Friday, October 17, 2014

Learning Tomography: Data Collection

Even though this blog is not focused on the experimental devices, it is interesting to have some ideas about the experimental data collection. I created videos to explain the various strategies used in science...

1. Data collection

To determine the 3D structure of the sample, we have to collect images from various viewpoints.  In the simplest strategy, all the images are obtained by rotating the sample around a single axis: we speak about axial tomography. In the other cases like in the "single particle" method used in cryo-electron microscopy, the sample is rotated in every directions.
1.1. With a Computed Tomography Scanner (or CT-Scanner) [Wikipedia]
The X-ray CT-scanner used in medicine is an example of axial tomography as shown in the video below. The X-ray emitter (in red) is located diametrically opposite to the detector. The bipartite device is rotating around the sample (here a human head) and collects a series of X-ray images.
According to the rotation angle, the collected X-ray image is not the same.

Note: This animation is a simplified version of a real CT-scanner especially for the shape of the X-ray beam which is conical and not cylindrical like in my video.
1.2. With an electron microscope
In electron microscopy, the principle is still the same, a series of images is collected but in this case, the device is static and the sample is rotated.
In the video, the electron gun (in red) produces an electron beam passing through the sample (in green) deposited on a grid itself maintained by a cryo-holder (tennis racket-shaped). The detector (CCD or CMOS) is capturing the image (a projection of the sample).
Compared to the CT-scanner, the mechanical constraints are much higher. Here, the rotation is limited by the holder  between -65° to +65°.

Note: In the video, for sake of convenience, the micrographs are not real projections (but only silhouettes) of the sample. The inner densities are not displayed in this clip.

2. Other crazybiocomputing posts

Further readings are available in ...
  • Learning Tomography Series  [Link]
  • Image Processing TOC [Link]

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