{"paper":{"title":"Toward an Automated HPC Pipeline for Processing Large Scale Electron Microscopy Data","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["eess.IV"],"primary_cat":"cs.DC","authors_text":"Hanyu Li, Jeffery Kinnison, Misha Salim, Murat Keceli, Narayanan Kasthuri, Nicola Ferrier, Rafael Vescovi, Thomas D. Uram","submitted_at":"2020-11-06T06:13:54Z","abstract_excerpt":"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 "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2011.03204","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2011.03204/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}