This is the code and data repository of the paper “Automated analysis of ultrastructure through large-scale hyperspectral electron microscopy”, submitted for review. Here, you can find links to view the full EM maps accompanying the paper, code to reproduce the experiments, and downloadable EDX-EM data for reuse.
Large-scale ColorEM (Figure 1)
HAADF and multi-channel abundance maps (Figure 3)
Abundance map composite image (Figure 3)
Skin HAADF and elemental maps (Figure S1)
Skin abundance maps (Figure S1)
The endmember extraction algorithm used in this study was inspired by the work of Vermeulen et al. (2021), and using code from the corresponding repository. Implementation of SAM segmentation (Figure 4) uses code adapted from the following repositories: SAM, SAMHQ. VCA from this repositoriy (used in preliminary testing; unused in paper).
Copyright (C) 2024 Ahmad Alsahaf and Peter Duinkerken.