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This dataset contains dark-field X-ray microscopy (DFXM) measurements of NaMnO₂ collected at the (20-2) Bragg reflection during two experiments conducted at Sector 6-ID-C of the Advanced Photon Source (APS) at Argonne National Laboratory.

The measurements were performed in July 2021 and December 2021 and consist primarily of diffraction images recorded during rocking curve imaging (RCI) scans. In RCI, the sample is rotated through the Bragg condition while recording diffraction images, allowing spatially resolved information about crystal orientation and domain structure to be obtained.

The December 2021 experiment includes measurements collected at temperatures ranging from 3.2 K to 300 K using a Montana Instruments cryostat, enabling investigation of temperature-dependent structural behavior in NaMnO₂.

The primary data consist of diffraction images recorded using an Andor sCMOS detector, along with associated experimental metadata including motor positions, cryostat temperature logs, and experimental logbooks.

Corresponding APS beamline scientist: Zahir Islam

Description of the data and file structure

Due to the large size of the diffraction image datasets, the repository is organized as a collection of compressed ZIP archives. Each archive contains data associated with a particular component of the experiment.

Image data for individual scans are stored in separate archives to allow incremental downloading and storage.

Archive naming convention:

Plumb_DFXM_<Experiment>_<DataType>.zip

Examples include:

Plumb_DFXM_DEC2021_data_S001.zip
Plumb_DFXM_DEC2021_motors.zip
Plumb_DFXM_DEC2021_cryostatData.zip
Plumb_DFXM_DEC2021_logs.zip

Two experiments are included in the dataset:

Plumb_DFXM_Jul2021
Plumb_DFXM_DEC2021

Diffraction image data

Each scan is stored as an individual archive:

Plumb_DFXM_DEC2021_data_S001.zip

Inside the archive:

S001/
    *.tiff

Each TIFF file contains a single detector image recorded during a rocking curve scan. Each image corresponds to a specific sample rocking angle (theta) and represents the spatial distribution of diffracted X-ray intensity from the sample.

The TIFF images can be opened using standard image software or scientific libraries such as Python tifffile.

Motor position logs

Motor logs are stored in:

Plumb_DFXM_DEC2021_motors.zip

Inside:

motors/
    S001_motorInfo.csv
    S002_motorInfo.csv
    ...

Each row in a motor log corresponds to one diffraction image and records the motor positions of the diffractometer and beamline optics at the time the image was acquired.

Columns in the motor log files:

Motor log files contain a standardized set of beamline motor parameters. Not all motors were actively used during every scan, therefore some columns may contain empty cells. Empty cells indicate that the corresponding motor position was not recorded or not relevant for that scan configuration. The column structure was preserved across all scans to maintain compatibility with beamline acquisition software.

Cryostat temperature logs

Cryostat temperature data are stored in:

Plumb_DFXM_DEC2021_cryostatData.zip

Inside:

temperatureData/
    S021.csv
    S022.csv
    ...
    S027.csv

These files contain temperature and control parameters recorded by the Montana Instruments cryostat during the December 2021 experiment.

Key columns include:

Additional columns labeled User1–User6 correspond to auxiliary temperature control channels recorded by the cryostat controller. Missing values in CSV files appear as empty cells and indicate parameters that were not recorded or were not applicable during a particular scan.

Experimental logbooks

Experimental notes recorded during beamtime are stored in:

Plumb_DFXM_DEC2021_logs.zip

Inside:

logs/
    *.docx

These files contain descriptions of scan conditions, experimental observations, and notes recorded during the measurements.

Optical microscope reference images

Reference optical microscope images of the NaMnO₂ sample were recorded during the experiments to aid in locating the region of interest on the crystal and to document the sample appearance at different temperatures.

These images are stored in the archive:

referenceImages.zip

The structure of this archive differs slightly between the July 2021 and December 2021 experiments. Optical reference images are not required for numerical analysis of the diffraction data but are included to provide visual documentation of the sample and experimental alignment.

December 2021 experiment

Archive:

Plumb_DFXM_DEC2021_referenceImages.zip

Directory structure:

referenceImages/
    NaMnO2_3.2K_Reference/
    NaMnO2_3.34K_Reference/
    NaMnO2_150K_Reference/
    NaMnO2_RoomTemp_Reference/

Each directory contains optical microscope images of the NaMnO₂ sample collected at the indicated temperature during the experiment.

Files are stored as TIFF or PNG images. These images were used during beamtime to relocate the sample and monitor changes in the sample surface as temperature varied.

July 2021 experiment

Archive:

Plumb_DFXM_Jul2021_referenceImages.zip

Directory structure:

referenceImages/
    *.tiff
    *.png
    Stitched/

The TIFF and PNG files in the referenceImages directory are individual optical microscope images of the sample.

