title: SmartTracing: self-learning-based Neuron reconstruction.
abstract: In this work, we propose SmartTracing, an automatic tracing framework that does not require substantial human intervention. There are two major novelties in SmartTracing. First, given an input image, SmartTracing invokes a user-provided existing neuron tracing method to produce an initial neuron reconstruction, from which the likelihood of every neuron reconstruction unit is estimated. This likelihood serves as a confidence score to identify reliable regions in a neuron reconstruction. With this score, SmartTracing automatically identifies reliable portions of a neuron reconstruction generated by some existing neuron tracing algorithms, without human intervention. These reliable regions are used as training exemplars. Second, from the training exemplars the most characteristic wavelet features are automatically selected and used in a machine learning framework to predict all image areas that most probably contain neuron signal. Since the training samples and their most characterizing features are selected from each individual image, the whole process is automatically adaptive to different images. Notably, SmartTracing can improve the performance of an existing automatic tracing method. In our experiment, with SmartTracing we have successfully reconstructed complete neuron morphology of 120 Drosophila neurons. In the future, the performance of SmartTracing will be tested in the BigNeuron project (bigneuron.org). It may lead to more advanced tracing algorithms and increase the throughput of neuron morphology-related studies.
authors.affiliation: Allen Institute for Brain Science, Seattle, WA, USA. cojoc.chen@gmail.com.|Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA. cojoc.chen@gmail.com.
authors.forename: Hanbo
authors.initials: H
authors.lastname: Chen
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Xiao
authors.affiliation: Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA.
authors.forename: Tianming
authors.initials: T
authors.lastname: Liu
authors.affiliation: Allen Institute for Brain Science, Seattle, WA, USA.
authors.forename: Hanchuan
authors.initials: H
authors.lastname: Peng
keywords: Machine learning; Neuron morphology; Neuron reconstruction; Reconstruction confidence; SmartTracing