Serial sections and 3D reconstruction of a Navajo Sandstone iron oxide concretion (Navajo sample A)

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Figure 1. Context

The Jurassic Navajo Sandstone of southern Utah in southwestern USA commonly hosts concretions cemented by iron oxides (Potter 2011, Loope 2012). The concretions appear to have formed by filling pore spaces between the aeolian sand grain matrix that hosts them, without disturbing the sand matrix.

Investigated here is the internal distribution of cements and colouration within an oblate spheroidal concretion encased in matrix about 15 cm in diameter and 8 cm high that was found resting on the surface (similar to figure 1). This particular sample was selected because the concretion is still partially encased within surrounding sandstone. Figure 2 shows views of the sample. Concretions in the vicinity more firmly attached to the bedrock were oriented identically, with their long dimension horizontal. The bedding planes visible in the side views are thought to have been subhorizontal (not slipface grainflow).

Figure 2. Top (left) and bottom

Figure 3. Sides, 90 degree rotations

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 4. Histogram of slice thickness (cm)

The sample was processed in two parts; it was first cut in unequal halves (to obtain secure mounting faces), then each of those halves was mounted and serially sectioned, and finally the two sets of images were concatenated. 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 0.18 cm per slice, as shown in the histogram in figure 4.

The resolution is much higher in the plane of the photographs than between slices. The resolution of the original photos is about 49 microns per pixel (7.94 cm in sample maps to 1613 pixels = 49.2 microns/pixel); the mean distance between slices is about 1800 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 200 microns/pixel and therefore true-shape voxels would be synthesized by 1800/200 = 9 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 (scaled down by half of video 1)

Video 3. Side view, orthogonal to video 1 (scaled down by half of video 1)

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.


Loope, David B., et al. (2012). Rinded iron-oxide concretions: hallmarks of altered siderite masses of both early and late diagenetic origin. Sedimentology 59.6 (2012): 1769-1781.

Potter, Sally L., et al. (2011). Characterization of Navajo Sandstone concretions: Mars comparison and criteria for distinguishing diagenetic origins. Earth and Planetary Science Letters 301.3 (2011): 444-456.


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