10. Quick links

• How to set up Python workspace for coding and installing libraries:

  • Section 4.1.

  • Section 1.1.

• How to read/write or explore hdf/nxs/h5 files:

  • Section 4.2.1.

  • Section 1.2.1

  • Broh5 software.

  • API of loading a hdf file.

  • API of writing to a hdf file.

  • Script for exploring a hdf file.

• How to read/write tiff images:

  • Section 1.2.2.

  • Section 4.2.2.

  • Loader/saver API.

• How to process standard tomography data:

  • Workflow:

    • Section 1.4.

    • Section 4.5.

  • Command line interface scripts: few-slices reconstruction, full reconstruction, data reduction:

    • Common data processing workflow.

  • Scripts:

    • Reconstructing a few slices of a standard scan.

    • Full size reconstruction of a standard scan.

• How to process half-acquisition tomography (360-degree scanning with offset center) data:

  • Demo script.

  • Section 1.4.8.2.

• How to apply distortion correction:

  • Reconstruct a scan with distortion correction.

  • Use Discorpy for finding distortion coefficients.

• How to choose ring artifact removal methods:

  • Section 4.4.

  • Section 4.5.4.

  • Sarepy documentation about ring artifacts in tomography.

• How to find center of rotation (rotation axis):

  • Section 4.5.3.

• How to process time-series tomography data:

  • Demo scripts

• How to process grid-scanning tomography data (tiled scans):

  • Reconstruct a few slices.

  • Full reconstruction: step 1.

  • Full reconstruction: step 2.

  • Full reconstruction: step 3.

• How to process helical tomography data:

  • Demo script.

• How to perform data reduction of reconstructed volume (cropping, rescaling, downsampling, reslicing,…):

  • Section 4.5.8.

  • Command line interface script.

• How to process speckle-based phase-contrast tomography data:

  • Section 5.1.

  • Demo scripts.

• How to correct tilted tomography data:

  • Demo script 1.

  • Demo script 2.

  • Tomography alignment tutorial.

• How to automate the workflow:

  • Section 4.5.7.

  • Utility scripts.

• How tomography works:

  • Section 1.3.

  • Section 1.6.

• How to generate simulated data:

  • Simulation module.

  • Demo script.

• How to customize ring-artifact removal methods:

  • Section 4.3.

• Tools for finding image shift, stitching images:

  • Correlation module.

  • Conversion module.

• Tools for phase unwrapping, phase retrieval:

  • Phase module.

  • Section 5.1.3.

• Datasets for testing algorithms:

  • Zenodo.

  • Tomobank.

• Parallel processing, GPU programming, and high-performance computing with Numba:

  • Section 1.5.

  • GPU programming.

  • Compiling python code.

• Common mistakes and useful tips:

  • Section 4.5.9.