EPiK-a Workflow for Electron Tomography in Kepler1

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.

Nanoscale 3D EM reconstructions reveal intrinsic mechanisms of structural diversity of chemical synapses

“…Double-tilt series were collected with 0.5 degree increments at 22,500X magnification on a 4k x 4k Gatan Ultrascan camera. Tomograms were generated with an iterative scheme in the TxBR package ( Chen et al, 2014 ).…”

Assembly of Excitatory Synapses in the Absence of Glutamatergic Neurotransmission

“…Double-tilt tilt-series were collected with 0.5 degree tilt increments at 22,500X magnification on a 4k × 4k Gatan Ultrascan camera. Tomograms were generated with an iterative scheme in the TxBR package (Chen et al, 2014). Segmentation of synaptic structures and vesicle pools were performed in IMOD.…”

Class IIa HDACs regulate learning and memory through dynamic experience-dependent repression of transcription

“…Double-tilt tilt-series were collected with 0.5° tilt increments at ×22,500 magnification on a 4k × 4k Gatan Ultrascan camera. Tomograms were generated with an iterative scheme in the TxBR package 70 . Segmentation of synaptic structures and vesicle pools were performed in IMOD 70,71 .…”