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Updated: Jul 4, 2026

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography
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Published on: January 30, 2016

An Automated Atom Probe Tomography Cluster Detection Approach Using Transfer Learning.

Yalei Tang1, Mukesh Bachhav1, Matthew W Anderson1

  • 1Idaho National Laboratory, Idaho Falls, ID 83415, USA.

Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
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PubMed
Summary

This study introduces an automated workflow for analyzing atom probe tomography (APT) data using deep learning. It enhances cluster detection accuracy and consistency in materials science, reducing manual parameter tuning.

Keywords:
HDBSCANatom probe tomographydensity-based clusteringtransfer learning

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Area of Science:

  • Materials Science
  • Data Analysis
  • Computational Science

Background:

  • Atom probe tomography (APT) enables atomic-scale visualization of solute distribution in materials.
  • Quantitative cluster analysis in APT is challenging due to subjective parameter selection in algorithms like HDBSCAN.
  • This sensitivity hinders reproducibility and accuracy in APT data interpretation.

Purpose of the Study:

  • To develop an automated, image-based deep learning workflow for parameter selection and cluster detection in APT data analysis.
  • To reduce reliance on manual parameter tuning for improved consistency and scalability.
  • To enable faster and more objective analysis of complex spatial patterns in APT datasets.

Main Methods:

  • Projecting 3D APT point clouds onto 2D planes for analysis.
  • Utilizing pretrained convolutional neural networks (ConvNeXt-Tiny, ResNet-50) with transfer learning.
  • Employing deep learning outputs to guide K-means clustering and estimate HDBSCAN parameters (min cluster size, min sample points).

Main Results:

  • Successfully automated parameter selection for clustering algorithms in APT data.
  • Demonstrated reduced subjectivity and improved consistency in cluster detection.
  • Validated the feasibility of using image-based deep learning for complex spatial pattern interpretation.

Conclusions:

  • The proposed deep learning-aided workflow significantly enhances the objectivity and efficiency of APT data analysis.
  • This method improves the reproducibility and scalability of quantitative cluster analysis in materials science.
  • The workflow and code are publicly available to foster further research and application.