Gao_et_al_2018_PS 0 6677

Projekt
Department BOPHY
Beschreibung
Supporting Data for:

Gao et al.: A shape-based method for automatic and rapid segmentation of roots in soil from X-ray computed tomography images: Rootine (submitted to Plant and Soil)

Description
This folder contains the Rootine Script. It also contains two small test images (500³ voxels, experiment I, experiment II) and a full X-ray CT image of an entire soil column split into a top and bottom image (1600 x 1600 x 1668 voxels each) to have some data for testing. The Rootine script was developed for a Linux OS (Ubuntu 18.04) is executed by running the shell script ./Rootine_v1.0.sh in a terminal. Open the shell script with a text editor to get more information about software installation, contact information for help, the required input for registration and to adapt folder locations, if necessary.

The shell script executes three main steps:
1. Image concatenation and attenuation correction with Fiji
2. Noise removal with a stand-alone 3D Non-local means filter implemented in ITK
3. Main Segmentation workflow with Fiji

Fiji workflows are run in the terminal via ImageJ macros (ijm files) followed by several input arguments .

Contents of the zipped folder

Images:
test_image_exp1.mhd – small test image from experiment I
test_image_exp2.mhd – small test image from experiment II
image_top.mhd - upper part of a full scan
image_bottom.mhd - lower part of a full scan

Note: the mhd-file contains meta-information and can only be opened in combination with the raw-file that contains the actual data

Scripts:
Rootine_v1.0.sh – Main shell script that executes the Rootine workflow

stitching_normalization.ijm - Image concatenation and attenuation correction with Fiji (can be ignored for small test images)

segmentation.ijm - Main Segmentation workflow with Fiji (note that for the small test data "Keep Largest Region" (line 164) and "Keep Largest Label" (line 195) need to be replaced by a size opening)

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