Counting molecules: Python based scheme for automated enumeration and categorization of molecules in scanning tunneling microscopy images

Scanning tunneling and atomic force microscopies (STM/nc-AFM) are rapidly progressing to offer unprecedented spatial resolution of a diverse array of chemical species. In particular, they are employed to characterize on-surface chemical reactions by directly examining precursors and products. Chiral effects and self-assembled structures can also be investigated. This open source, modular, python based scheme automates the categorization of a variety of molecules present in medium sized (10 × 10 to 100 × 100 nm) scanned probe images.