Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

Whole Slide Imaging Technology and Its Applications: Current and Emerging Perspectives

Background. Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. It utilizes virtual microscopy wherein glass slides are converted into digital slides and are viewed by pathologists by automated image analysis. Its impact on pathology workflow, reproducibility, dissemination of educational material, expansion of service to underprivileged areas, and institutional collaboration exemplifies a significant innovative movement. The recent US Food and Drug Administration approval to WSI for its use in primary surgical pathology diagnosis has opened opportunities for wider application of this technology in routine practice. Main Text. The ongoing technological advances in digital scanners, image visualization methods, and the integration of artificial intelligence-derived algorithms with these systems provide avenues to exploit its applications. Its benefits are innumerable such as ease of access through the internet, avoidance of physical storage space, and no risk of deterioration of staining quality or breakage of slides to name a few. Although the benefits of WSI to pathology practices are many, the complexities of implementation remain an obstacle to widespread adoption. Some barriers including the high cost, technical glitches, and most importantly professional hesitation to adopt a new technology have hindered its use in routine pathology. Conclusions. In this review, we summarize the technical aspects of WSI, its applications in diagnostic pathology, training, and research along with future perspectives. It also highlights improved understanding of the current challenges to implementation, as well as the benefits and successes of the technology. WSI provides a golden opportunity for pathologists to guide its evolution, standardization, and implementation to better acquaint them with the key aspects of this technology and its judicial use. Also, implementation of routine digital pathology is an extra step requiring resources which (currently) does not usually result increased efficiency or payment.

E-learning module for cytopathology education based on virtual microscopy

INTRODUCTION

In cytopathology education, Virtual Microscopy e-learning modules (VM-eLM) have achieved remarkable results in the improvement and personalization of learning. However, it remains to be determined whether these modules can significantly contribute to improving the accuracy of cytological diagnosis. The aim of this work was to create a VM-eLM for gynecologic cytopathology education designed to improve screening and interpretation skills in two groups of cytologists: experienced and nonexperienced.

MATERIALS AND METHODS

The module was designed in Moodle with both Whole Slide Images and Static Images taken from Papanicolaou smears that were diagnosed as: negative for intraepithelial lesion, low-grade squamous intraepithelial lesion, high-grade squamous intraepithelial lesion, squamous cell carcinoma, or adenocarcinoma. We assessed the effectiveness of the module using 1) clinical quality indicators to measure skill development and 2) a user survey.

RESULTS

After training, participants significantly improved their cytological screening skills, decreasing their false negative diagnosis by 78% in the non-experienced group and eliminating them entirely in the experienced group. Nonexperienced participants also significantly increased their recognition of low-grade squamous intraepithelial lesion and high-grade squamous intraepithelial lesion by 31% and 50%, respectively. Participants positively evaluated the module, highlighting its novelty, the possibility to train remotely, the immediate feedback and the quality of the Whole Slide Images.

CONCLUSIONS

We designed, implemented and tested a VM-eLM for Gynecologic Cytopathology Education that improved cytological screening skills for both non-experienced and experienced cytologists, also increasing the diagnostic accuracy of preinvasive lesions by less experienced cytologists. The module was positively evaluated by participants, who perceived an improvement in their interpretive skills.

Preparing Data for Artificial Intelligence in Pathology with Clinical-Grade Performance

The pathology is decisive for disease diagnosis but relies heavily on experienced pathologists. In recent years, there has been growing interest in the use of artificial intelligence in pathology (AIP) to enhance diagnostic accuracy and efficiency. However, the impressive performance of deep learning-based AIP in laboratory settings often proves challenging to replicate in clinical practice. As the data preparation is important for AIP, the paper has reviewed AIP-related studies in the PubMed database published from January 2017 to February 2022, and 118 studies were included. An in-depth analysis of data preparation methods is conducted, encompassing the acquisition of pathological tissue slides, data cleaning, screening, and subsequent digitization. Expert review, image annotation, dataset division for model training and validation are also discussed. Furthermore, we delve into the reasons behind the challenges in reproducing the high performance of AIP in clinical settings and present effective strategies to enhance AIP's clinical performance. The robustness of AIP depends on a randomized collection of representative disease slides, incorporating rigorous quality control and screening, correction of digital discrepancies, reasonable annotation, and sufficient data volume. Digital pathology is fundamental in clinical-grade AIP, and the techniques of data standardization and weakly supervised learning methods based on whole slide image (WSI) are effective ways to overcome obstacles of performance reproduction. The key to performance reproducibility lies in having representative data, an adequate amount of labeling, and ensuring consistency across multiple centers. Digital pathology for clinical diagnosis, data standardization and the technique of WSI-based weakly supervised learning will hopefully build clinical-grade AIP.

Digital Versus Conventional Teaching of Surgical Pathology: A Comparative Study

OBJECTIVE

To compare the digital method and the conventional method of teaching surgical pathology to medical students.

METHODS

A prospective case-control study was conducted on second-year students during the period of August 20, 2022, through January 15, 2023. Students, divided into two groups of 45 each, were taught surgical pathology via both conventional and digital methods. Four specimens and four slides were taught in total to the same set of students. A pre-test and a post-test were used to evaluate students' performance and the impact of the teaching method. The answers were analyzed using a paired t-test. In the end, students' responses were obtained regarding their views on a better method of teaching on a Likert scale.

RESULTS

To study gross pathology, 50.7% of students were in favor of the digital method, and 21% were not in favor. For the microscopic examination of tissues, 56.92% of students were in favor of the digital method, and 15% were not in favor. There was a significant increase in post-test scores (12.54-9.79 = 2.75, p=0.007) when digital methods for teaching surgical pathology were applied.

CONCLUSION

The Likert scale demonstrated that the digital method of teaching surgical pathology not only improved student performance but also resulted in a better understanding of the subject.

