SPP2089_P21_Phalempin_et_al_Plant_Methods 0 10553

Projekt
POF3 - T123D631 - Rhizosphere
Beschreibung
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.

Funding:
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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