Counting Molecules

9-azidophenanthrene produces a rich manifold of products when deposited on Ag(111).

The images we took for this study inspired this work to develop a lightweight script to count the molecules we observed, and categorize them.

Our personal journey of computer vision rediscovery led us to Zernike moments, a rotationally invariant basis set that solves the problem of identifying the same molecules with relative rotations, in an image.

We put some effort into making this module user-friendly, the example scripts offer a reasonable template to apply to any old SXM file you might want to histogram.

Hellerstedt, J., et. al. (2022). Counting Molecules: Python based scheme for automated enumeration and categorization of molecules in scanning tunneling microscopy images. Software Impacts https://doi.org/10.1016/j.simpa.2022.100301

github repo

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