Virtual Versus Light Microscopy Usage among Students: A Systematic Review and Meta-Analytic Evidence in Medical Education

BACKGROUND

The usage of whole-slide images has recently been gaining a foothold in medical education, training, and diagnosis.

OBJECTIVES

The first objective of the current study was to compare academic performance on virtual microscopy (VM) and light microscopy (LM) for learning pathology, anatomy, and histology in medical and dental students during the COVID-19 period. The second objective was to gather insight into various applications and usage of such technology for medical education.

MATERIALS AND METHODS

Using the keywords "virtual microscopy" or "light microscopy" or "digital microscopy" and "medical" and "dental" students, databases (PubMed, Embase, Scopus, Cochrane, CINAHL, and Google Scholar) were searched. Hand searching and snowballing were also employed for article searching. After extracting the relevant data based on inclusion and execution criteria, the qualitative data were used for the systematic review and quantitative data were used for meta-analysis. The Newcastle Ottawa Scale (NOS) scale was used to assess the quality of the included studies. Additionally, we registered our systematic review protocol in the prospective register of systematic reviews (PROSPERO) with registration number CRD42020205583.

RESULTS

A total of 39 studies met the criteria to be included in the systematic review. Overall, results indicated a preference for this technology and better academic scores. Qualitative analyses reported improved academic scores, ease of use, and enhanced collaboration amongst students as the top advantages, whereas technical issues were a disadvantage. The performance comparison of virtual versus light microscopy meta-analysis included 19 studies. Most (10/39) studies were from medical universities in the USA. VM was mainly used for teaching pathology courses (25/39) at medical schools (30/39). Dental schools (10/39) have also reported using VM for teaching microscopy. The COVID-19 pandemic was responsible for the transition to VM use in 17/39 studies. The pooled effect size of 19 studies significantly demonstrated higher exam performance (SMD: 1.36 [95% CI: 0.75, 1.96], p < 0.001) among the students who used VM for their learning. Students in the VM group demonstrated significantly higher exam performance than LM in pathology (SMD: 0.85 [95% CI: 0.26, 1.44], p < 0.01) and histopathology (SMD: 1.25 [95% CI: 0.71, 1.78], p < 0.001). For histology (SMD: 1.67 [95% CI: -0.05, 3.40], p = 0.06), the result was insignificant. The overall analysis of 15 studies assessing exam performance showed significantly higher performance for both medical (SMD: 1.42 [95% CI: 0.59, 2.25], p < 0.001) and dental students (SMD: 0.58 [95% CI: 0.58, 0.79], p < 0.001).

CONCLUSIONS

The results of qualitative and quantitative analyses show that VM technology and digitization of glass slides enhance the teaching and learning of microscopic aspects of disease. Additionally, the COVID-19 global health crisis has produced many challenges to overcome from a macroscopic to microscopic scale, for which modern virtual technology is the solution. Therefore, medical educators worldwide should incorporate newer teaching technologies in the curriculum for the success of the coming generation of health-care professionals.

Stain normalization using score-based diffusion model through stain separation and overlapped moving window patch strategies

Hematoxylin and eosin (H&E) staining is the gold standard modality for diagnosis in medicine. However, the dosage ratio of hematoxylin to eosin in H&E staining has not been standardized yet. Additionally, H&E stains fade out at various speeds. Therefore, the staining quality could differ among each image, and stain normalization is a critical preprocessing approach for training deep learning (DL) models, especially in long-term and/or multicenter digital pathology studies. However, conventional methods for stain normalization have some significant drawbacks, such as collapsing in the structure and/or texture of tissue. In addition, conventional methods must require a reference patch or slide. Meanwhile, DL-based methods have a risk of overfitting and/or grid artifacts. We developed a score-based diffusion model of colorization for stain normalization. However, mistransfer, in which the model confuses hematoxylin with eosin, can occur using a score-based diffusion model due to its high diversity nature. To overcome this mistransfer, we propose a stain separation method using sparse non-negative matrix factorization (SNMF), which can decompose pathology slide into Hematoxylin and Eosin to normalize each stain component. Furthermore, inpainting with overlapped moving window patches was used to prevent grid artifacts of whole slide image normalization. Our method can normalize the whole slide pathology images through this stain normalization pipeline with decent performance.

An international collaborative approach to learning histology using a virtual microscope

Histology is often taught in higher education settings using online virtual microscopes (VM). This study aimed to develop and evaluate the use of VM in teaching on a BSc degree at the University of Nottingham by surveying students and staff. A key development was the use of an e-workbook so that students were actively engaged in creating their own bespoke revision material. Subsequently, this approach was used in a second study evaluating the use of VM in teaching the histology and pathology of the gastrointestinal (GI) tract via group work with students from two BSc courses at the University of Nottingham; one based at Derby (RDHC) and the other in Malaysia (UNMC). Students worked together in groups to complete an e-workbook, develop a presentation, and decide how to collaborate and communicate. An evaluation of these activities revealed advantages in developing transferrable skills, and good engagement with both the histology topic and group work. Analysis of assessment of the module at UNMC showed that student performance improved in the histology-based module after the intervention (p < 0.01) and that this improvement was not evident in other modules taken by the cohort. Furthermore, when interrogating the questions from the examination paper that asked students to identify features from histological images, fewer questions were seen as 'difficult' (p < 0.001) and more were seen as 'average' (p < 0.01). This study demonstrates that the use of VM in histology combined with active learning in creating a revision resource enhances engagement and depth of learning. When further combined with collaborative active group work, students developed a range of histology knowledge and transferrable skills, with notable improvement in examination performance relative to other contemporaneous modules.

