Annotation practices in computational pathology: a European Society of Digital and Integrative Pathology (ESDIP) survey study.

Integrating digital pathology (DP) and artificial intelligence (AI) algorithms can potentially improve diagnostic practice and precision medicine. Developing reliable, generalizable, and comparable AI algorithms depends on access to meticulously annotated data. However, achieving this requires robust collaboration among pathologists, computer scientists and other researchers to ensure data quality and consistency.

A survey on cell nuclei instance segmentation and classification: Leveraging context and attention.

Nuclear-derived morphological features and biomarkers provide relevant insights regarding the tumour microenvironment, while also allowing diagnosis and prognosis in specific cancer types. However, manually annotating nuclei from the gigapixel Haematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features for artificial intelligence (AI) tools. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&E-stains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance.

Improved recovery of urinary small extracellular vesicles by differential ultracentrifugation.

Extracellular vesicles (EVs) are lipid-membrane enclosed structures that are associated with several diseases, including those of genitourinary tract. Urine contains EVs derived from urinary tract cells. Owing to its non-invasive collection, urine represents a promising source of biomarkers for genitourinary disorders, including cancer.

Cervical cytology and HPV distribution in Cape Verde: A snapshot of a country taken during its first HPV nation-wide vaccination campaign.

Cervical cancer ranks as the third most common female cancer in Cape Verde and is the leading cause of cancer-related deaths among women in the country. While Human Papillomavirus (HPV) vaccination, which started in 2021, is anticipated to significantly reduce disease incidence, cervical screening remains crucial for non-vaccinated women. We retrospectively reviewed gynecologic cytology exams and HPV tests performed in Cape Verde between 2017 and April 2023 and processed at IMP Diagnostics.

An interpretable machine learning system for colorectal cancer diagnosis from pathology slides.

Considering the profound transformation affecting pathology practice, we aimed to develop a scalable artificial intelligence (AI) system to diagnose colorectal cancer from whole-slide images (WSI). For this, we propose a deep learning (DL) system that learns from weak labels, a sampling strategy that reduces the number of training samples by a factor of six without compromising performance, an approach to leverage a small subset of fully annotated samples, and a prototype with explainable predictions, active learning features and parallelisation. Noting some problems in the literature, this study is conducted with one of the largest WSI colorectal samples dataset with approximately 10,500 WSIs.

Invisible for a few but essential for many: the role of Histotechnologists in the establishment of digital pathology.

Digital pathology (DP) is indisputably the future for histopathology laboratories. The process of digital implementation requires deep workflow reorganisation which involves an interdisciplinary team. This transformation may have the greatest impact on the Histotechnologist (HTL) profession.

A CAD system for automatic dysplasia grading on H&E cervical whole-slide images.

Cervical cancer is the fourth most common female cancer worldwide and the fourth leading cause of cancer-related death in women. Nonetheless, it is also among the most successfully preventable and treatable types of cancer, provided it is early identified and properly managed. As such, the detection of pre-cancerous lesions is crucial.

Annotating for Artificial Intelligence Applications in Digital Pathology: A Practical Guide for Pathologists and Researchers.

Training machine learning models for artificial intelligence (AI) applications in pathology often requires extensive annotation by human experts, but there is little guidance on the subject. In this work, we aimed to describe our experience and provide a simple, useful, and practical guide addressing annotation strategies for AI development in computational pathology. Annotation methodology will vary significantly depending on the specific study's objectives, but common difficulties will be present across different settings.

Vimentin epigenetic deregulation in Bladder Cancer associates with acquisition of invasive and metastatic phenotype through epithelial-to-mesenchymal transition.

Bladder cancer (BlCa) is the ninth most common cancer worldwide, associated with significant morbidity and mortality. Thus, understand the biological mechanisms underlying tumour progression is of great clinical significance. Vimentin (VIM) is (over)expressed in several carcinomas, putatively in association with EMT.

Quality Control in Digital Pathology: Automatic Fragment Detection and Counting.

Manual assessment of fragments during the pro-cessing of pathology specimens is critical to ensure that the material available for slide analysis matches that captured during grossing without losing valuable material during this process. However, this step is still performed manually, resulting in lost time and delays in making the complete case available for evaluation by the pathologist. To overcome this limitation, we developed an autonomous system that can detect and count the number of fragments contained on each slide.

iMIL4PATH: A Semi-Supervised Interpretable Approach for Colorectal Whole-Slide Images.

Colorectal cancer (CRC) diagnosis is based on samples obtained from biopsies, assessed in pathology laboratories. Due to population growth and ageing, as well as better screening programs, the CRC incidence rate has been increasing, leading to a higher workload for pathologists. In this sense, the application of AI for automatic CRC diagnosis, particularly on whole-slide images (WSI), is of utmost relevance, in order to assist professionals in case triage and case review.

Digital Pathology Implementation in Private Practice: Specific Challenges and Opportunities.

Digital pathology (DP) is being deployed in many pathology laboratories, but most reported experiences refer to public health facilities. In this paper, we report our experience in DP transition at a high-volume private laboratory, addressing the main challenges in DP implementation in a private practice setting and how to overcome these issues. We started our implementation in 2020 and we are currently scanning 100% of our histology cases.

