Microtomography

1 - Principle of the Technique

Microtomography is an imaging technique based on radiography. It is the same principle as the medical scanner, but using synchrotron radiation allows to reach much higher resolution.

 

2 - Principle of the reconstruction algorithm

 

Synchrotron radiation leads to a parallel beam geometry.

From the acquisition of about 1500 radiographs, volume is obtained using filtered backprojection algorithm.

Demonstration 
See the following page: http://bigwww.epfl.ch/demo/jtomography/

 

3 - Acquisition

3.1 - Basis to perform a microtomography experiment at ID19

     Step by step experiment document

3.2 - First reconstructed slice during experiment

     Computing during experiment

4 - Database: tomoDB

All scans performed on ID19 are registered in a Database (First version created by Ludovic Launer in 1999). This Database contains a lot of information about acquisition like energy, exposure_time, distance between sample and detector, image of a projection, image of a slice, ...

The first version of tomoDB was improved by Véronique Chaffard and Hyacinthe Meniet in July 2004.

Access to this database is possible onsite only.

User name: guest   password: tomodb

The user manual of tomoDB is available here (in French).

5 - Reconstruction

Using rnice cluster: see here

 

 

We use pyHST (High Speed Tomography in python version) software as reconstruction program. It has been created by Andy Hammersley and optimised by Alessandro Mirone.
The documentation of the last version of PyHST is available here: this web page
 

6 - Rescaling volumes in 8 bits: .vol --> .raw

 

To know more about rescaling, see here

 

 

 

7 - Visualization

7.1 - Projections

ImageJ

7.2 - Movie of projections

 

You can create an /avi file from scan projections

 

7.3 - Volumes

ImageJ: slice by slice

VGStudio: 3D rendering  (Documentation)

 

8 - Possible bugs

 

What to do in case of ...:

 

possible bugs