Virtual Microscopy Goes Global: The Images Are Virtual and the Problems Are Real

For the last two centuries, the scholarly education of histology and pathology has been based on technology, initially on the availability of low-cost, high-quality light microscopes, and more recently on the introduction of computers and e-learning approaches to biomedical education. Consequently, virtual microscopy (VM) is replacing glass slides and the traditional light microscope as the main instruments of instruction in histology and pathology laboratories. However, as with most educational changes, there are advantages and disadvantages associated with a new technology. The use of VM for the teaching of histology and pathology requires an extensive infrastructure and the availability of computing devices to all learners, both posing a considerable financial strain on schools and students. Furthermore, there may be valid reasons for practicing healthcare professionals to maintain competency in using light microscopes. In addition, some educators may be reluctant to embrace new technologies. These are some of the reasons why the introduction of VM as an integral part of histology and pathology instruction has been globally uneven. This paper compares the teaching of histology and pathology using traditional or VM in five different countries and their adjacent regions, representing developed, as well as developing areas of the globe. We identify general and local roadblocks to the introduction of this still-emerging didactic technology and outline solutions for overcoming these barriers.

The utility of a gross dissection anatomical model for simulation-based learning in pathology

INTRODUCTION

The examination of morphological alterations in tissues is fundamental in Pathology. Traditional training in gross dissection has several limitations, including the risk of transmissible diseases, formaldehyde exposure and limited specimen availability. We describe a teaching method using anatomical simulators.

METHODS

Liquid silicone-based artisan neoplastic anatomical models were used in conjunction with clinical scenarios. Eighty-five medical students participated in a gross dissection experience and were asked to complete a feedback questionnaire. Additionally, a workshop was organized for students to compare three different teaching methods. The first one used still images (Group1-G1), the second a video explanation (Group2-G2), and the third directly observed a pathologist while grossing (Group3-G3).

RESULTS

The knowledge acquisition questionnaire showed an average value of 4.4 out of 5 (1-5) (range 3.4-4.7, σ0.89). The categories 'knowledge of resection margins' and 'macroscopic diagnosis' received the highest values (4.8, σ0.11 and 4.7, σ0.32, respectively), followed by 'understanding of handling and gross examination of the surgical specimen' (4.5, σ0.49), 'prognosis' (4.3, σ0.67) and 'understanding of a tumor resection' (3.9, σ0.96) (p<0.05). Regarding teaching methods, G3 spent less time than G2 and G1 with mean times of 15'39″ (σ2'12″), 16'50″ (σ3'45″), and 17'52″ (σ2'12″), respectively (p<0.05). Gross dissection marks (0-5) showed statistically significant differences (p<0.05). G2 obtained better results (3.7;σ0.54) than G3 (3.4;σ0.94) or G1 (3.1;σ0.8).

CONCLUSIONS

This preliminary study demonstrates that it is possible to implement a gross dissection simulation module at medical school and thus enable the acquisition of skills in a secure environment.

Virtual Pathology Education in Medical Schools Worldwide during the COVID-19 Pandemic: Advantages, Challenges Faced, and Perspectives

The COVID-19 pandemic shifted pathology education in medical schools worldwide towards online delivery. To achieve this goal, various innovative platforms were used by pathology educators and medical students, facilitating both synchronous and asynchronous learning. The aim of this study was to review the published evidence regarding remote pathology teaching at the medical school level during this period, present our own experience, and provide some perspectives regarding the best mode of pathology teaching post-pandemic. Among its advantages, virtual pathology education was considered among students and educators as convenient, flexible, and engaging, while learning outcomes were met and students’ academic performance was in general satisfactory. However, several challenges were faced. For instance, suboptimal internet connection compromised the flow of classes and was even associated with a lower academic performance. The lack of hands-on laboratory activities, such as operating the light microscope and tissue grossing, and the reduced student interactions among themselves and their instructors, were also pointed out as significant drawbacks of remote pathology education. Whereas online education has multiple advantages, experiencing the physical university environment, in-person interactions and teamwork, exposure to the “hidden curriculum”, and hands-on activities are vital for medical school education and future student development. In conclusion, the implementation of a blended approach in pathology education—where online and face-to-face sessions are jointly used to promote students’ engagement, interaction with their instructors and peers, and learning—could be the most optimal approach to pathology teaching in medical schools post-pandemic.

Validation of whole slide imaging for frozen section diagnosis of lymph node metastasis: A retrospective study from a tertiary care hospital in Thailand

BACKGROUND

The use of whole slide imaging (WSI) for frozen section (FS) diagnosis is helpful, particularly in the context of pathologist shortages. However, there is minimal data on such usage in resource-limited settings. This study aims to validate the use of WSI for FS diagnosis of lymph node metastasis using a low-cost virtual microscope scanner with consumer-grade laptops at a tertiary care hospital in Thailand.

METHODS

FS slides were retrieved for which the clinical query was to evaluate lymph node metastasis. They were digitized by a virtual microscope scanner (MoticEasyScan, Hong Kong) using up to 40× optical magnification. Three observers with different pathology experience levels diagnosed each slide, reviewing glass slides (GS) followed by digital slides (DS) after two weeks of a wash out period. WSI and GS diagnoses were compared. The time used for scanning and diagnosis of each slide was recorded.

RESULTS

295 FS slides were retrieved and digitized. The first-time successful scanning rate was 93.6 %. The mean scanning time was 2 min per slide. Both intraobserver agreement and interobserver agreement of WSI and GS diagnoses were high (Cohen's K; kappa value >0.84). The time used for DS diagnosis decreased as the observer's experience with WSI increased.

CONCLUSIONS

Despite varying pathological experiences, observers using WSI provided accurate FS diagnoses of lymph node metastasis. The time required for DS diagnoses decreased with additional observer's experience with WSI. Therefore, a WSI system containing low-cost scanners and consumer-grade laptops could be used for FS services in hospital laboratories lacking pathologists.

