Work

A seamless workflow for STXM-NEXAFS data analysis using napari: implementation of an ROI spectrum extraction function

Year: 2026

Type: article

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.

Source: MethodsX

DOI: 10.1016/j.mex.2026.104212

Authors: Koya Kobayashi, Shohei Yamashita, Maki Asano, Rota Wagai

Institutions: The University of Tokyo, High Energy Accelerator Research Organization, Institute of Materials Structure Science, Photon Factory, University of Tsukuba

Language: English

Topic: X-ray Spectroscopy and Fluorescence Analysis

Subfield: Radiation

Field: Physics and Astronomy

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $1,260

Funder: Japan Society for the Promotion of Science