Serial sections and 3D reconstruction of a block of Kanab Goldenstone

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Figure 1. A block of Kanab Goldenstone, mounted on a carrier for sectioning

Investigated here is the internal distribution of cements and colouration within a quarried block of 'Kanab Goldenstone' (also called 'Kanab Wonderstone'), from the Triassic Shinarump Formation (Burgess, 2014), about 20 cm wide, 6 cm high, and 6 cm deep (figure 1).

The concretion was sectioned serially at approximately 2mm intervals to produce a stack of images, using the procedure described at Serial Sections. The resulting stack of images was assembled into the frames of a video (below).

Figure 2. Histogram of slice thickness (cm)

Although the aim was to remove 2mm of sample per slice, the actual measured thickness of the remaining sample showed some jitter around a mean of 1.87 mm per slice, as shown in the histogram in figure 2.

The resolution is much higher in the plane of the photographs than between slices. The resolution of the original photos is about 61 microns per pixel (20.2 cm in sample maps to 3306 pixels = 61.1 microns/pixel); the mean distance between slices is about 1870 microns. To approximate the true shape of the voxels in synthesized images, the photographed image plane is repeated or interpolated. The number of repetitions required to approximate true shape depends on the processed size of the photographic plane. For example, at quarter size the photographic plane would have a resolution of approximately 244 microns/pixel and therefore true-shape voxels would be synthesized by 1870/244 = 7 repetitions of the image plane. Since there is some jitter in slice thickness, better would be to set the repetitions of a particular slice proportional to the measured thickness of that slice, instead of using the average.

QuickTime offers the best 'scrubbing' control (the ability to move forward/backwards smoothly, frame by frame), but HTML5 (using a controller I wrote) has reasonable frame control and better 'poster image' control. Select which you'd like using the controls below. If none work for you, here are direct links to the video files: video 1, video 2, video 3.

Video 1. Side view

The two synthesized views below are orthogonal to the view above.

Video 2. Top view (same scale as video 1)

Video 3. Side view, orthogonal to video 1 and 2 (same scale as above)

Excellent tools are available to explore these image stacks offline, eg., ImageJ; see serial sections for more information. An image stack can be obtained by downloading video 1 (by right-clicking on the link above and saving it to your computer) and using Quicktime or similar tools (eg., VLC) to export the video to an image sequence, which can then be imported into ImageJ (eg., for Orthogonal Views).

All videos here have been downsized. To obtain full resolution images, contact me below.


Burgess, D.T. (2014). Early and late iron diagensis in the upper Triassic Shinarump Member of the Chinle Formation (Utah and Arizona) (MS Thesis). University of Nebraska, Lincoln, NE


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