An Analysis of Pathologists’ Viewing Processes as They Diagnose Whole Slide Digital Images

Although pathologists have their own viewing habits while diagnosing, viewing behaviors leading to the most accurate diagnoses are under-investigated. Digital whole slide imaging has enabled investigators to analyze pathologists' visual interpretation of histopathological features using mouse and viewport tracking techniques. In this study, we provide definitions for basic viewing behavior variables and investigate the association of pathologists' characteristics and viewing behaviors, and how they relate to diagnostic accuracy when interpreting whole slide images. We use recordings of 32 pathologists' actions while interpreting a set of 36 digital whole slide skin biopsy images (5 sets of 36 cases; 180 cases total). These viewport tracking data include the coordinates of a viewport scene on pathologists' screens, the magnification level at which that viewport was viewed, as well as a timestamp. We define a set of variables to quantify pathologists' viewing behaviors such as zooming, panning, and interacting with a consensus reference panel's selected region of interest (ROI). We examine the association of these viewing behaviors with pathologists' demographics, clinical characteristics, and diagnostic accuracy using cross-classified multilevel models. Viewing behaviors differ based on clinical experience of the pathologists. Pathologists with a higher caseload of melanocytic skin biopsy cases and pathologists with board certification and/or fellowship training in dermatopathology have lower average zoom and lower variance of zoom levels. Viewing behaviors associated with higher diagnostic accuracy include higher average and variance of zoom levels, a lower magnification percentage (a measure of consecutive zooming behavior), higher total interpretation time, and higher amount of time spent viewing ROIs. Scanning behavior, which refers to panning with a fixed zoom level, has marginally significant positive association with accuracy. Pathologists' training, clinical experience, and their exposure to a range of cases are associated with their viewing behaviors, which may contribute to their diagnostic accuracy. Research in computational pathology integrating digital imaging and clinical informatics opens up new avenues for leveraging viewing behaviors in medical education and training, potentially improving patient care and the effectiveness of clinical workflow.

Shift to emergency remote preclinical medical education amidst the Covid-19 pandemic: A single-institution study

The Covid-19 pandemic disrupted medical education, shifting it towards emergency remote delivery. This cross-sectional study aimed to assess the impact of the pandemic on preclinical medical education and identify predictors of the virtual learning experience and perceived stress. An anonymous survey was delivered electronically to the students of the authors' medical school that attended either histology or pathology. This survey contained two scales, the virtual learning experience (VLE) and the perceived stress scale-10 (PSS-10). A total of 173/255 (68%) responded, showing a positive perception towards the remote delivery of both courses. An exploratory factor analysis was performed on the VLE scale items and four new dimensions were formed: "course quality and learning outcomes", "student motivation", virtual against F2F learning", and "virtual laboratory sessions". The following significant predictors of enhanced VLE, in at least one dimension, were identified: female gender, pathology course, final examination grade >80%, lower perceived stress levels, studying in home country, and holding of another degree before medical school. In addition, the following predictors were significantly associated with higher levels of student perceived stress: female gender, pathology course, studying away from home, and suboptimal internet connection. Notably, the quality of internet connection was significantly associated with the students' final examination performance. Concerning the best mode for future delivery of both courses, most students proposed a blended, rather than an entirely on-campus or online approach. In conclusion, despite its problems, a high-quality remote preclinical medical education was possible in the authors' school and offered tremendous opportunities for future improvement.

Frozen section telepathology service: Efficiency and benefits of an e-health policy in South Tyrol

Objective/Background

Telepathology has been widely adopted to allow intraoperative pathology examinations to be performed remotely and for obtaining second opinion teleconsultation. In the Italian northern region of South Tyrol, the widespread geographical distances and consequent cost for the health system of having a travelling pathologist cover intraoperative consultations in peripheral hospitals was a key driver for the implementation of a telepathology system.

Methods

In 2010, four Menarini D-Sight whole slide scanners to digitize entire pathology slides were placed in the peripheral hospitals of Merano, Bressanone, Brunico, and in the hub hospital of Bolzano. Digital workstations were also installed to allow pathologists to remotely perform intraoperative consultations with digital slides. This study reviews the outcome after 12 years of telepathology for this intended clinical use.

Results

After an initial validation phase with 100 cases which yielded a sensitivity of 65% (CI 43–84%) and specificity of 100% (CI 95–100%), there were 2058 intraoperative consultations handled by telepathology. The cases evaluated were mainly breast sentinel lymph nodes, followed by urological, gynecological and general surgical pathology frozen section specimens. There were no false-positive cases and 165 (8%) false-negative cases, yielding an overall sensitivity and specificity of 65% (CI 61–69%) and 100% (CI 99–100%), respectively.

Conclusion

Telepathology is reliable for remote intraoperative diagnosis and, despite technical issues and initial acquaintance issues, proved beneficial for patient care in satellite hospitals, improved standardization, promoted innovation, and resulted in cost savings for the health system.

Virtual Microscopy in Undergraduate Pathology Education: An early transformative experience in clinical reasoning

Objectives

Whole-slide imaging and virtual microscopy (VM) have revolutionised teaching, diagnosis and research in histopathology. This study aimed to establish the feasibility of achieving early integration of clinical reasoning with undergraduate pathology teaching on a VM platform and to determine its student-centricity through student feedback.

Methods

This study was conducted at the Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates, between August and December 2017. A total of 38 VM-centred clinical cases were introduced to 49 students in an integrated undergraduate medical curriculum. The cases were aligned to curricular objectives, reinforced the pathologic basis of disease with critical thinking and were delivered across 15 interactive small-group sessions. A simulated cross-disciplinary integration and judicious choice of pertinent diagnostic investigations were linked to principles of management. Feedback was obtained through a mixed-methods approach.

