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

Toward an Automated HPC Pipeline for Processing Large Scale Electron Microscopy Data