Editing Scanco User Instructions (section)

==Micro-CT Image Basics==
Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed.  Micro-CT refers to CT in which the [http://www.scanco.ch/index.php?id=faq_general#c779 resolution] lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT.  Structural detail provided by CT depends on differences in x-ray attenuation properties.  Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish. 

===Dark Field===
Detector response with x-rays off.  Enables corrections of non-uniformities of the detector.  Acquired automatically by the scanning software before each scan.

[[File:Dark_field_single.img_assist_custom-400x97.jpg|400px]]

===Bright Field===
Detector response with x-rays on but no sample.  Enables corrections of non-uniformities of the x-ray beam.  Acquired automatically by the scanning software before each scan.

[[File:Bright_field_single.jpg|400px]]

===Raw Projection===
A raw x-ray projection of a mouse leg.  The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example).  Projections are acquired at many incremental rotations around the sample.

[[File:Raw_projection_notes.jpg|400px]]

===Sinogram===
The sinogram is a different representation of the projection data.  The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

[[File:Sinogram.jpg|400px]]

===Attenuation Projection===
Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample.  Bright regions correspond with higher attenuation.

[[File:Attenuation_projection.jpg|400px]]

===Reconstructed Image===
From the attenuation projections, the original structure can be calculate using filtered back projection.

*[https://youtu.be/DBLYSETYbe8 CT Back-projection Reconstruction]
*[https://youtu.be/NWeM35_KR2w CT Reconstruction of a Head]

[[File:Reconstruction_xy_yz_planes.jpg|400px]]


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