Results

User-friendliness, gradual learning curve of VM and annotation-capacity were scored as 4–5 (on a Likert scale of 1–5) by 91.84%, 87.76% and 83.67% of the participants, respectively. Most students agreed that the content matched the stage of learning (81.63%), theme of the week (91.84%) and development of a strong clinical foundation (77.55%). Integration (85.71%) and clinico-pathological correlation (83.67%) were the strengths of this educational effort. High student attendance (~100%) and improved assessment scores on critical thinking (80%) were observed. Software lacunae included frequent logouts and lack of note-taking tools. Easy access was a significant student-centric advantage.

Conclusion

A VM-centred approach with a clinico-pathological correlation has been successfully introduced to inculcate integrated learning. Using the pathologic basis of disease as a fulcrum and critical reasoning as an anchor, a digitally-enabled generation of medical students have embraced this educational tool for tutor-guided, student-centred learning.

Whole slide imaging is a high-throughput method to assess Candida biofilm formation

New strategies that enable fast and accurate visualization of Candida biofilms are necessary to better study their structure and response to antifungals agents. Here, we applied whole slide imaging (WSI) to study biofilm formation of Candida species. Three relevant biofilm-forming Candida species (C. albicans ATCC 10231, C. glabrata ATCC 2001, and C. tropicalis ATCC 750) were cultivated on glass coverslips both in presence and absence of widely used antifungals. Accumulated biofilms were stained with fluorescent markers and scanned in both bright-field and fluorescence modes using a WSI digital scanner. WSI enabled clear assessment of both size and structural features of Candida biofilms. Quantitative analyses readily detected reductions in biofilm-covered surface area upon antifungal exposure. Furthermore, we show that the overall biofilm growth can be adequately assessed across both bright-field and fluorescence modes. At the single-cell level, WSI proved adequate, as morphometric parameters evaluated with WSI did not differ significantly from those obtained with scanning electron microscopy, considered as golden standard at single-cell resolution. Thus, WSI allows for reliable visualization of Candida biofilms enabling both large-scale growth assessment and morphometric characterization of single-cell features, making it an important addition to the available microscopic toolset to image and analyse fungal biofilm growth.

Pushed Across the Digital Divide: COVID-19 Accelerated Pathology Training onto a New Digital Learning Curve

Bringing digital teaching materials into residency training programs has seen slow adoption, expected for many new technologies. The COVID-19 pandemic dramatically shifted the paradigm for many resident teaching modalities as institutions instituted social distancing to prevent spread of the novel coronavirus. The impact of this shift on pathology trainee education has not been well studied. We conducted an online survey of pathology trainees, program directors, and faculty to assess pre- and post-COVID-19 use of, and response to, various digital pathology modalities. Responses were solicited through both social media and directed appeals. A total of 261 respondents (112 faculty, 52 program directors, and 97 trainees) reported a dramatic and significant increase in the use of digital pathology-related education tools. A significant majority of faculty and program directors agreed that this shift had adversely affected the quality (59% and 62%, respectively) and effectiveness (66%) of their teaching. This perception was similar among learners relative to the impact on quality (59%) and effectiveness (64%) of learning. Most respondents (70%-92%) anticipate that their use of digital pathology education tools will increase or remain the same post-COVID. The global COVID-19 pandemic created a unique opportunity and challenge for pathology training programs. Digital pathology resources were accordingly readily adopted to continue supporting educational activities. The learning curve and utilization of this technology was perceived to impair the quality and effectiveness of teaching and learning. Since the use of digital tools appears poised to continue to grow post-COVID19, challenges due to impaired quality and effectiveness will need to be addressed.

Experience Reviewing Digital Pap Tests using a Gallery of Images

Introduction:

Hologic is developing a digital cytology platform. An educational website was launched for users to review these digitized Pap test cases. The aim of this study was to analyze data captured from this website.

Materials and Methods:

ThinPrep^® Pap test slides were scanned at ×40 using a volumetric (14 focal plane) technique. Website cases consisted of an image gallery and whole slide image (WSI). Over a 13 month period data were recorded including diagnoses, time participants spent online, and number of clicks on the gallery and WSI.

Results:

51,289 cases were reviewed by 918 reviewers. Cytotechnologists spent less time (M [Median] = 65.0 s) than pathologists (M = 82.2 s) reviewing cases (P < 0.001). Longer times were associated with incorrect diagnoses and cases with organisms. Cytotechnologists matched the reference diagnoses in 85% of cases compared to pathologists who matched in 79.8%. While in 62% of cases reviewers only examined the gallery, they attained the correct diagnosis 92.7% of the time. Pathologists made more clicks on the gallery and WSI than cytotechnologists (P < 0.001). Diagnostic accuracy decreased with increasing clicks.

Conclusions:

Website participation provided feedback about how cytologists interact with a digital platform when reviewing cases. These data suggest that digital Pap test review when comprised of an image gallery displaying diagnostically relevant objects is quick and easy to interpret. The high diagnostic concordance of digital Pap tests with reference diagnoses can be attributed to high image quality with volumetric scanning, image gallery format, and ability for users to freely navigate the entire digital slide.

Digital pathology and computational image analysis in nephropathology

The emergence of digital pathology - an image-based environment for the acquisition, management and interpretation of pathology information supported by computational techniques for data extraction and analysis - is changing the pathology ecosystem. In particular, by virtue of our new-found ability to generate and curate digital libraries, the field of machine vision can now be effectively applied to histopathological subject matter by individuals who do not have deep expertise in machine vision techniques. Although these novel approaches have already advanced the detection, classification, and prognostication of diseases in the fields of radiology and oncology, renal pathology is just entering the digital era, with the establishment of consortia and digital pathology repositories for the collection, analysis and integration of pathology data with other domains. The development of machine-learning approaches for the extraction of information from image data, allows for tissue interrogation in a way that was not previously possible. The application of these novel tools are placing pathology centre stage in the process of defining new, integrated, biologically and clinically homogeneous disease categories, to identify patients at risk of progression, and shifting current paradigms for the treatment and prevention of kidney diseases.

