RT Journal Article
SR Electronic
T1 Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.02.18.955237
DO 10.1101/2020.02.18.955237
A1 Samik Banerjee
A1 Lucas Magee
A1 Dingkang Wang
A1 Xu Li
A1 Bingxing Huo
A1 Jaik-ishan Jayakumar
A1 Katie Matho
A1 Adam Lin
A1 Keerthi Ram
A1 Mohanasankar Sivaprakasam
A1 Josh Huang
A1 Yusu Wang
A1 Partha P. Mitra
YR 2020
UL http://biorxiv.org/content/early/2020/02/19/2020.02.18.955237.abstract
AB Understanding of neuronal circuitry at cellular resolution within the brain has relied on tract tracing methods which involve careful observation and interpretation by experienced neuroscientists. With recent developments in imaging and digitization, this approach is no longer feasible with the large scale (terabyte to petabyte range) images. Machine learning based techniques, using deep networks, provide an efficient alternative to the problem. However, these methods rely on very large volumes of annotated images for training and have error rates that are too high for scientific data analysis, and thus requires a significant volume of human-in-the-loop proofreading. Here we introduce a hybrid architecture combining prior structure in the form of topological data analysis methods, based on discrete Morse theory, with the best-in-class deep-net architectures for the neuronal connectivity analysis. We show significant performance gains using our hybrid architecture on detection of topological structure (e.g. connectivity of neuronal processes and local intensity maxima on axons corresponding to synaptic swellings) with precision/recall close to 90% compared with human observers. We have adapted our architecture to a high performance pipeline capable of semantic segmentation of light microscopic whole-brain image data into a hierarchy of neuronal compartments. We expect that the hybrid architecture incorporating discrete Morse techniques into deep nets will generalize to other data domains.