EPiK-a Workflow for Electron Tomography in Kepler.

Authors:
Xiaohua Wan
Xiaohua Wan
Beijing Tongren Hospital
Ilkay Altintas
Ilkay Altintas
University of California San Diego
United States
Jianwu Wang
Jianwu Wang
South China Agricultural University
China
Daniel Crawl
Daniel Crawl
San Diego Supercomputer Center
Sebastien Phan
Sebastien Phan
University of California at San Diego
United States
Albert Lawrence
Albert Lawrence
University of California
United States
Mark Ellisman
Mark Ellisman
University of California San Diego
United States

Procedia Comput Sci 2014 ;20:2295-2305

National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.

Scientific workflows integrate data and computing interfaces as 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 EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (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.

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Source
http://dx.doi.org/10.1016/j.procs.2014.05.214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304086PMC

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January 2014
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