Immune contexture analysis in immuno-oncology: applications and challenges of multiplex fluorescent immunohistochemistry

The tumor microenvironment is an integral player in cancer initiation, tumor progression, response and resistance to anti-cancer therapy. Understanding the complex interactions of tumor immune architecture (referred to as 'immune contexture') has therefore become increasingly desirable to guide our approach to patient selection, clinical trial design, combination therapies, and patient management. Quantitative image analysis based on multiplexed fluorescence immunohistochemistry and deep learning technologies are rapidly developing to enable researchers to interrogate complex information from the tumor microenvironment and find predictive insights into treatment response. Herein, we discuss current developments in multiplexed fluorescence immunohistochemistry for immune contexture analysis, and their application in immuno-oncology, and discuss challenges to effectively use this technology in clinical settings. We also present a multiplexed image analysis workflow to analyse fluorescence multiplexed stained tumor sections using the Vectra Automated Digital Pathology System together with FCS express flow cytometry software. The benefit of this strategy is that the spectral unmixing accurately generates and analyses complex arrays of multiple biomarkers, which can be helpful for diagnosis, risk stratification, and guiding clinical management of oncology patients.

The use of digital microscopy as a teaching method for human pathology: a systematic review

Since digital microscopy (DM) has become a useful alternative to conventional light microscopy (CLM), several approaches have been used to evaluate students' performance and perception. This systematic review aimed to integrate data regarding the use of DM for education in human pathology, determining whether this technology can be an adequate learning tool, and an appropriate method to evaluate students' performance. Following a specific search strategy and eligibility criteria, three electronic databases were searched and several articles were screened. Eight studies involving medical and dental students were included. The test of performance comprised diagnostic and microscopic description, clinical features, differential, and final diagnoses of the specimens. The students' achievements were equivalent, similar or higher using DM in comparison with CLM in four studies. All publications employed question surveys to assess the students' perceptions, especially regarding the easiness of equipment use, quality of images, and preference for one method. Seven studies (87.5%) indicated the students' support of DM as an appropriate method for learning. The quality assessment categorized most studies as having a low bias risk (75%). This study presents the efficacy of DM for human pathology education, although the high heterogeneity of the included articles did not permit outlining a specific method of performance evaluation.

Virtual Microscopy Is More Effective Than Conventional Microscopy for Teaching Cytology to Veterinary Students: A Randomized Controlled Trial

Virtual microscopy (VM) using scanned slides and imaging software is increasingly used in medical curricula alongside instruction in conventional microscopy (CM). Limited reports suggest that VM is useful in the veterinary education setting, and generally well-received by students. Whether students can apply knowledge gained through VM to practical use is unknown. Our objective was to determine whether instruction using VM, compared to CM, is a successful method of training veterinary students for the application of cytology in practice (i.e., using light microscopes). Seventy-one veterinary students from Colorado State University who attended a voluntary 3-hour cytology workshop were randomized to receive the same instruction with either VM (n = 35) or CM (n = 36). We compared these students to a control group (n = 22) of students who did not attend a workshop. All students took a post-workshop assessment involving the interpretation of four cases on glass slides with CM, designed to simulate the use of cytology in general practice. Students also took an 18-question survey related to the effectiveness of the workshop, providing their opinions on cytology instruction in the curriculum and their learning preference (VM or CM). The mean assessment score of the VM group (14.18 points) was significantly higher than the control group (11.33 points, p = .003), whereas the mean of the CM group (12.77 points) was not statistically significantly different from controls (p = .170). Not only is VM an effective method of teaching cytology to veterinary students that can be translated to a real-world case scenario, but it outperformed CM instruction in this study.

HISTOBREAST, a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue

Modern histopathology workflows rely on the digitization of histology slides. The quality of the resulting digital representations, in the form of histology slide image mosaics, depends on various specific acquisition conditions and on the image processing steps that underlie the generation of the final mosaic, e.g. registration and blending of the contained image tiles. We introduce HISTOBREAST, an extensive collection of brightfield microscopy images that we collected in a principled manner under different acquisition conditions on Haematoxylin - Eosin (H&E) stained breast tissue. HISTOBREAST is comprised of neighbour image tiles and ensemble of mosaics composed from different combinations of the available image tiles, exhibiting progressively degraded quality levels. HISTOBREAST can be used to benchmark image processing and computer vision techniques with respect to their robustness to image modifications specific to brightfield microscopy of H&E stained tissues. Furthermore, HISTOBREAST can serve in the development of new image processing methods, with the purpose of ensuring robustness to typical image artefacts that raise interpretation problems for expert histopathologists and affect the results of computerized image analysis.

Simple Shading Correction Method for Brightfield Whole Slide Imaging

Whole slide imaging (WSI) refers to the process of creating a high-resolution digital image of a whole slide. Since digital images are typically produced by stitching image sequences acquired from different fields of view, the visual quality of the images can be degraded owing to shading distortion, which produces black plaid patterns on the images. A shading correction method for brightfield WSI is presented, which is simple but robust not only against typical image artifacts caused by specks of dust and bubbles, but also against fixed-pattern noise, or spatial variations in pixel values under uniform illumination. The proposed method comprises primarily of two steps. The first step constructs candidates of a shading distortion model from a stack of input image sequences. The second step selects the optimal model from the candidates. The proposed method was compared experimentally with two previous state-of-the-art methods, regularized energy minimization (CIDRE) and background and shading correction (BaSiC) and showed better correction scores, as smooth operations and constraints were not imposed when estimating the shading distortion. The correction scores, averaged over 40 image collections, were as follows: proposed method, 0.39 ± 0.099; CIDRE method, 0.67 ± 0.047; BaSiC method, 0.55 ± 0.038. Based on the quantitative evaluations, we can confirm that the proposed method can correct not only shading distortion, but also fixed-pattern noise, compared with the two previous state-of-the-art methods.

