Schlueter_et_al_ES&T 0 6322

Project
Department BOPHY
Description
Supporting Data for:

Schlüter et al.: Correlative imaging reveals holistic view on soil microenvironments, Environ. Sci. Technol. 2019, 53, 829−837

Description
This folder contains a minimum example to demonstrate the registration of a 3D computed tomography (CT) file into a 2D light microscopy (LM) image using Elastix (http://elastix.isi.uu.nl/). The demo was developed for a Linux OS (Ubuntu 16.04), tested with elastix version 4.700 and requires 3GB of RAM. The CT file is cropped and does not cover the full sample to save disk space and memory. Images are stored an ITK format which consists of the binary file containing the data (.raw) and a text file containing important meta information (.mhd). The registration is executed by running the shell script ./elastix.sh in a terminal. Open the shell script with a text editor to get more information about the required input for registration and to adapt folder locations, if necessary. Please consult the elastix homepage on how to download and install the software.

Contents of the zipped folder

Images:
CT.mhd – 3D X-ray CT image
LM.mhd – light microscopy image
CT_psd.mhd – pore size distribution derived from the segmented CT image (to demonstrate transformix)

Scripts:
elastix.sh – Shell script that executes elastix and transformix commands

Text files:
elastix_parameters.txt – contains all the parameters tun run the 2D-3D registration
CT_landmarks.txt – contains all corresponding landmark coordinates located in the CT image
LM_landmarks.txt – contains all corresponding landmark coordinates located in the LM image

Size
812,2 MB
License and Terms of Use
LICENSE and TERMS OF USE
Data quality
quality assured data
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Metadata Catalogues
Dublin Core
URI
http://www.ufz.de/record/dmp/archive/6322
Subject
2D-3D Image Registration example
Type of data
picture / image
Text
Data quality
quality assured data
Status of data
raw data
derived data
Data format
mhd
txt
sh
Creators
Schlüter, Steffen
Contributors
Müller, Carsten
Eickhorst, Thilo
Publisher
Helmholtz-Zentrum für Umweltforschung
Rights holders
Helmholtz-Zentrum für Umweltforschung
Source/Origin
DOI: 10.1021/acs.est.8b05245
References to related data
DOI: 10.1021/acs.est.8b05245
Citation note
Schlüter, S., Eickhorst, T. & Mueller, C. W. Correlative Imaging Reveals Holistic View of Soil Microenvironments. Environmental Science & Technology 53, 829-837, doi:10.1021/acs.est.8b05245 (2019).
Contact
Steffen Schlüter (steffen.schlueter@ufz.de
Time or Period of creation
04.12.2018 11:00
Language of the content
English
Access permissions
free access