Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets
This work addresses a critical bottleneck in neuroscience for researchers analyzing neural circuits, though it is incremental as it builds on prior methods to handle both synapse types.
The paper tackles the problem of detecting synaptic connectivity in neural reconstruction from EM data by predicting both cleft location and direction for both dyadic and polyadic synapses, and it outperforms existing methods on rodent and fruit fly brain datasets.
Synaptic connectivity detection is a critical task for neural reconstruction from Electron Microscopy (EM) data. Most of the existing algorithms for synapse detection do not identify the cleft location and direction of connectivity simultaneously. The few methods that computes direction along with contact location have only been demonstrated to work on either dyadic (most common in vertebrate brain) or polyadic (found in fruit fly brain) synapses, but not on both types. In this paper, we present an algorithm to automatically predict the location as well as the direction of both dyadic and polyadic synapses. The proposed algorithm first generates candidate synaptic connections from voxelwise predictions of signed proximity generated by a 3D U-net. A second 3D CNN then prunes the set of candidates to produce the final detection of cleft and connectivity orientation. Experimental results demonstrate that the proposed method outperforms the existing methods for determining synapses in both rodent and fruit fly brain.