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

TL;DR

This paper introduces an open-source Python scheme that automates the identification and categorization of molecules in high-resolution scanning probe microscopy images, aiding chemical analysis and surface studies.

Contribution

It presents a novel, modular Python tool for automated molecule enumeration and categorization in microscopy images, enhancing efficiency and accuracy over manual methods.

Findings

Automates molecule detection in microscopy images

Supports medium-sized images (10x10 to 100x100 nm)

Open source and modular design

Abstract

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$\times$10 to 100$\times$100 nm) scanned probe images.