Ring Correction for Tomographic Slices

This MATLAB package provides scripts for correcting ring artifacts in tomographic datasets. The correction can be previewed on a selected slice and then applied to the entire stack if the results are satisfactory.

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Setup

1. Open MATLAB
   Start MATLAB in the directory where this repository is located.

2. Add the current folder to the MATLAB path
   This ensures all scripts can be accessed:

   addpath('.');

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Testing the Correction

1. Navigate to the image directory, for example:

   cd 52.76um_lung_complete-organ

2. Run a test correction on a sample slice
   In MATLAB, execute:

   stack_rings_master_2022_slurm(20, 'preset_stack_rings.m');

   • The first argument (20) refers to the index of the slice to test.
   • This will display a comparison showing the effect of the ring correction.

3. Check the preview
   Below is an example of the ring correction preview on slice 20:

   

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Applying the Correction

If the result looks satisfactory:

• Press 'y' when prompted to apply the correction to all slices.
• Alternatively, to skip the preview and directly process the full dataset, run:

  stack_rings_master_2022_slurm(0, 'preset_stack_rings.m');

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File Overview

• preset_stack_rings.m: Contains preset parameters for ring correction.
• stack_rings_master_2022_slurm.m: Main script to manage the correction process.
• stack_rings_slave_2022_slurm.m: Helper script called by the master.
• Other .m files: Supporting utilities for filtering, image handling, and I/O.