  We present a fully modular and scalable software pipeline for processing
electron microscope (EM) images of brain slices into 3D visualization of
individual neurons and demonstrate an end-to-end segmentation of a large EM
volume using a supercomputer. Our pipeline scales multiple packages used by the
EM community with minimal changes to the original source codes. We tested each
step of the pipeline individually, on a workstation, a cluster, and a
supercomputer. Furthermore, we can compose workflows from these operations
using a Balsam database that can be triggered during the data acquisition or
with the use of different front ends and control the granularity of the
pipeline execution. We describe the implementation of our pipeline and
modifications required to integrate and scale up existing codes. The modular
nature of our environment enables diverse research groups to contribute to the
pipeline without disrupting the workflow, i.e. new individual codes can be
easily integrated for each step on the pipeline.
