Abstract
Recent advances in 3d electron microscopy are yielding ever larger reconstructions of brain tissue, encompassing thousands of individual neurons interconnected by millions of synapses. Interpreting reconstructions at this scale demands advances in the automated analysis of neuronal morphologies, for example by identifying morphological and functional subcompartments within neurons. We present a method that for the first time uses full 3d input (voxels) to automatically classify reconstructed neuron fragments as axon, dendrite, or somal subcompartments. Based on 3d convolutional neural networks, this method achieves a mean f1-score of 0.972, exceeding the previous state of the art of 0.955. The resulting predictions can support multiple analysis and proofreading applications. In particular, we leverage finely localized subcompartment predictions for automated detection and correction of merge errors in the volume reconstruction, successfully detecting 90.6% of inter-class merge errors with a false positive rate of only 2.7%.
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Acknowledgments
We thank Philipp Schubert and Jörgen Kornfeld for sharing detailed CMN results and training data, as well as the EM volume. We thank Jeremy Maitin-Shepard and the anonymous reviewers for comments on the manuscript.
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Li, H., Januszewski, M., Jain, V., Li, P.H. (2020). Neuronal Subcompartment Classification and Merge Error Correction. In: Martel, A.L., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science(), vol 12265. Springer, Cham. https://doi.org/10.1007/978-3-030-59722-1_9
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DOI: https://doi.org/10.1007/978-3-030-59722-1_9
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