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Multi-class segmentation of neuronal electron microscopy images using deep learning

Study of connectivity of neural circuits is an essential step towards a better understanding of functioning of the nervous system. With the recent improvement in imaging techniques, high-resolution and high-volume images are being generated requiring automated segmentation techniques. We present a pixel-wise classification method based on Bayesian SegNet architecture. We carried out multi-class segmentation on serial section Transmission Electron Microscopy (ssTEM) images of Drosophila third instar larva ventral nerve cord, labeling the four classes of neuron membranes, neuron intracellular space, mitochondria and glia / extracellular space. Bayesian SegNet was trained using 256 ssTEM images of 256 x 256 pixels and tested on 64 different ssTEM images of the same size, from the same serial stack. Due to high class imbalance, we used a class-balanced version of Bayesian SegNet by re-weighting each class based on their relative frequency. We achieved an overall accuracy of 93% and a mean class accuracy of 88% for pixel-wise segmentation using this encoder-decoder approach. On evaluating the segmentation results using similarity metrics like SSIM and Dice Coefficient, we obtained scores of 0.994 and 0.886 respectively. Additionally, we used the network trained using the 256 ssTEM images of Drosophila third instar larva for multi-class labeling of ISBI 2012 challenge ssTEM dataset.