MicroCT Facility (MCT) X-Ray Computed Microtomography X-Ray Micro-Computed Tomography

Data File Explanation

Overview

Below are brief explanations and examples of the files in the data collected at the MCT. The files are separated into the following subclasses: raw data, reconstructed data and metadata. A note is made if there is variance in file location/naming convention between standard scans (i.e. one scan at one height) and stamina scans (i.e. multiple scans at different heights to be merged into one file).

Raw Data

  • Folder Location: (Standard) Top-level folder; (Stamina): In each folder with the naming convention of scanXXXXXXX
  • File Naming Convention: scan_XXXXXX.tif, diXXXXXX_XXXXXX.tif, ioXXXXXX_XXXXXX.tif

The raw data are the 2D x-ray projection images at each scanning angle around the sample. These are the TIFF files that start with "scan." The other two files are the dark field (starts with "di") and white field (starts with "io") images. This data has not been processed at all and is therefore usually only important for three use cases: 

  1. The user wants to have the raw data in order to implement their own 3D reconstruction algorithm.
  2. The user wants to keep the raw data in the event they would want to change the pre-processing settings at some point.
  3. The x-ray projection images are important for their analysis/visualization.
2D X-ray projection of a toy

Reconstructed Data

  • Folder Location: (Standard) In the "recon" folder; (Stamina): In the "merge" folder
  • File Naming Convention: (Standard) scan_XXXXXX.tif; (Stamina): merged_XXXXXX.tif

The reconstructed (recon) data are a collection of 2D tiff files where each file is a slice in the Z-direction through the 3D reconstructed sample. Each slice has a thickness equal to that of the voxel size of the acquisition. All the files have been reconstructed with the pre-processing settings chosen in the reconstruction software such as beam hardening correction, x-ray scattering correction, ring-artifact filtering, etc.

These data files are usually the most useful for users. By loading all the recon files at once into a image processing program (e.g. ImageJ, Dragonfly, Avizo, etc.) the full 3D digital reconstruction of the sample can be visualized.

Reconstructed slice of the toy

Metadata

The rest of the files are classified as metadata files, or files that contain data about how the data was collected. They are listed below in assumed order of importance to the user and with brief explanations about each:

  1. 'scan settings.txt'
    • Highest importance to average user. Contains the most important metadata for the average user. Researchers can find most relevant information needed for publication of microCT data in this file.
  2. 'Acquisition settings XRE.txt'
    • High importance to average user. Includes all the metadata of the acquisition. Metadata is organized into categories such as the tube settings (voltage, power, in-line filter, etc.), camera settings (detector used, exposure time, averages, etc.), acquisition settings (number of projections, motor positions, etc.) and CT parameters (source-object-distance, source-detector-distance, voxel size, etc.).
  3. 'data set settings.ini'
    • Low importance to average user. An initialization file for opening the data with relevant metadata in TESCAN's software. It does provide a succinct list of important data settings such as source-object-distance, source-detector-distance, tilt, skew, slant, etc.
  4. 'script.txt'
    • Low importance to average user. This file contains the script that was generated by the Acquila software when the scan was initiated. Important for users that want to duplicate conditions of previous scans or to understand the steps that the scanner actually takes when collecting the data.
  5. 'Reference_***.tif' files
    • Minimal importance to average user. These image files are sometimes collected after a long scan or a scan that is highly likely to exhibit movement during the scan. They act as reference points for the Scan Monitor add-on in TESCAN's acquisition software, Acquila. This add-on calculates a correction for slight shifts in the position of the sample during scanning (output as 'shiftcurve.txt') to reduce movement artifacts in the reconstructed image.
  6. 'shiftcurve.txt'
    • Minimal importance to average user. This is the output of the shift correction in the Scan Monitor add-on in TESCAN's acquisition software, Acquila. It includes a list of the calculated x, y, and magnitude shifts that correspond with each acquisition. The file is used during reconstruction to reduce movement artifacts.
  7. 'data settings XRE.txt'
    • Minimal importance to average user. Identical to 'Acquisition settings XRE.txt' unless a pre-reconstruction calculation is performed in Acquila such as shift correction, then some metadata is appended to the bottom of the file.
  8. 'tubelog.txt'
    • No importance to average user. Log of the x-ray tube conditions throughout the scan. Usually only important to the operator to help diagnose issues in the event of a failed scan.
  9. '***.xml' file extensions
    • No importance to average user. Files with the ".xlm" file extension are only important should the user want to open the files back up in TESCAN's reconstruction software, Panthera.
  10. 'scan__diagnostics.txt'
    • No importance to average user. Usually only important to the operator to help diagnose collection issues if the scan failed.
  11. 'script_executed.txt'
    • No importance to average user. Contains the output of the script that was updated after each step of the 'script.txt' file was executed.