EPiK-a Workflow for Electron Tomography in Kepler

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https://www.sciencedirect.com/science/article/pii/S1877050914003913

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https://doi.org/10.1016/j.procs.2014.05.214
 http://hdl.handle.net/11603/31600

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UMBC Information Systems Department
UMBC Center for Accelerated Real Time Analysis
UMBC Center for Real-time Distributed Sensing and Autonomy
UMBC Computer Science and Electrical Engineering Department
UMBC Data Science
UMBC Joint Center for Earth Systems Technology (JCET)

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https://orcid.org/0000-0002-9933-1170

Date

2014-06-06

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journal articles
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Citation of Original Publication

Chen, Ruijuan, Xiaohua Wan, Ilkay Altintas, Jianwu Wang, Daniel Crawl, Sébastien Phan, Albert Lawrence, and Mark Ellisman. “EPiK-a Workflow for Electron Tomography in Kepler1.” Procedia Computer Science, 2014 International Conference on Computational Science, 29 (January 1, 2014): 2295–2305. https://doi.org/10.1016/j.procs.2014.05.214.

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UMBC Big Data Analytics Lab

Abstract

Scientific workflows integrate data and computing interfacesas configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiKworkflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered back projection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.