CAD systems for colorectal cancer from WSI are still not ready for clinical acceptance.

Most oncological cases can be detected by imaging techniques, but diagnosis is based on pathological assessment of tissue samples. In recent years, the pathology field has evolved to a digital era where tissue samples are digitised and evaluated on screen. As a result, digital pathology opened up many research opportunities, allowing the development of more advanced image processing techniques, as well as artificial intelligence (AI) methodologies.

A Multiplex Test Assessing and in Urine Accurately Discriminates Bladder Cancer from Inflammatory Conditions.

Bladder cancer (BlCa) is a common malignancy with significant morbidity and mortality. Current diagnostic methods are invasive and costly, showing the need for newer biomarkers. Although several epigenetic-based biomarkers have been proposed, their ability to discriminate BlCa from common benign conditions of the urinary tract, especially inflammatory diseases, has not been adequately explored.

Variants of Papillary Thyroid Carcinoma: An Algorithmic Cytomorphology-Based Approach to Cytology Specimens.

Background: Thyroid cancer accounts for 1% of cancer cases in developed countries, in which papillary thyroid carcinoma (PTC) is the most common type. There are multiple variants of PTC described to date, some of them with aggressive behavior and poor clinical outcome. These variants are well described and accepted in recent guidelines of many international societies, and the prognostic and management implications are well laid out.

Breast Fine Needle Aspiration Biopsy Cytology Using the Newly Proposed IAC Yokohama System for Reporting Breast Cytopathology: The Experience of a Single Institution.

Objective: Recently the International Academy of Cytology (IAC) proposed a new reporting system for breast fine needle aspiration biopsy (FNAB) cytology. We aimed to categorize our samples according to this classification and to assess the risk of malignancy (ROM) for each category as well as the diagnostic yield of breast FNAB.

Study Design: Breast FNAB specimens obtained between January 2007 and December 2017 were reclassified according to the newly proposed IAC Yokohama reporting system.

"The other side of the coin": understanding noninvasive follicular tumor with papillary-like nuclear features in unifocal and multifocal settings.

The recent description of noninvasive follicular tumor with papillary-like nuclear features (NIFTP) creates several diagnostic and therapeutic challenges for both the pathologist and the attending clinician. Given the concern about overtreatment of these neoplasms, the best way to manage the patients by a surgical procedure and postsurgical follow-up is still under discussion. We aimed to identify predictors of synchronous disease (eg, bilateral cancers) that can influence the appropriate type of surgery and long-term surveillance.

A comparison study of the reporting systems for salivary gland fine needle aspirations: Are they really different?

Background: Recently a new system for reporting salivary gland fine-needle aspiration (FNA) cytology was proposed, the Milan System for Reporting Salivary Gland Cytopathology (MSRSGC). Herein, we evaluated diagnostic accuracy of salivary gland FNA, comparing the system previously used in our hospital with the Milan system.

Methods: Salivary gland specimens obtained between 2011 and 2017 were reclassified according to MSRSGC.

The new guidelines of Papanicolaou Society of Cytopathology for respiratory specimens: Assessment of risk of malignancy and diagnostic yield in different cytological modalities.

Background: In 2016, the Papanicolaou Society of Cytopathology (PSC) issued a new classification scheme for respiratory cytology. We aim to evaluate our samples according to this classification and to assess risk of malignancy and diagnostic yield of different cytological modalities.

Methods: Respiratory specimens (sputum, bronchial wash/brush, BAL and FNA) obtained between 2007 and 2016 were reclassified according to PSC guidelines.

Sialyl-Tn identifies muscle-invasive bladder cancer basal and luminal subtypes facing decreased survival, being expressed by circulating tumor cells and metastases.

Objectives: To evaluate the potential of sialyl-Tn (STn), a cancer-associated glycan antigen present in membrane glycoproteins, to improve a recent molecular model for stratification and prognostication of advanced stage bladder tumors based on keratins (KRT14, 5, and 20) expression. In addition, determine the association between STn and disease dissemination based on the evaluation of circulating tumor cells (CTCs) and the metastasis, which is a critical matter to improve patient management.

Patients And Methods: A retrospective series of 80 muscle-invasive primary bladder tumors and associated metastasis were screened for KRT14, 5, and 20 and STn by real-time polymerase chain reaction and immunohistochemistry.

Identification of somatic TERT promoter mutations in familial nonmedullary thyroid carcinomas.

Objective: The genes causing familial nonmedullary thyroid carcinoma (FNMTC) identified to date are only involved in a small fraction of the families. Recently, somatic mutations in TERT promoter region and in EIF1AX gene were reported in thyroid tumours of undefined familial status. The aim of this study was to investigate the role of TERT and EIF1AX mutations in familial thyroid tumours.

MicroRNA promoter methylation: a new tool for accurate detection of urothelial carcinoma.

Background: Urothelial carcinoma (UC) is the most common cancer affecting the urinary system, worldwide. Lack of accurate early detection tools entails delayed diagnosis, precluding more efficient and timely treatment. In a previous study, we found that miR-129-2 and miR-663a were differentially methylated in UC compared with other genitourinary tract malignancies.