Stitched images

The Stitched directory contains composite images generated by stitching together multiple microscope images using ImageJ.

Directory structure:

Stitched/
    *.tiff
    *.txt
    LeftHalf/
    RightHalf/
    total/

These directories contain intermediate and final outputs produced by the ImageJ stitching process.

• LeftHalf and RightHalf contain partial stitched images and associated metadata.
• total contains the final stitched images representing the full field of view.
• .txt files store stitching parameters and coordinate information generated by ImageJ.

These stitched images provide a larger field-of-view reference of the sample surface and were used for spatial context during the experiment.

Structure files

Crystallographic structure files (.cif) for α- and β-phase NaMnO₂ are included for reference.

Scan grouping

During analysis, scans were grouped according to their experimental purpose.

July 2021 experiment

• Exposure time: 2.5 s
• X-ray energy: 13 keV

December 2021 experiment

• Exposure time: 10 s
• X-ray energy: 10 keV
• Temperature range: 3.2–300 K

Scans 3–20 correspond to temperature points:

9, 15, 22, 28, 38, 42, 45, 47, 52, 66, 80, 91, 103, 121, 143, 149, 161, 196 K

Sharing / Access information

Dataset hosted on Dryad.

If used in research, please cite the associated publication:

Dark field X-ray microscopy below liquid-helium temperature: The case of NaMnO₂.

Data collected at the Advanced Photon Source (APS) at Argonne National Laboratory.

Code/Software

Basic preprocessing and analysis scripts used during this project are included in the dataset.

Two archives contain analysis code associated with the experiments:

Plumb_DFXM_Jul2021_scripts.zip
Plumb_DFXM_DEC2021_scripts.zip

Each archive contains a directory:

repo_scripts/

which includes Python scripts used for preprocessing and analysis of the rocking curve imaging scans.

Scan group analysis scripts

Individual Python scripts are provided for each scan group.

Example naming convention:

DC21_SGA_basicAnalysis.py
DC21_SGB_basicAnalysis.py
...
DC21_SGJ_basicAnalysis.py

Where:

These scripts perform basic preprocessing steps including:

• loading diffraction images
• constructing rocking curves
• fitting Gaussian functions to rocking curve intensity profiles
• generating parameter maps describing domain structure

The scripts are intended as examples of analysis workflows used during the study.

DiffractionMaster software

The repo_scripts directory also contains a subdirectory:

DiffractionMaster/

This directory contains a Python-based graphical analysis tool used for diffraction image analysis.

Key files include:

Additional directories within this package include source code, logs, and legacy modules used during development.

These scripts were last updated June 2024.

These files are included to preserve the full analysis environment used during the project, but are not required to access or interpret the raw dataset.

Software requirements

The analysis scripts were written in Python (version ≥3.9) and use common scientific libraries including:

• numpy
• scipy
• matplotlib
• tifffile
• tkinter (for the graphical interface)

The diffraction images themselves are standard TIFF files and can be opened using common scientific image software or libraries.

Results / Summary images

Preprocessed summary images generated during the initial analysis are included in the archives:

Plumb_DFXM_Jul2021_results.zip
Plumb_DFXM_DEC2021_results.zip

Each archive contains the directory:

repo_results/

This directory contains PNG files summarizing the diffraction images collected in each scan group.

These images were generated during preprocessing to verify scan alignment, cropping regions, and signal quality before performing detailed rocking curve analysis.

File naming convention

Files follow the naming pattern:

<Experiment><ScanGroup>_<Description>.png

Examples:

DC21A_manualCroppingCheck.png
DC21A_manualCroppingIntCheck.png

Where:

Types of result images

Two types of summary images are provided for each scan group.

Rocking curve summed image

*_manualCroppingCheck.png

This image shows the sum of all diffraction images across the rocking curve scan.

It provides a spatial overview of the diffracted intensity across the detector field and was used to visually verify that the correct region of interest was selected during analysis.

Rocking curve summed intensity plot

*_manualCroppingIntCheck.png

This figure shows the total integrated diffraction intensity as a function of rocking angle (theta).

These plots were used to verify that the rocking curve scan captured the full Bragg peak and to check overall signal quality.

Purpose of these files

The PNG files are diagnostic outputs from the preprocessing stage of the analysis workflow.

They are included to provide a quick visual overview of each scan group and to document intermediate analysis steps, but they are not required for reanalysis of the dataset, which can be performed directly using the raw diffraction images and motor position logs.

Contact information

For questions regarding this dataset:

Jayden C. Plumb
jaydencplumb@gmail.com