TLCellClassifier: Machine Learning Based Cell Classification for Bright-Field Time-Lapse Images

Abstract

AbstractImmunotherapies have shown promising results in treating patients with hematological malignancies like multiple myeloma, which is an incurable but treatable bone marrow-resident plasma cell cancer. Choosing the most efficacious treatment for a patient remains a challenge in such cancers. However, pre-clinical assays involving patient-derived tumor cells co-cultured in anex vivoreconstruction of immune-tumor micro-environment have gained considerable notoriety over the past decade. Such assays can characterize a patient’s response to several therapeutic agents including immunotherapies in a high-throughput manner, where bright-field images of tumor (target) cells interacting with effector cells (T cells, Natural Killer (NK) cells, and macrophages) are captured once every 30 minutes for upto six days. Cell detection, tracking, and classification of thousands of cells of two or more types in each frame is bound to test the limits of some of the most advanced computer vision tools developed to date and requires a specialized approach. We propose TLCellClassifier (time-lapse cell classifier) for live cell detection, cell tracking, and cell type classification, with enhanced accuracy and efficiency obtained by integrating convolutional neural networks (CNN), metric learning, and long short-term memory (LSTM) networks, respectively. State-of-the-art computer vision software like KTH-SE and YOLOv8 are compared with TLCellClassifier, which shows improved accuracy in detection (CNN) and tracking (metric learning). A two-stage LSTM-based cell type classification method is implemented to distinguish between multiple myeloma (tumor/target) cells and macrophages/monocytes (immune/effector cells). Validation of cell type classification was done both using synthetic datasets andex vivoexperiments involving patient-derived tumor/immune cells.Availability and implementationhttps://github.com/QibingJiang/cell classification ml