Sub-Micrometer X-ray Tomography of Radiolarians: Computer Modeling and Skeletonization
Roger C. Wagner , 1 * John R. Jungck , 1 and Denis Van Loo 2 1 Department of Biological Sciences , 005 McKinly Lab. University of Delaware , Newark , Delaware 19716 2 UGCT-N12 , Proeſt uinstraat 86 , 9000 , Ghent , Belgium
*
rags@udel.edu Introduction
X-ray tomography is used to visualize the surface and interior structure of solid objects on the basis of X-ray attenuation (the proportion of X rays scattered or absorbed as they pass through an object) [ 1 ]. A tomographic series is acquired by rotating an X-ray source around a specimen and collecting transmitted X-ray intensity on a series of detectors. T e detectors acquire a set of images, which are X-ray projec- tions. T ese are converted to a voxelated 3D fi le that can be visualized and analyzed with a wide variety of 3D-based imaging programs. Resolution of these image fi les (designated as voxel pitch) depends on X-ray intensity, focal spot size of the X-ray source, detector size, and noise reduction. Using a combination of these factors, X-Ray Engineering, Belgium XRE (
www.xre.be ), has developed custom-made X-ray scanning systems designed for a variety of applications. T ese instruments generate tomographic information well into the sub-micrometer range.
Radiolarians are amoeboid protists with elaborate, radially symmetrical mineral skeletons [ 2 ]. Fossilized radiolarian skeletons (also called tests) consist of SiO 2 , which is X-ray attenuating. This provides the mechanism for acquisition of 3D data sets by X-ray tomography. With the development of high-resolution computerized tomography (CT), detailed 3D data sets of radiolarians can be acquired with sub-micrometer resolution. We report here the recording of X-ray tomograms (0.103 µm voxel pitch) of selected radiolarian tests and subsequent computer modeling of 3D data sets that reveal intricate details of the exterior and interior of the specimens. Also, digital skeletonization of some of the rendered models reveals their essential geomet- rical features, which can be measured with great accuracy based on the voxel size of the original data set.
Methods and Materials Washed radiolarians [ 3 ] were obtained from Dr. Richard Howey (Univeristy of Wyoming). T ese specimens originated from sediments collected from the seas of Barbados and were dated to the Tertiary period. X-Ray tomography . A custom-made, high-resolution CT imaging system, built via a collaboration between UGCT (Ghent University Centre for X-ray Tomography) and its spin-off company, X-Ray Engineering (
www.xre.be ), was used to acquire tomographic data sets of radiolarians. Several thousand radiolarians were mailed to Ghent, Belgium, on the sticky tab of a post-it-note. Single skeletons or groups of specimens were selected under a stereoscopic microscope and mounted on the tip of a 0.9 mm carbon
18
sample-holder stick using nitrocellulose as an adhesive. The sticks were inserted into the CT system on a custom sample holder. The X-ray CT system consisted of a transmission X-ray source with a 1 µm thick tungsten target, a high- resolution CCD-based sensor, and eight motorized stages on a damped optical table in a temperature-controlled, shielded room.
The detector was used in a 995×664 pixel mode with
a 36 µm pixel size. The X-ray source operated at 50 kV and 0.7 W. For each sample, typically 1,600 two-second projec- tions were acquired over a rotation of 360 degrees. The scan time was approximately 45–60 minutes, using the acquisition software ACQUILA (
www.xre.be ). The recorded data were processed and reconstructed using XRE dynamic reconstruction code into data sets with voxel size between 300 and 950 nm.
Computer modeling and rendering . 3D image stacks (DICOMM or TIFF) were thresholded and surface-rendered with AMIRA 5.6 (FEI, Houston, TX) running on a Mac-Pro platform. Rendered models were rotated and sliced digitally at several angles to reveal the specimen’s internal structure. The motion of a virtual camera was scripted to move around and within the modeled radiolarian test to produce a fly-through video for closer assessment of the interior structure.
Figure 1 : Rendered model of a group of radiolarians embedded in nitrocellulose adhesive. Several forms are present exhibiting cage-like tests with polygonal elements.
doi: 10.1017/S1551929515000747
www.microscopy-today.com • 2015 September
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