HistomicsML is an interactive machine-learning system for analyzing whole-slide imaging digital pathology datasets. The web-server enables interaction with whole-slide imaging datasets and image analysis metadata to train and validate classification rules for identifying microanatomic objects. HistomicsML operates using data generated by image segmentation and feature extraction algorithms applied to whole-slide images that characterize objects like cell nuclei, and can operate interchangeably with any image segmentation and feature extraction algorithms. The web-interface facilitates classifier training and also provides interfaces for generating ground-truth validation data, validating classifiers, loading data, and exporting results.