MCT Data Processing

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Last updated: Nov 11, 2024
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All experiment data will be stored in the Australian synchrotron for one year period. Please copy your data to your institutional data storage before the expiry date.

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 this link, 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 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 file:

For fine tuning the COR (Center of Rotation):

For loading .h5 file on ImageJ

 

 

 

image-20240110-022243.png

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.

Analysis software such as ORS-Dragonfly and Avizo 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, please use the plugin file in this link: plugin: new version. You can open .h5 file by clicking on the MCT menu: Capture.JPG

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. Avizo tutorial can be seen in this link Avizo learning center.   

People who are listed in the Experimental Authorization Form will have access to the data automatically.

 

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:

 

 

Or see this link Data_Download