Deep learning introduces the potential for autonomous S/TEM characterization, a step towards unsupervised data acquisition and analysis through machine learning. Whole image classification is the first step towards the long-term goal of autonomous image data acquisition and analysis. We have successfully retrained AlexNet, b-FCN, and U-Net, pre-existing deep learning Convolutional Neural Networks(CNNs), for autonomous, whole image classification and analysis, on TEM image datasets.