Lattice Hub Analyser

A unified, semi-automated toolkit for STM lattice analysis, unit cell averaging, and atomic site detection.

Lattice Hub Analyser takes post-cleansed/mean-plane subtracted Gwyddion STM files (.npy) and provides an end-to-end pipeline to visualize, cut, average, and analyze atomic lattices. Whether you want to quickly average a noisy unit cell or run rigorous quantitative comparisons across different datasets, this tool handles the heavy lifting.

Features

• Interactive Lattice Picker: Visually map origin and Bravais vectors.
• NaN-Median Averaging & Tiling: Select multiple unit cells across a noisy image to generate a high-precision, averaged, and seamless unit cell.
• Auto-Detector: Locate atomic sites automatically using strict spatial constraints and local intensity peaks.
• Total Lattice Editor: A multi-window interface to manually refine, map, and export atomic coordinates.
• Advanced Analysis Suite:
  • 2D FFT Visualization.
  • Real $\to$ Fractional coordinate conversion.
  • Hungarian Algorithm Bipartite Matching & RMSD calculation to quantify variance between different unit cells.

Installation

Option 1: For Python Users Install directly via pip:

pip install latticehubanalyser

Option 2: Standalone Executable (Windows) Head over to the Releases tab and download LatticeHub.exe. Double-click to run—no Python installation required.

Methodology

For more information on the underlying algorithms, check out the methods_explained.ipynb notebook in the notebooks/ folder for a complete mathematical breakdown.

Citation

This project is licensed under the MIT License. If you use this tool in your published research, please see the CITATION.cff file or use the "Cite this repository" button on GitHub.