We demonstrate identification of position, material, orientation and shape of objects imaged by an $^{85}$Rb atomic magnetometer performing electromagnetic induction imaging supported by machine learning. Machine learning maximizes the information extracted from the images created by the magnetometer, demonstrating the use of hidden data. Localization 2.6 times better than the spatial resolution of the imaging system and successful classification up to 97$%$ are obtained. This circumvents the need of solving the inverse problem, and demonstrates the extension of machine learning to diffusive systems such as low-frequency electrodynamics in media. Automated collection of task-relevant information from quantum-based electromagnetic imaging will have a relevant impact from biomedicine to security.