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Applying Simian to High Mag Electron Tomography Data
November 2003 reash41
The following images are based on a tomography data
showing a number of different features on a sub-cellular scale.
The 8-bit grayscale image at right is a slice of a three
dimensional volume.
The images below are close ups of the features labeled Cx43-TC in the labeled image above, all produced with the Simian purely via volume rendering. Normals were assigned using the gradient vector and used to add convincing lighting, revealing geometry which would otherwise be quite difficult to make out. The result is remarkably similar in appearance to what could be produced using time-intensive level set techniques. Rotation and scaling of the model in Simian provides
cues showing the three dimensional structure of the data that are
absent in the slice and two dimensional capture shown here.
The image below at center
corresponds to a camera position that shows the data in the same
orientataion as the labeled slice above. The image below at right shows
the data somewhat rotated in an effort to illustrate the structural
information
that can be conveyed with an interactive three dimensional model.
reash15
The leftmost image below is a slice (number 300 of 670) taken from a massive 1.3 GB data set showing a gap junction between cells. The second image below was created by projecting through all 600 slices of the data set, showing the minimum value in each "column" of voxels; the third shows column maxima; the last shows column mean values. Slice extraction and projections were done using the unu tool created by Gordon Kindlmann. At right is a first pass effort at visualizing the same data
using Joe Kniss'
Simian
volume renderer. The ammount of information that can be taken from
the Simian's treatment of the data is dramatic when looked at
side-by-side with slice and projection images - especially when
viewed interactively. Simian 2.8 is freely available.
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