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We present a new method for rapid, automated, large-scale 3D mitochondria instance segmentation, developed in response to the ISBI 2021 MitoEM Challenge. In brief, we trained separate machine learning algorithms to predict (1) mitochondria areas and (2) mitochondria boundaries in image volumes acquired from both rat and human cortex with multi-beam scanning electron microscopy. The predictions from these algorithms were combined in a multi-step post-processing procedure, that resulted in high semantic and instance segmentation performance. All code is provided via a public repository.