Dataset Open Access

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

Tabb, Amy; Duncan, Keith E.; Topp, Christopher N.

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.

 

 

 

 

The README file in the code repository has documentation for running the code.
Files (4.6 GB)
Name Size
CassavaDataset.zip
md5:006ddb4d6e0c174e76053b6e7b013442
805.9 MB Download
CassavaResultJul12_A.zip
md5:bfc4fdf995d4385f34524a7ba5b21397
32.0 MB Download
CassavaResultJul12_B.zip
md5:75bafaa8edfc94454d4203dabbb93837
1.5 GB Download
CassavaResultJul12_C.zip
md5:3afe60deca68c7794d0088771e766a76
3.0 MB Download
CassavaSlices.zip
md5:88cf9b83b5178b369f1708f233cd3327
795.3 MB Download
SoybeanDataset.zip
md5:a458e7df6a1d7a36f54f7bb99df9aa87
533.7 MB Download
SoybeanResultJul11.zip
md5:67e49eb8c6a5c534a31ced9a27ed974e
990.3 MB Download
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