Schlueter_et_al_ES&T 0 6322

Projekt
Department BOPHY
Beschreibung
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

Größe
812,2 MB
Lizenz- und Nutzungsbedingungen
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Metadaten Kataloge
Dublin Core
URI
http://www.ufz.de/record/dmp/archive/6322
Thema
2D-3D Image Registration example
Datenart
Bild / Grafik
Text
Datenqualität
qualitätsgesicherte Daten
Datenstatus
Rohdaten
abgeleitete Daten
Datenformat
mhd
txt
sh
Urheber
Schlüter, Steffen
Beitragende
Müller, Carsten
Eickhorst, Thilo
Herausgeber
Helmholtz-Zentrum für Umweltforschung
Rechteinhaber
Helmholtz-Zentrum für Umweltforschung
Quelle/Ursprung
DOI: 10.1021/acs.est.8b05245
Beziehungen zu verwandten Daten
DOI: 10.1021/acs.est.8b05245
Hinweis zur Zitation
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).
Kontakt
Steffen Schlüter (steffen.schlueter@ufz.de
Zeitpunkt oder -bereich der Erzeugung der Daten
04.12.2018 11:00
Sprache des Inhalts
Englisch
Zugriffsrechte
freier Zugriff