MCT Data Processing
All experimental data will be stored at the Australian Synchrotron for a period of one year. Please ensure you copy your data to your institutional storage before the expiry date. Regularly check the status of your experimental data using Data Records. You can use Globus for transferring your data, see Data_Download.
ASCI Desktop is used for data processing, reconstruction, and analysis. It provides a simple interface to the cluster computer at the Australian synchrotron. ASCI Desktop can be accessed → in https://asci.synchrotron.org.au/, during the beam time and/or after the beam time. The experimental projection data and the reconstructed data are saved in hdf5 file format. However, they can be converted to tiff or other file format. MCT reconstruction pipeline is available in ASCI Desktop to reconstruct the projection data into 3D reconstructed data. See the detail instruction below:
The MCT reconstruction code is written in jupyter notebook. MCT reconstruction pipeline includes:
TIE Hom phase-retrieval
Tomography artifact correction such as beam hardening, ring correction
Horizontal and vertical stitching algorithm.
For conversion .h5 file to .tiff or other file format:
For fine tuning the COR (Center of Rotation):
For loading .h5 file on ImageJ
For changing parameter in hdf5 file:
Phase retrieval of meteor sample with variation of gamma values. Phase contrast fringes reduce with increasing gamma value. Different density increases with increasing gamma value. Note that the gamma values vary depending on the material density, material type, and X-ray energy.
Analysis software such as ORS-Dragonfly and 3D Slicer are also available in the ASCI desktop for 3D viewing, image rendering, image segmentation and other data analysis. The Dragonfly plugin to open .h5 file can be found in this link (and please follow the instruction in this link): https://github.com/AustralianSynchrotron/dragonfly_mct_import . For new version of Dragonfly 2024.1, the plugin file in this link is also valid. You can open .h5 file by clicking on the MCT menu:
Dragonfly is only available for online users or the users are having the beam-time. Dragonfly tutorial can be seen in this link Dragonfly learning center. 3D Slicer is available for online and offline users. The tutorial for 3D Slicer can be seen 3D Slicer learning center.
The minimum computer specification required is 1 GB of RAM to open 1 GB .h5 files. This means that larger file sizes will require proportionally more RAM.
People who are listed in the Experimental Authorization Form will have access to the data automatically.
Globus is a secure, reliable platform for transferring and sharing large research data between institutions and storage systems. It automates transfers, verifies data integrity, and supports easy collaboration.
Or see this link for using Globus: Data_Download
You can access to your experimental data remotely via Secure FTP (SFTP) to download your experimental data. You can use a graphical client such as FileZilla with the following connection details:
Protocol : SFTP – SSH File Transfer Protocol
Host: sftp://sftp.synchrotron.org.au
Port: 22
Username is the same email address you use to log in the User Portal
Password:
