TXM-Wizard is a specialized, MATLAB-based software GUI designed for advanced data collection, pre-processing, and analysis in full-field Transmission X-ray Microscopy (TXM) and X-ray Absorption Near Edge Structure (XANES) imaging. When configuring parameters or running automated modules like mosaic stitching and energy scanning, users often encounter common calibration, alignment, or file errors.
The primary configuration errors in TXM-Wizard and how to fix them include: Mosaic Stitcher GUI Freezing or Unresponsive
The Cause: This error occurs during the merging of image tiles to form a larger field of view (FOV). If the GUI hangs, there is insufficient overlap between the single-shot images due to physical motor errors. The phase correlation (PhCo) auto-alignment algorithm fails because it cannot find matching conditions between the tiles.
The Fix: Open the Mosaic Stitcher properties, uncheck “PhCo Alignment,” and rerun the process. If a low-alignment image successfully compiles, you have confirmed an overlap deficit. Permanently fix this by increasing your raster configuration’s pixel size or adjusting the tile motor overlap bounds. Invalid Mosaic Configuration Layout
The Cause: When setting up a multi-tile scan, the overview panel fails to display yellow or green tiles, indicating an invalid layout matrix.
The Fix: If you configure the layout without a central tile, you cannot enter zero for both the “Up and Down” or “Left and Right” tile bounds simultaneously. Adjust your directional tile numbers from the center matrix until the visual layout updates, then click Submit. Magnification Shifts During Energy Scans
The Cause: Fresnel zone plate focal lengths change based on the X-ray energy level being targeted. If your structural images alter sizes dynamically across a XANES stack, the energy configurations are mismatched.
The Fix: Ensure that bicubic interpolation is active within your script pre-processing settings. This scales the variations across the energy stack back into consistent, uniform image dimensions before executing local alignments. Phase Correlation Alignment Failures
The Cause: Random relative shifts occur between images due to motorized stage corrections or zone plate stage errors during scanning. Mismatched coordinates create broken image stacks.
The Fix: Ensure that your original spatial metadata coordinates remain unchanged during format conversions (e.g., via the TXRM2Bin sub-GUI). Utilizing the raw, encoded motor positions within the TXM-Wizard Mosaic Image Stitcher significantly increases alignment success compared to manual pixel parsing. High R-Factor / Bad Linear Combination Fits
The Cause: During least-squares linear combination fitting of your XANES map, certain high-concentration element regions produce a high R-factor (poor fit quality). This indicates a systemic error in the reference configuration.
The Fix: This error points to a missing or incorrect reference dataset within your .mat parameters. Isolate the pixel clusters via the built-in correlation plot GUI, check the element absorption edge boundaries, and re-upload the appropriate reference standards to the model.
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