Editing Scanco Administration (section)

===Attenuation measured by µCT===
A micro-CT 3D image of an object is basically a 3D map of local x-ray absorption in the object. The reconstruction from multiple angular views provides information on how much x-ray absorption is happening within each cubic voxel element of the scanned volume.

It is important to understand what is meant by “density” in a µCT image. The reconstructed grey-scale intensity of each image voxel does not relate directly to mass density alone, thus do not expect it to correspond with measurements of weight per volume, e.g. g.cm-3. The primary entity that is measured is x-ray absorption, defined as the x-ray linear attenuation coefficient in units of
1/distance, specifically, 1/cm. This is determined both by mass density and x-ray mass attenuation coefficient which is determined by the elemental composition of the material. The x-ray linear attenuation coefficients of typical material is shown blow.

[[File:Mu_comparison.JPG|thumb|center|600px|X-ray linear attenuation coefficient µ of typical material (image curtesy of Dr. Ying Zhu)]]

The images we obtain from the scanner are in a special scanner manufacturer format called AIM files. Each voxel in these images contains a scaled linear attenuation value (mu-value) to save disk space. 

{| class="wikitable"
|-
! scope="col"| Symbol
! scope="col"| Name
! scope="col"| Unit
! scope="col"| Value Range
! scope='col'| Meaning or Comments
|-
! scope="row"| µ
| x-ray linear attenuation coefficient
| 1/cm
| µ > 0 
| A constant that describes the fraction of attenuated incident photons in a monoenergetic beam per unit thickness of a material
|-
! scope="row"| mu_value
| linear attenuation in Scanco images
| 1/cm
| -8～8 typically
| mu value represented in Scanco images
|-
! scope="row"| pixel_Scanco
| pixel intensity value in Scanco images
| -
| −32768～32767
| Original format of Scanco images in 16-bit signed
|-
! scope="row"| pixel_uint
| pixel intensity value in converted Scanco images
| -
| 0～65535
| Converted format of Scanco images in 16-bit unsigned, using the same slope (unscaled) but an updated intercept
|}

<pre>
pixel_Scanco = mu-value * scaling_factor
</pre>


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