SPP2089_P21_Phalempin_et_al_Plant_Methods 0 10553

POF3 - T123D631 - Rhizosphere
This folder contains image processing protocols bundled under the name Rootine v.2. In addition,
there is one X-ray CT raw data set from the worse case scenario for testing and the Rootine v.2 segmentation result for checking reproducibility.

The compressed folder contains three subfolders and a README.txt which are described below :

1. images: bottom and top part of a whole-column X-ray CT scan in mhd/raw format, incl. text files containing necessary parameters to run Rootine v.2.

2. macro: the bash.sh shell script carries out a series of commands bundled under the name Rootine v.2 on a Linux computer.
- Part 1 is a ImageJ macro which prepares the image before filtering by stitching both image parts together and normalizing gray values
- Part 2 does the Non-Local Means filtering in a stand-alone program that needs to be installed before and (see instructions in bash.sh)
- Part 3 contains the main root segmentation work flow as an ImageJ macro

3. our_results: Root length density and Root diameter results for the test image stored in txt files

4. README.txt: provides additional comments regarding the modification of the test image which were required to obtain reasonable results for the root diameter distribution with Rootine v.2.

This data was produced in the framework of the priority programme 2089 “Rhizosphere spatiotemporal organization - a key to rhizosphere functions” funded by Deutsche Forschungsgemeinschaft (project number 403640293).
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