AI-powered transmitted light microscopy for functional analysis of live cells

Transmitted light microscopy can readily visualize the morphology of living cells. Here, we introduce artificial-intelligence-powered transmitted light microscopy (AIM) for subcellular structure identification and labeling-free functional analysis of live cells. AIM provides accurate images of subcellular organelles; allows identification of cellular and functional characteristics (cell type, viability, and maturation stage); and facilitates live cell tracking and multimodality analysis of immune cells in their native form without labeling

Classification of normal versus malignant cells in B-ALL microscopic images based on a tiled convolution neural network approach.

In this paper we present a method based on the existing convolution neural network architecture of AlexNet for the purpose of classifying microscopic images of B-ALL white blood cancer cells. This classification problem is especially challenging due to lack of conspicuous morphological differences between normal and malignant cell nuclei. Therefore, we designed a machine learning pipeline that focused on the texture of the staining images. Briefly, our approach divides the cell image into several overlapping tiles and trains a modified version of AlexNet on the tiles. Only those tiles are retained which are fully contained within the cell image. Several such networks were trained in an ensemble fashion using different training–validation data splits. For a given test image, the tiles are generated and ran through all the trained networks. The outputs of all networks along with the nucleus area are then fed into a simple decision tree, which generates the final prediction. The proposed method was developed in the context of the ISBI 2019 C-NMC challenge. The final testing results demonstrated a classification-weighted F1 score of 0.8307 using 2586 test images. The results demonstrate the possibility of making relatively accurate predictions using only local texture features

Interactive classification of whole-slide imaging data for cancer researchers

Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists. In this article, we describe HistomicsML2, a software tool for learn-by-example training of machine learning classifiers for histologic patterns in whole-slide images. This tool improves training efficiency and classifier performance by guiding users to the most informative training examples for labeling and can be used to develop classifiers for prospective application or as a rapid annotation tool that is adaptable to different cancer types. HistomicsML2 runs as a containerized server application that provides web-based user interfaces for classifier training, validation, exporting inference results, and collaborative review, and that can be deployed on GPU servers or cloud platforms. We demonstrate the utility of this tool by using it to classify tumor-infiltrating lymphocytes in breast carcinoma and cutaneous melanoma. Significance: An interactive machine learning tool for analyzing digital pathology images enables cancer researchers to apply this tool to measure histologic patterns for clinical and basic science studies

Triage-driven diagnosis of Barrett's esophagus for early detection of esophageal adenocarcinoma using deep learning.

Deep learning methods have been shown to achieve excellent performance on diagnostic tasks, but how to optimally combine them with expert knowledge and existing clinical decision pathways is still an open challenge. This question is particularly important for the early detection of cancer, where high-volume workflows may benefit from (semi-)automated analysis. Here we present a deep learning framework to analyze samples of the Cytosponge-TFF3 test, a minimally invasive alternative to endoscopy, for detecting Barrett's esophagus, which is the main precursor of esophageal adenocarcinoma. We trained and independently validated the framework on data from two clinical trials, analyzing a combined total of 4,662 pathology slides from 2,331 patients. Our approach exploits decision patterns of gastrointestinal pathologists to define eight triage classes of varying priority for manual expert review. By substituting manual review with automated review in low-priority classes, we can reduce pathologist workload by 57% while matching the diagnostic performance of experienced pathologists