Code and Data from: Segmenting Root Systems in X-Ray Computed Tomography Images Using Level Sets

This record contains code and data for segmentation using a three-dimensional level-set method, written by Amy Tabb in C++.  The record also contains two datasets of root systems in media imaged with X-Ray CT, and the results of running the code on those datasets.  The code will also perform a pre-processing task in three-dimensional image sets, and a dataset for that purpose is included as well.  This work is a companion to the paper : "Segmenting root systems in X-ray computed tomography images using level sets" (WACV 2018) by the authors or this record, and and open-access version of the paper is here -- https://arxiv.org/abs/1809.06398 .   The code is also available from Github: https://github.com/amy-tabb/tabb-level-set-segmentation , using a DOI and stable releases https://doi.org/10.5281/zenodo.3344906.

Format of the data:

Three input datasets are provided; two for the segmentation functionality of the code, and one to test the pre-processing functionality.  The two segmentation sets are the same as were used in the paper, and are CassavaDataset, and SoybeanDataset.  The pre-processing set is CassavaSlices.  The output set for Soybean is SoybeanResultsJul11.  The Cassava result set is large, so I broke it into three compressed folders, CassavaResultsJul12_A, _B, _C.  _B is the largest, and only contains the results overwritten on the original X-Ray images.  Unless your connection to Zenodo is extremely fast, it will be faster to compute the result than to download it.