strategy to incorporate image features derived from H and E stained slides into predictive models of OS. In addition, we showed how these image-derived phenotypic characteristics correlate with molecular signaling activity underlying the etiology or behavior of LGG.

Background: Numerous validation studies in digital pathology confirmed its value as a diagnostic tool. However, a longer time to diagnosis than traditional microscopy has been seen as a significant barrier to the routine use of digital pathology. As a part of our validation study, we compared a digital and microscopic diagnostic time in the routine diagnostic setting. Materials and Methods: One senior staff pathologist reported 400 consecutive cases in histology, nongynecological, and fine needle aspiration cytology (20 sessions, 20 cases/session), over 4 weeks. Complex, difficult, and rare cases were excluded from the study to reduce the bias. A primary diagnosis was digital, followed by traditional microscopy, 6 months later, with only request forms available for both. Microscopic slides were scanned at ×20, digital images accessed through the fully integrated laboratory information management system (LIMS) and viewed in the image viewer on double 23” displays. A median broadband speed was 299 Mbps. A diagnostic time was measured from the point slides were made available to the point diagnosis was made or additional investigations were deemed necessary, recorded independently in minutes/session and compared. Results: A digital diagnostic time was 1841 and microscopic 1956 min; digital being shorter than microscopic in 13 sessions. Four sessions with shorter microscopic diagnostic time included more cases requiring extensive use of magnifications over ×20. Diagnostic time was similar in three sessions. Conclusions: A diagnostic time in digital pathology can be shorter than traditional microscopy in the routine diagnostic setting, with adequate and stable network speeds, fully integrated LIMS and double displays as default parameters. This also related to better ergonomics, larger viewing field, and absence of physical slide handling, with effects on both diagnostic and nondiagnostic time. Differences with previous studies included a design, image size, number of cases, specimen type, network speed, and participant's level of confidence and experience in digital reporting. Further advancements in working stations and gained experience in digital reporting are expected to improve diagnostic time and widen routine applications of digital pathology.

Background: The electronic health record (EHR) provides opportunity to improve health and enhance appropriate test utilization through decision support. Electronic alerts in the order entry system can guide test use. Few published reports have assessed the impact of automated alerts on compliance of Pap ordering with published screening guidelines. Methods: Programming rules for Pap test ordering were developed within the EHR (Epic, Madison, WI) of the University of California, Davis Health System using American College of Obstetrics and Gynecology's 2009 guidelines and implemented in primary care clinics in 2010. Alerts discouraged Pap orders in women <21 and >71 years and displayed when an order was initiated. Providers were not prevented from placing an order. Results were measured during four calendar periods: (1) pre-alert (baseline) (July 2010 to June 2011), (2) post alert (alerts on) (July 2011 to December 2011), (3) inadvertent alert turn-off ("glitch") (January 2012 to December 2012), (5) post-glitch (alerts re-instated) (1/2013-7/2013). Metrics used to measure alert impact were between time and period seasonally adjusted relative frequency ratios. Results: Alerts were most effective in the <21 year old age group. During the baseline period 2.7 Pap tests were order in patients less than age 21 for every 100 Paps in those 21-71 years of age. This relative frequency decreased to 1.7 in the post-alert period and 1.4 during the glitch, with an even greater decline to 0.8 post-glitch when alerts were reinstated. Less impact was observed in the >70 year old group where the baseline relative frequency was 2.4 and declined to 2.1 post-alert, remained stable at 2.0 during the glitch period, and declined again to 1.7 post-glitch when alerts were reinstated. This likely reflects inclusion of women with a history of abnormal Pap tests for whom continued Pap testing is indicated, as well as reluctance by providers and patients to accept discontinuation of Pap testing for women with a history of normal Pap results. In both age groups, decreases in ordering were greatest when the alerts were functioning, indicating that the alerts had an effect beyond the influences of the environment. Conclusions: Discouraging alerts can impact ordering of Pap tests and improve compliance with established guidelines, thus avoiding unnecessary follow-up tests that can create potential patient harm and unnecessary expense. Alerts represent a potential model to address utilization of other lab tests. Longer study intervals are necessary to determine if provider compliance is maintained.