Article template for Elemental Microscopy

Colin Ophus; Georgios Varnavides

doi:10.69761/TAMJ0615

Computational Article

Contents

While most microscopy images are often obtained in projection, advanced techniques such as electron tomography and multislice ptychography enable the 3D reconstruction of structures. Due to the limitations of print journals, these results are often presented as 2D slices of the 3D objects of interest or at-best as 360° orbit movies. These make the results difficult to interpret and evaluate.

To overcome these limitations, we can embed interactive 3D visualization libraries directly on the page including volumetric rendering as in Figure 3.2 and volume slicing as in Figure 3.1.

Volume Slicing

Volume Rendering

Joint ptychographic-tomographic reconstruction of a simulated CNT with a missing wedge of 60 deg.
Reproduced from. — Figure 3.1:Joint ptychographic-tomographic reconstruction of a simulated CNT with a missing wedge of 60 deg. Reproduced fromVarnavides *et al.*, 2024.

References¶

Varnavides, G., Ribet, S. M., Zeltmann, S. E., Yu, Y., Savitzky, B. H., Byrne, D. O., Allen, F. I., Dravid, V. P., Scott, M. C., & Ophus, C. (2024). Iterative phase retrieval algorithms for scanning transmission electron microscopy. arXiv Preprint arXiv:2309.05250. https://doi.org/10.48550/arXiv.2309.05250

EM Template

Movies and Movie Widgets

EM Template

Complex interactive examples

[cite-varnavides2024iterative] Varnavides, G., Ribet, S. M., Zeltmann, S. E., Yu, Y., Savitzky, B. H., Byrne, D. O., Allen, F. I., Dravid, V. P., Scott, M. C., & Ophus, C. (2024). Iterative phase retrieval algorithms for scanning transmission electron microscopy. arXiv Preprint arXiv:2309.05250. https://doi.org/10.48550/arXiv.2309.05250

3D Plots and 3D Widgets