A Taxonomic Index for Retrieval of Digitized Whole Slide Images from an Electronic Database for Medical School and Pathology Residency Education

Since the advent of whole slide imaging, the utility of digitized slides for education in medical school and residency has been amply documented. Pathology departments at most major academic medical centers have made digitized slides available to pathology residents for study, even before the use of digitized slides for clinical purposes (i.e., primary diagnosis) has become commonplace. This article describes the experience of one academic medical center with the storage and indexing of large volumes of digitized slides. Our goal was to be able to retrieve scanned slides for a variety of educational applications and thereby maximize the heuristic value of the slides. This posed a formidable challenge in terms of development and deployment of an index system that would allow exemplary slides to be identified and retrieved irrespective of the purpose for which the slide was scanned. We used the structure inherent in Aperio's image management software (eSlide Manager) to build an educational database that allowed each image to be appended with a unique taxonomic identifier so that the individual files could be retrieved in a flexible and utilitarian manner.

Optical Versus Virtual Microscope for Medical Education: A Systematic Review

Many technological innovations have changed the traditional practice of medical education and clinical practice. Whole slide imaging (WSI) technology provided an unique way of viewing conventional glass slides in histology and pathology laboratories. The WSI technology digitalized glass slide images and made them readily accessible via the Internet using tablets or computers. Users utilized the pan-and-zoom function to view digital images of slides, also referred to as the virtual microscope (VM), simulating use of an optical microscope (OM). Several articles have reported various outcomes on the utility of VM in teaching laboratories. Recently, the Royal College of Physicians and Surgeons of Canada certification examinations for anatomical pathologists ha completely adopted VM for the national licensing examination. To better inform medical educators, there is an urgent need for more structured reviews to draw evidence-based conclusions on the effectiveness of VM and learner's perceptions, in comparison to OM. The current study provides a descriptive summary of published outcomes using the systematic review approach. In conclusion, medical students' performance was improved with adoption of VM into the curriculum and recognized as a preferred learning modality, compared to OM. On the contrary, resident learners' performance was comparable between using OM and VM, with OM being the favored slide-viewing modality.

Overcoming Barriers in a Traditional Medical Education System by the Stepwise, Evidence-Based Introduction of a Modern Learning Technology

INTRODUCTION

Histology teaching in India and in other developing countries has not changed much over the past decades and has not joined the global movement of using virtual microscopy (VM). Many factors may have contributed to this academic inertia-including curricular requirements for traditional microscopy (TM) skills, assessments that are heavily based on TM, and unfamiliarity with modern technology among faculty, as well as infrastructural shortcomings. This study is aimed at overcoming these roadblocks by using a blended approach combining VM with TM in a tradition-centered curricular setting.

METHODS

For validation of this approach, the authors conducted a non-randomized controlled trial with a crossover design on first year medical students at the Government Medical College, Thiruvananthapuram, India. Examination scores and responses of a student group taught with VM as an adjunct to TM were compared with a student group taught with TM only.

RESULTS

The test group had significantly better results when compared to the control group for knowledge-based tests (p = 0.012; analysis of co-variance) and for an unannounced visual-based test conducted 1 month later (p = 0.001; Mann-Whitney U test). Feedback collected from students showed highly favorable responses to the use of VM for teaching histology.

CONCLUSION

This study should encourage Indian medical colleges and schools in other developing countries to start using VM as a supplementary approach for their histology education programs. Furthermore, as the Medical Council of India recommends the introduction of new competency-based integrated curriculum in India starting in 2019, the use of VM may facilitate more effective learning in the new scenario.

TRIAL REGISTRATION

CTRI/2018/04/012928.

Characterizing Diagnostic Search Patterns in Digital Breast Pathology: Scanners and Drillers

Following a baseline demographic survey, 87 pathologists interpreted 240 digital whole slide images of breast biopsy specimens representing a range of diagnostic categories from benign to atypia, ductal carcinoma in situ, and invasive cancer. A web-based viewer recorded pathologists' behaviors while interpreting a subset of 60 randomly selected and randomly ordered slides. To characterize diagnostic search patterns, we used the viewport location, time stamp, and zoom level data to calculate four variables: average zoom level, maximum zoom level, zoom level variance, and scanning percentage. Two distinct search strategies were confirmed: scanning is characterized by panning at a constant zoom level, while drilling involves zooming in and out at various locations. Statistical analysis was applied to examine the associations of different visual interpretive strategies with pathologist characteristics, diagnostic accuracy, and efficiency. We found that females scanned more than males, and age was positively correlated with scanning percentage, while the facility size was negatively correlated. Throughout 60 cases, the scanning percentage and total interpretation time per slide decreased, and these two variables were positively correlated. The scanning percentage was not predictive of diagnostic accuracy. Increasing average zoom level, maximum zoom level, and zoom variance were correlated with over-interpretation.

Interactive Digital Microscopy at the Center for a Cross-Continent Undergraduate Pathology Course in Mozambique

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.

