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Nonnegative matrix factorization incorporating domain specific constraints for four dimensional scanning transmission
Koji Kimoto1, Fumihiko Uesugi2, Koji Harano3,4
1Center for Basic Research on Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. kimoto.koji@nims.go.jp.
Scientific Reports
|November 7, 2025
Summary
We developed a new machine learning method for electron microscopy data analysis. This technique enhances material insights by improving data decomposition and classification, outperforming existing methods.
Area of Science:
- Materials Science
- Data Science
- Microscopy
Background:
- Modern electron microscopy generates large datasets requiring advanced analysis.
- Existing machine learning methods like PCA and NMF struggle with microscopy-specific data features.
- Domain-specific constraints are crucial for accurate interpretation of microscopy data.
Purpose of the Study:
- To develop a novel nonnegative matrix factorization (NMF) technique for analyzing four-dimensional (4D) scanning transmission electron microscopy (STEM) data.
- To integrate domain-specific constraints from electron microscopy into the NMF algorithm.
- To improve the decomposition and classification of material features in large microscopy datasets.
Main Methods:
- Proposed a constrained nonnegative matrix factorization (NMF) integrating spatial resolution and continuous intensity features.
- Applied the constrained NMF to simulated and experimental 4D STEM data.
- Optimized hierarchical clustering using diffraction similarity (polar coordinate transformation and uniaxial cross-correlation).
Main Results:
- Successfully decomposed 4D STEM data into interpretable diffractions and maps, surpassing PCA and standard NMF.
- Detected and classified nanometer-sized crystalline precipitates in ZrCuAl metallic glass using optimized clustering.
- Demonstrated superior performance over conventional machine learning techniques lacking domain knowledge.
Conclusions:
- The constrained NMF method effectively extracts material insights from large electron microscopy datasets.
- The developed technique accurately decomposes and classifies complex microstructures.
- This approach is broadly applicable to various characterization techniques and mitigates common machine learning artifacts.

