# Nonnegative matrix factorization incorporating domain specific constraints for four dimensional scanning transmission electron microscopy

https://mdr.nims.go.jp/datasets/e1a00e7f-4bc6-4321-98ff-46d84a6877c2

## File

- [SciRep(2025)Kimoto.pdf](https://mdr.nims.go.jp/filesets/29cdcb68-0441-4dda-a98e-f1018c8145bc/download) ([Detail](https://mdr.nims.go.jp/filesets/29cdcb68-0441-4dda-a98e-f1018c8145bc.md))
- [Supplementary Material.pdf](https://mdr.nims.go.jp/filesets/f037cf96-3e66-44ff-87cc-d6e30228e95a/download) ([Detail](https://mdr.nims.go.jp/filesets/f037cf96-3e66-44ff-87cc-d6e30228e95a.md))

## Id

e1a00e7f-4bc6-4321-98ff-46d84a6877c2

## Local identifier



## Visibility

open_to_public

## State

published

## Created at

2025-11-28T08:51:28.694511Z

## Updated at

2025-12-01T03:30:04.391351Z

## Published at

2025-12-01T03:23:45.020234Z

## Doi



## First published url

https://doi.org/10.1038/s41598-025-23541-7

## Date published

2025-11-07

## Recorded date published



## Resource type

journal_article

## Manuscript type

vor

## Collection



## Title

- title: Nonnegative matrix factorization incorporating domain specific constraints
    for four dimensional scanning transmission electron microscopy
  title_type: original
  lang: en

## Description

- description: We propose a novel nonnegative matrix factorization (NMF) technique
    that integrates domain-specific constraints inherent to electron microscopy. This
    constrained NMF was applied to four-dimensional (4D) scanning transmission electron
    microscopy (STEM). Using the constrained NMF 4D-STEM data were successfully decomposed
    into interpretable diffractions and maps that cannot be achieved using principal
    component analysis (PCA) and primitive NMF. Additionally, hierarchical clustering
    was optimized based on diffraction similarity, which is a combination of a polar
    coordinate transformation and cross-correlation. Nanometer-sized crystalline precipitates
    embedded in an amorphous metallic glass, ZrCuAl, were successfully detected and
    classified according to their diffraction patterns. The present scheme is broadly
    applicable across various characterization techniques, including hyperspectral
    imaging, and effectively mitigates the known artifacts found in conventional machine
    learning techniques that rely solely on mathematical constraints without domain-specific
    knowledge.
  description_type: abstract
  lang: und

## Creator

- name: Koji Kimoto
  role: author
  orcid: https://orcid.org/0000-0002-3927-0492
- name: Fumihiko Uesugi
  role: author
  orcid: https://orcid.org/0000-0003-3346-4218
- name: Koji Harano
  role: author
  orcid: https://orcid.org/0000-0001-6800-8023
- name: Jun Kikkawa
  role: author
  orcid: https://orcid.org/0000-0003-0659-1844
- name: Ovidiu Cretu
  role: author
  orcid: https://orcid.org/0000-0002-1822-8172
- name: Yuki Shibazaki
  role: author
  orcid: https://orcid.org/0000-0002-0550-6719
- name: Motoki Shiga
  role: author
  orcid: https://orcid.org/0000-0003-2434-4716
- name: Atsushi Togo
  role: author
  orcid: https://orcid.org/0000-0001-8393-9766

## Contact agent



## Publisher

organization: Springer Science and Business Media LLC

## Managing organization



## Keyword

- subject: 4D-STEM
  schema: not_defined
- subject: unsupervised machine learning
  schema: not_defined
- subject: nonnegative matrix factorization
  schema: not_defined
- subject: scanning transmission electron microscopy
  schema: not_defined
- subject: metallic glass
  schema: not_defined
- subject: amorphous
  schema: not_defined
- subject: ZrCuAl
  schema: not_defined

## Rights

- identifier: https://creativecommons.org/licenses/by/4.0/

## Other identifier(s)



## Data origin



## Embargo



## Journal

- title: Scientific Reports
  issn: '20452322'
  volume: '15'
  issue: '1'
  article_number: '39143'

## Conference



## Related item



## Funding

- identifier: JP 22H05145
  funder_name: Japan Society for the Promotion of Science
- identifier: JP23H04874
  funder_name: Japan Society for the Promotion of Science
- identifier: 20H02624
  funder_name: Japan Society for the Promotion of Science
- identifier: 20H02624
  funder_name: Japan Society for the Promotion of Science

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## Measurement method



## Specimen



## Chemical composition



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## Fileset

- id: 29cdcb68-0441-4dda-a98e-f1018c8145bc
  filename: SciRep(2025)Kimoto.pdf
  content_type: application/pdf
  size: 5731112
  md5: 8a401f591f9ae86017a0271a2dd36285
- id: f037cf96-3e66-44ff-87cc-d6e30228e95a
  filename: Supplementary Material.pdf
  content_type: application/pdf
  size: 3363326
  md5: db13419d98d8187bbe2a6e171e0eb2b2

## Thumbnail

fileset_id: 29cdcb68-0441-4dda-a98e-f1018c8145bc
filename: SciRep(2025)Kimoto.pdf