A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association

Context.—

Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. Its basic function is to digitize glass slides, but its impact on pathology workflows, reproducibility, dissemination of educational material, expansion of service to underprivileged areas, and intrainstitutional and interinstitutional collaboration exemplifies a significant innovative movement with far-reaching effects. Although the benefits of WSI to pathology practices, academic centers, and research institutions are many, the complexities of implementation remain an obstacle to widespread adoption. In the wake of the first regulatory clearance of WSI for primary diagnosis in the United States, some barriers to adoption have fallen. Nevertheless, implementation of WSI remains a difficult prospect for many institutions, especially those with stakeholders unfamiliar with the technologies necessary to implement a system or who cannot effectively communicate to executive leadership and sponsors the benefits of a technology that may lack clear and immediate reimbursement opportunity.

Objectives.—

To present an overview of WSI technology—present and future—and to demonstrate several immediate applications of WSI that support pathology practice, medical education, research, and collaboration.

Data Sources.—

Peer-reviewed literature was reviewed by pathologists, scientists, and technologists who have practical knowledge of and experience with WSI.

Conclusions.—

Implementation of WSI is a multifaceted and inherently multidisciplinary endeavor requiring contributions from pathologists, technologists, and executive leadership. Improved understanding of the current challenges to implementation, as well as the benefits and successes of the technology, can help prospective users identify the best path for success.

Whole-Slide Imaging for Esophageal Adenocarcinoma

Whole-slide imaging revolutionizes the field of pathology especially in the areas of facilitation of research, long-term storages, exchange of information, and image analysis. In this process, a scanning equipment (scanner) scans the whole glass slide into a digital file. In research in esophageal adenocarcinoma or other cancers, whole-slide imaging could help in production of high-resolution images for studying and sharing of research information, assessment of tissue microarray slides as well as allowing digital image analysis of the tissue information such as level of staining (e.g., HER2) in a more efficient and objective manner. In this chapter, we will elaborate the concepts, advantages, barriers, and the operations of whole-slide imaging scanning.

Validation of whole-slide imaging in the primary diagnosis of liver biopsies in a University Hospital

BACKGROUND

Experience in the use of whole slide imaging (WSI) for primary diagnosis is limited and there are no comprehensive reports evaluating this technology in liver biopsy specimens.

AIMS

To determine the accuracy of interpretation of WSI compared with conventional light microscopy (CLM) in the diagnosis of needle liver biopsies.

METHODS

Two experienced liver pathologists blindly analyzed 176 consecutive biopsies from the Pathology Department at the Hospital Clinic of Barcelona. One of the observers performed the initial evaluation with CLM, and the second evaluation with WSI, whereas the second observer performed the first evaluation with WSI and the second with CLM. All slides were digitized in a Ventana iScan HT at 400× and evaluated with the Virtuoso viewer (Roche diagnostics). We used kappa statistics (κ) for two observations.

RESULTS

Intra-observer agreement between WSI and CLM evaluations was almost perfect (96.6%, κ=0.9; 95% confidence interval [95% CI]: 0.9-1 for observer 1, and 90.3%, κ=0.9; 95%CI: 0.8-0.9 for observer 2). Both native and transplantation biopsies showed an almost perfect concordance in the diagnosis.

CONCLUSION

Diagnosis of needle liver biopsy specimens using WSI is accurate. This technology can reliably be introduced in routine diagnosis.

E-learning for medical imaging specialists: introducing blended learning in a nuclear medicine specialist course

Background

While e-learning has become an important tool in teaching medical students, the training of specialists in medical imaging is still dominated by lecture-based courses.

Purpose

To assess the potential of e-learning in specialist education in medical imaging.

Material and Methods

An existing lecture-based five-day course in Clinical Nuclear Medicine (NM) was enhanced by e-learning resources and activities, including practical exercises. An anonymized survey was conducted after participants had completed and passed the multiple choice electronic course examination.

Results

Twelve out of 15 course participants (80%) responded. Overall satisfaction with the new course format was high, but 25% of the respondents wanted more interactive elements such as discussions and practical exercises. The importance of lecture handouts and supplementary online material such as selected original articles and professional guidelines was affirmed by all the respondents (92% fully, 8% partially), while 75% fully and 25% partially agreed that the lectures had been interesting and relevant.

Conclusion

E-learning represents a hitherto unrealized potential in the education of medical specialists. It may expedite training of medical specialists while at the same time containing costs.

Dermatopathology education in the era of modern technology

Continuing technological advances are inevitably impacting the study and practice of dermatopathology (DP). We are seeing the transition from glass slide microscopy to virtual microscopy, which is serving both as an accessible educational medium for medical students, residents and fellows in the form of online databases and atlases, as well as a research tool to better inform us regarding the development of visual diagnostic expertise. Expansion in mobile technology is simplifying slide image attainment and providing greater opportunities for phone- and tablet-based microscopy, including teledermatopathology instruction and consultation in resource-poor areas with lack of specialists. Easily accessible mobile and computer-based applications ("apps"), including myDermPath and Clearpath, are providing an interactive medium for DP instruction. The Internet and social networking sites are enabling rapid global communication of DP information and image-sharing, promoting collaborative diagnostic research and scholastic endeavors.

RecutClub.com: An Open Source, Whole Slide Image-based Pathology Education System

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.

Turning Microscopy in the Medical Curriculum Digital: Experiences from The Faculty of Health and Medical Sciences at University of Copenhagen

Familiarity with the structure and composition of normal tissue and an understanding of the changes that occur during disease is pivotal to the study of the human body. For decades, microscope slides have been central to teaching pathology in medical courses and related subjects at the University of Copenhagen. Students had to learn how to use a microscope and envisage three-dimensional processes that occur in the body from two-dimensional glass slides. Here, we describe how a PathXL virtual microscopy system for teaching pathology and histology at the Faculty has recently been implemented, from an administrative, an economic, and a teaching perspective. This fully automatic digital microscopy system has been received positively by both teachers and students, and a decision was made to convert all courses involving microscopy to the virtual microscopy format. As a result, conventional analog microscopy will be phased out from the fall of 2016.