The present approach relates, in some aspects, to a multi-level and a multi-channel frame work for segmentation using model-based or “shallow” classification (i.e. learning processes such as linear regression, clustering, support vector machines, and so forth) followed by deep learning. This framework starts with a very low resolution version of the multi-channel data and constructs an shallow classifier with simple features to generate a coarser level tissue mask that in turn is used to crop patches from the high-resolution volume. The cropped volume is then processed using the trained convolution network to perform a deep learning based segmentation within the slices.