{"doi":"10.48550/arxiv.2011.03204","title":"Toward an Automated HPC Pipeline for Processing Large Scale Electron\\n Microscopy Data","abstract":"We present a fully modular and scalable software pipeline for processing\\nelectron microscope (EM) images of brain slices into 3D visualization of\\nindividual neurons and demonstrate an end-to-end segmentation of a large EM\\nvolume using a supercomputer. Our pipeline scales multiple packages used by the\\nEM community with minimal changes to the original source codes. We tested each\\nstep of the pipeline individually, on a workstation, a cluster, and a\\nsupercomputer. Furthermore, we can compose workflows from these operations\\nusing a Balsam database that can be triggered during the data acquisition or\\nwith the use of different front ends and control the granularity of the\\npipeline execution. We describe the implementation of our pipeline and\\nmodifications required to integrate and scale up existing codes. The modular\\nnature of our environment enables diverse research groups to contribute to the\\npipeline without disrupting the workflow, i.e. new individual codes can be\\neasily integrated for each step on the pipeline.\\n","journal":"arXiv (Cornell University)","year":2020,"id":134838,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9507,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":590403,"name":"Hanyu Li","orcid":"0000-0002-7848-731X","position":1,"is_corresponding":false},{"id":590404,"name":"Jeffery Kinnison","orcid":"0000-0001-5643-1123","position":2,"is_corresponding":false},{"id":590405,"name":"Murat Keçeli","orcid":"0000-0001-8588-9272","position":3,"is_corresponding":false},{"id":590770,"name":"Misha Salim","orcid":null,"position":4,"is_corresponding":false},{"id":271833,"name":"Narayanan Kasthuri","orcid":"0000-0003-3825-931X","position":5,"is_corresponding":false},{"id":590406,"name":"Thomas Uram","orcid":"0000-0002-5631-0142","position":6,"is_corresponding":false},{"id":590407,"name":"Nicola Ferrier","orcid":"0000-0003-1444-0624","position":7,"is_corresponding":false},{"id":590402,"name":"Rafael Vescovi","orcid":"0000-0002-0652-1128","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-18T23:16:27.963294Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}