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Computer Vision for Electron Tomography

Researchers: Sami Brandt and Jukka Heikkonen

In structural biology, electron tomography is used in reconstructing three-dimensional objects such as macromolecules, viruses, and cellular organelles to learn their three-dimensional structures and properties. The reconstruction is made from a set of transmission electron microscope (TEM) images which may be obtained either by tilting the specimen stage by small angular increments (single axis tilting) or a fixed angle and rotating by constant increments in the specimen plane (conical tilting).

In order to successfully perform the 3D reconstruction in electron tomography, transmission electron microscope images have to be accurately aligned or registered. So far, the problem is solved either by manually showing the corresponding fiducial markers from the set of images or automatically using simple correlation between the images on several rotations and scales. The present solutions, however, share the problem of being inefficient and/or inaccurate. We have therefore developed a method where the registration is automated using conventional colloidal gold particles as reference markers between images. The results we have obtained show the reliability of the approach as well as high accuracy in alignment is provided (Figure 12).

Always it is not, however, possible to sprinkle gold particles on the preparation. In addition, the gold beads interfere with the three-dimensional reconstruction of the object. Therefore, we have also studied the automatic registration problem when there are no fiducial markers in the images. This approach is based on tracking the high curvature points of the intensity surface in the image chain. The main problem lies in identifying and localizing these interest points and their robust matching from image to image. The results we have obtainded in this problem have also been promising.

  
Figure 12
Figure 12: Stereo image pair of a reconstructed chromosome where the auomatic alignment procedure with gold markers have been used. The gold beads are shown as red.


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