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%.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Manuscript expanded based on reviewer comments. The main text is now in sync with the conference version of the paper, but the supplemental material is more detailed here.