title: EPiK-a Workflow for Electron Tomography in Kepler.
abstract: 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.
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Ruijuan
authors.initials: R
authors.lastname: Chen
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.|Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Wan
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Ilkay
authors.initials: I
authors.lastname: Altintas
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Jianwu
authors.initials: J
authors.lastname: Wang
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Crawl
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Phan
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Albert
authors.initials: A
authors.lastname: Lawrence
authors.affiliation: National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Ellisman
keywords: EPiK; Electron Tomography; Kepler; Scientific workflows; TxBR