SPP2089_P21_Phalempin_et_al_Plant_Methods 0 10553

Project
POF3 - T123D631 - Rhizosphere
Description
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).
Size
6,5 GB
Data quality
quality assured data
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Metadata Catalogues
Dublin Core
URI
http://www.ufz.de/record/dmp/archive/10553
Subject
X-ray CT data
Type of data
collection of various data
Data quality
quality assured data
Status of data
raw data
derived data
Data format
raw
txt
ijm
sh
Creators
Schlüter, Steffen
Phalempin, Maxime
Publisher
Helmholtz-Zentrum für Umweltforschung
Rights holders
Helmholtz-Zentrum für Umweltforschung
Contact
Contact person : Steffen Schlüter (steffen.schlueter@ufz.de)
Time or Period of creation
15.03.2021
Language of the content
English
Update policy
stored data will not be extended
Access permissions
free access