Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images

We address a central problem of neuroanatomy, namely, the automatic segmentation of neuronal structures depicted in stacks of electron microscopy (EM) images. This is necessary to efficiently map 3D brain structure and connectivity. To segment biological neuron membranes, we use a special type of deep artificial neural network as a pixel classifier. The label of each pixel (membrane or nonmembrane) is predicted from raw pixel values in a square window centered on it.