Automated Object Tracing for Biomedical Image Segmentation Using a Deep Convolutional Neural Network

Convolutional neural networks (CNNs) have been used for fast and accurate segmentation of medical images. In this paper, we present a novel methodology that uses CNNs for segmentation by mimicking the human task of tracing object boundaries. The architecture takes as input a patch of an image with an overlay of previously traced pixels and the output predicts the coordinates of the next m pixels to be traced. We also consider a CNN architecture that leverages the output from another semantic segmentation CNN, e.g., U-net, as an auxiliary image channel. To initialize the trace path in an image, we use either locations identified as object boundaries with high confidence from a semantic segmentation CNN or a short manually traced path. By iterating the CNN output, our method continues the trace until it intersects with the beginning of the path. We show that our network is more accurate than the state-of-the-art semantic segmentation CNN on microscopy images from the ISBI cell tracking challenge. Moreover, our methodology provides a natural platform for performing human-in-the-loop segmentation that is more accurate than CNNs alone and orders of magnitude faster than manual segmentation.