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Processing Script for Cryostratigraphy Using X-ray Computed Tomography Scans of Permafrost Cores

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This script processes DICOM images resulting in gas-ice-sediment volumetric content.



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A script has been developed to process images of permafrost cores from X-ray computed tomography scans that semi-automatically results in gas, ice, sediment (and other inclusions) volumetric content. The material here complements the paper entitled “Quantitative processing of X-ray CT images of permafrost cores for cryostratigraphy: limitations and prospects” submitted to Permafrost and Periglacial Processes by W. R. Clavano, F. Calmels, and D. G. Froese (DOI: 10.1002/ Check back for an update on the actual DOI.

XrayCTscript.m is written in script format to allow the user to evaluate the code in Cell Mode and facilitate comments and commenting. More guidance can be found in the m-file. Pre-processing starts out by getting the information on the proper sequencing of image files and showing a profile plot for visual inspection. An initial ice-air threshold is automatically selected during this step to facilitate the boundary delineation step. The main processing includes automatically selecting blocks of slices depending on size and shape of the objects in each slice, segmenting each image slice into a number of clusters the user specifies, determining image classifiers from the gas-ice and ice-solids thresholds, defining an image mask to exclude image pixels of the bench, and finally classifying each image into pixels identified as gas, ice, or solids. In post-processing, results are presented in a histogram image, vertical profiles, volume plots, as well as sample slice images.

A sample data set is temporarily available via FTP using the following details:

Username: xrayct
Password (case-sensitive): anonymouS1

The data is in its "raw" directory structure, which preserves all the database files that the scanning instrument created. It is however compressed (~560MB) and will need to be expanded (~1.5GB) before it can be used.

Please email me if you have problems accessing the data. The data includes the sequence of images of the natural sample discussed and presented in the Permafrost and Periglacial Processes paper. The script has been tested to work with the sample data, and may be used to test that the script works in a particular system or setup. The data set resides in a file structure as follows:


where DVD22 is an arbitrary name, DICOM is the folder containing the data file structure, PA stands for patient, ST for study, SE for series, and IM for image. In general, the PA, ST, and SE folders may contain any number of subfolders and is automatically indexed as 000000, 000001, 000002, and so on. Individual images are contained in the IM files and numbered sequentially beginning with 000000, for each scan set.

Note: under the DVD22 directory is a dynamically linked library that should be left untouched for use in other applications. An executable file called DICOMDIR is also included and ideally left unaltered.

The script and the associated code is available free of charge. Any revision, adaptation, or extension is welcome without prior permission; however, appropriate credit for their use would be greatly appreciated. The following is a recommendation for citation.

Clavano, W. R. 2011. Cryostratigraphy from X-ray CT Scans of Permafrost (, MATLAB Central File Exchange. Retrieved 25 Sept 2011.

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