SerialTrack-X-ray 2D

Purpose

This repository contains scripts for running a custom implementation of ("SerialTrack",https://github.com/FranckLab/SerialTrack) designed for 2D X-ray projection images taken during in situ micro-X-ray computed tomography (XCT) experiments. The particle tracking-based technique allows for surface displacement and strain fields to be measured during, for example, mini-tensile test motions. This provides quantitative visualization of non-uniformities in the strain field (i.e., necking, shear banding), direct measurement of applied strain to supplement crosshead-based data, and quantification of system drift, among other uses.

Requirements and Content

Dependencies

This is a Matlab-based code. It was developed using Releases 2021b - 2023b under Windows 10. The following toolboxes are used, although it may be straightforward to adapt to code to reduce these dependencies we have not tested this:

• Curve Fitting Toolbox
• Image Processing Toolbox
• Parallel Computing Toolbox
• Statistics and Machine Learning Toolbox
• System Identification Toolbox
• Wavelet Toolbox

Directory structure

Since this is a derivative of the SerialTrack package, it follows similar workflow and usage and has similar content. The codebase has been streamlined and updated for the specific needs of the measurement task. The folder structure is as follows:

• function contains the library of supporting function scripts that SerialTrack relies on for pre-processing, running the algorithm, and post-processing. Licenses for 3rd party functions are included as .txt file.
• imgFolder contains subdirectories with images sequences that are the input data for the algorithm. These can be elsewhere, but since the user is usually prompted to select a file or folder and the selection window starts at the top level direction this is a convenient organizational method.
• results output folder for results, typically for automatically saved .mat files, .fig files saved by the user, etc.
• src core source scripts to run SerialTrack.
• The main_hardpar_inc_xray_particles.m file is the script used to input experiment specifications and is the run-script to execute the full process.

Running the SerialTrack code

See also the HowToRun_SerialTrack-XR.txt document.

Briefly, the major steps are as follows:

1. Prepare images in a directory you can find. Usually this will be an image sequence named in alphanumerical order of the time-series in which they were acquired. Typically image loading method "0" works well for this type of data.
2. If the images have not been brightfield corrected save the brightfield image in a directory you can find.
3. If you wish to use an image mask (although it is not typically required) prepare the mask according to the "Image binary mask file" mode you indent to use.
4. In the main script"
5. Update the MPTPara.xstep variable with the micro-to-pixel ratio from your instrument.
6. Update any tracking parameters according to your problem: usually the defaults are a good starting point to get a sense of the tracking performance, but, for example, for different particle densities n_neighborsMax and n_neighborsMin might be changed, or for lower resolution images edge_width and/or grid_spaceing might be reduced.
7. Run the script and follow the prompts.
8. Save output, visualize results.

Other links and info

For the data used in the development and calibration of the model see:

Kafka, Orion L., Landauer, Alexander K., Benzing, Jake T., Moser, Newell H., Mansfield, Elisabeth, Garboczi, Edward J. (2023), Dataset for: A technique for in-situ displacement and strain measurement with laboratory-scale X-ray Computed Tomography, National Institute of Standards and Technology, https://doi.org/10.18434/mds2-3127

For a static, archival version of the code at version 1.0.0 see: https://doi.org/10.18434/mds2-3118

Please cite this code as:

Landauer, Alexander K, Kafka, Orion L (2023), Code for SerialTrack-XR particle tracking, National Institute of Standards and Technology, https://doi.org/10.18434/mds2-3118

Contact and support

For questions, please open a new entry in the "Issues" tab. If needed, you can also find authors' contact information via the associated paper (see above).

The corresponding author is Orion Kafka (NIST MML Applied Chemicals and Materials Division). Alex Landauer (NIST MML Materials Measurement Science Division) is the primary developers of the code.

License

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