A seamless workflow for STXM-NEXAFS data analysis using napari: implementation of an ROI spectrum extraction function
- 1Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- 2Institute of Materials Structure Science Photon Factory, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
- 3Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
Abstract
Scanning transmission soft X-ray microscopy (STXM), combined with near-edge X-ray absorption fine structure (NEXAFS), enables the mapping of elemental distributions and chemical properties at a spatial resolution of tens of nanometers. A common approach for analyzing STXM data is to compare NEXAFS spectra obtained from regions of interest (ROIs). However, ROI-based spectral comparison typically requires frequent switching among multiple software applications. ROI spectrum extraction, spectrum normalization, and figure creation are often performed using separate applications, which increase analytical time and the likelihood of errors.•We developed a Python-based workflow for STXM-NEXAFS data analysis that implements functions for extracting mean ROI spectra in napari, an open-source multidimensional image viewer.•These napari-based functions provide a seamless workflow from ROI selection to figure preparation within Python, without switching between multiple software applications.•The seamless workflow improves analytical efficiency and facilitates broader use of STXM-NEXAFS analysis.
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BibTeX
@article{kobayashi2026seamless,
title = {{A seamless workflow for STXM-NEXAFS data analysis using napari: implementation of an ROI spectrum extraction function}},
author = {Koya Kobayashi and Shohei Yamashita and Maki Asano and Rota Wagai},
journal = {MethodsX},
year = {2026},
month = oct,
doi = {10.1016/j.mex.2026.104212},
url = {https://europepmc.org/article/PMC/PMC13718659},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - A seamless workflow for STXM-NEXAFS data analysis using napari: implementation of an ROI spectrum extraction function
AU - Koya Kobayashi
AU - Shohei Yamashita
AU - Maki Asano
AU - Rota Wagai
PY - 2026
DA - 2026/10/17
JO - MethodsX
DO - 10.1016/j.mex.2026.104212
UR - https://europepmc.org/article/PMC/PMC13718659
AB - Scanning transmission soft X-ray microscopy (STXM), combined with near-edge X-ray absorption fine structure (NEXAFS), enables the mapping of elemental distributions and chemical properties at a spatial resolution of tens of nanometers. A common approach for analyzing STXM data is to compare NEXAFS spectra obtained from regions of interest (ROIs). However, ROI-based spectral comparison typically requires frequent switching among multiple software applications. ROI spectrum extraction, spectrum normalization, and figure creation are often performed using separate applications, which increase analytical time and the likelihood of errors.•We developed a Python-based workflow for STXM-NEXAFS data analysis that implements functions for extracting mean ROI spectra in napari, an open-source multidimensional image viewer.•These napari-based functions provide a seamless workflow from ROI selection to figure preparation within Python, without switching between multiple software applications.•The seamless workflow improves analytical efficiency and facilitates broader use of STXM-NEXAFS analysis.
SN - 2215-0161
ER -