Synapse Detection Efficiency in EM Drosophila Connectomics

Researchers have long noted the differences in synapse count between different EM reconstructions of similar circuitry. In this paper we attempt to determine the portion of these differences that may be due to different sample preparation and imaging techniques, in particular serial-section transmission imaging (SS-TEM) compared to focused ion beam with scanning electron microscopy (FIB-SEM). To do this, we compare synapse detection in the major Drosophila EM reconstructions - FANC, MANC, FAFB (with original and new synapses), male CNS, BANC, and HemiBrain, plus several smaller reconstructions. We look at raw synapse counts to avoid any dependence on proofreading, and compensate insofar as possible for the confounds of sample sizes differences and different software detection efficiency. The result are estimates, per compartment and for the sample as a whole, of the number of synapses that would be visible to a skilled human observer. These are then compared across all samples, using regions which are reconstructed in common for each sample pair. We find that in almost all known cases where a volume has been reconstructed by both techniques, isotropic FIB-SEM reconstructions show more human-visible synapses than microtome sliced reconstructions, typically by more than 40%. This strongly suggests, but does not conclusively prove, that synapses are easier to see in isotropic FIB-SEM data.