Progress towards a methodology for high throughput 3D reconstruction of soot nanoparticles via electron tomography

Abstract

The aim of this work is to make progress towards the development of 3D reconstruction as a legitimate alternative to traditional 2D characterization of soot. Time constraints are the greatest opposition to its implementation, as currently reconstruction of a single soot particle takes around 5-6 h to complete. As such, the accuracy and detail gains are currently insufficient to challenge 2D characterization of a representative sample (e.g. 200 particles). This work is a consideration of the optimization of the steps included within the computational reconstruction and manual segmentation of soot particles. Our optimal process reduced the time required by over 70% in comparison to a typical procedure, whilst producing models with no appreciable decrease in quality.

Assessing the Accuracy of Soot Nanoparticle Morphology Measurements Using Three-Dimensional Electron Tomography

“…Okyay's SEM tomography study of soot used a simple sphere model, and observed no elongation for a ±80° reconstruction [64]. Our own study performed similar work and saw 15% Z-elongation for ±60° reconstruction of a sphere [63]. It is common for simplified structures to be used as model systems due to difficulties associated with the creation of synthetic data-sets.…”

“…At this point, three variations of each tilt-series were made for each model: the full ±80° tilt-series (161 images), a ±60° tilt-series (121 images), and a ±60° tilt-series with 3° increments (41 images; henceforth referred to as ±60_3°). These represent the maximum tilt series that can be reconstructed with the IMOD/Etomo software (±80°), the largest tilt range that can routinely be recorded experimentally with TEM (±60°), and the optimum tilt-series as per our previous publication (±60° with 3° increments) [63]. Figure 3 shows an example of images from a simulated tilt-series For each of the models, all 3 tilt-series were reconstructed and tomograms produced (39 reconstructions total).…”

“…Figure 3 shows an example of images from a simulated tilt-series For each of the models, all 3 tilt-series were reconstructed and tomograms produced (39 reconstructions total). Reconstructions were performed using IMOD with Etomo [72], utilizing the weighted back-projection (WBP) algorithm, as per the optimized results of our previous publication [63]. For all 3 versions of reconstruction for each model, the maximum Z-length of the particle in the tomogram was measured to assess the extent of the missing-wedge elongation.…”

“…In the limit of infinite iterations, the SIRT tomogram is exactly equal to the original object. Both have been used to study soot nanoparticles [18,53,63,64].…”

“…However, little followup work has been carried out primarily due to the technique being too slow to be a viable alternative. Recent work by the authors has presented efforts towards improving the throughput of 3D-TEM [63], though as yet due consideration has not been given to ensuring its accuracy. The purpose of this study is to quantify the accuracy of 3D-TEM, and in particular our optimized methodology.…”