Recent advances in ultra-high-throughput microscopy have enabled a new generation of cell classification methodologies using image-based cell phenotypes alone. In contrast to current single-cell analysis techniques that rely solely on slow and costly genetic/epigenetic analysis, these image-based analyses allow morphological profiling and screening of thousands or even millions of single cells at a fraction of the cost, and have been proven to demonstrate the statistical significance required for understanding the role of cell heterogeneity in diverse biological applications, ranging from cancer screening to drug candidate identification/validation processes. This paper examines the efficacies and opportunities presented by machine learning algorithms in processing large scale datasets with millions of label-free cell images. An automatic single-cell classification framework using convolutional neural network (CNN) has been developed. A comparative analysis of its efficiency in classifying large datasets against conventional k-nearest neighbors (kNN) and support vector machine (SVM) based methods are also presented. Experiments have shown that our proposed framework can efficiently identify multiple types cells with over 99% accuracy based on the phenotypic label-free bright-field images; and CNN-based models perform well and relatively stable against data volume compared with kNN and SVM.