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Analysis of 3D elemental mapping artifacts in biological specimens using Monte Carlo simulation



Keana C. Scott, Nicholas W. Ritchie


In this paper, we present the Monte Carlo simulation results demonstrating the feasibility of the focused ion beam based X-ray microanalysis technique (FIB-EDS) for the 3D elemental analysis of biological samples. We used a marine diatom Thalassiosira pseudonana as our model organism and NISTMonte for the Monte Carlo simulations. We explored several beam energies commonly used for the X-ray microanalysis to examine their effects on the resulting 3D elemental volume of the model organism. We also performed a preliminary study on the sensitivity of X-ray analysis for detecting nanoparticles in the model. For the conditions considered in this work, we show that the mapping energy greater than 5 keV results in a 3D elemental distributions that do not reflect the elemental distributions in the original model. At 5 keV, the depth resolution of the X-ray maps is about 250 nm for biological samples. We also show that the nanoparticles that are 50 nm in diameter or greater are easily located but may not be resolved as separate features if several of them are located close to each other. Although much work is still needed in generating more accurate biological models and simulating experimental conditions relevant to these samples, our results demonstrate that FIB-EDS is a promising technique for the 3D elemental analysis of bulk biological specimens.
Journal of Microscopy-Oxford
Report Number
233, Part 2


X-ray microanalysis, EDS, focused ion beam, FIB, SEM, Monte Carlo, 3D elemental mapping, diatom


Scott, K. and Ritchie, N. (2009), Analysis of 3D elemental mapping artifacts in biological specimens using Monte Carlo simulation, Journal of Microscopy-Oxford, [online], (Accessed July 24, 2024)


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Created January 29, 2009, Updated February 5, 2009