Tomographic techniques for the study of exceptionally preserved fossils

Sutton, Mark D.

doi:10.1098/rspb.2008.0263

Cited by 162 publications

(152 citation statements)

References 53 publications

(64 reference statements)

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“…Bones are commonly imaged in computed tomographic (CT) and X-ray microtomographic (μCT) systems for research purposes, such as investigating trabecular and cortical changes in osteoporosis [1,2], comparative anatomy [3,4], and non-destructive examination of fossil skeletons [5,6]. We had hundreds of CT, μCT and synchrotron μCT scans of whole bones and trabecular bone cubes to analyse for studies on allometric bone scaling [7,8] and osteogenesis imperfecta.…”

Section: Introductionmentioning

confidence: 99%

BoneJ: Free and extensible bone image analysis in ImageJ

Doube

Kłosowski

Arganda‐Carreras

et al. 2010

Bone

1,754

1,239

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Bone geometry is commonly measured on computed tomographic (CT) and X-ray microtomographic (μCT) images. We obtained hundreds of CT, μCT and synchrotron μCT images of bones from diverse species that needed to be analysed remote from scanning hardware, but found that available software solutions were expensive, inflexible or methodologically opaque. We implemented standard bone measurements in a novel ImageJ plugin, BoneJ, with which we analysed trabecular bone, whole bones and osteocyte lacunae. BoneJ is open source and free for anyone to download, use, modify and distribute.

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Section: Introductionmentioning

confidence: 99%

BoneJ: Free and extensible bone image analysis in ImageJ

Doube

Kłosowski

Arganda‐Carreras

et al. 2010

Bone

1,754

1,239

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“…19 for comparative review of the various methods mentioned above and their application to paleontology); these are primarily zoological studies. SRXTM provides several advantages over CT. Modern, third-generation synchrotrons make use of hard X-rays, a monochromatic beam, and a high beam intensity to scan specimens.…”

mentioning

confidence: 99%

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

Smith

Collinson

Rudall

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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While more commonly applied in zoology, synchrotron radiation X-ray tomographic microscopy (SRXTM) is well-suited to nondestructive study of the morphology and anatomy of both fossil and modern plants. SRXTM uses hard X-rays and a monochromatic light source to provide high-resolution data with little beam-hardening, resulting in slice data with clear boundaries between materials. Anatomy is readily visualized, including various planes of section from a single specimen, as clear as in traditional histological sectioning at low magnifications. Thus, digital sectioning of rare or difficult material is possible. Differential X-ray attenuation allows visualization of different layers or chemistries to enable virtual 3-dimensional (3D) dissections of material. Virtual potential fossils can be visualized and digital tissue removal reveals cryptic underlying morphology. This is essential for fossil identification and for comparisons between assemblages where fossils are preserved by different means. SRXTM is a powerful approach for botanical studies using morphology and anatomy. The ability to gain search images in both 2D and 3D for potential fossils gives paleobotanists a tool-virtual taphonomy-to improve our understanding of plant evolution and paleobiogeography.anatomy ͉ morphology ͉ palaeobotany ͉ synchrotron radiation X-ray tomographic microscopy V arious methods now exist for visualizing plant material in 3-dimension (3D). Confocal laser-scanning microscopy, electron tomography, and optical coherence microscopy are used for imaging thin (often sectioned) and (semi-)transparent material (1), in conjunction with modern computer programs for 3D reconstruction. Complementing this, other techniques for examining larger specimens or to avoid sectioning ''difficult'' material include neutron imaging, nuclear magnetic resonance (NMR) imaging, X-ray computed tomography (CT), highresolution X-ray computed tomography (HRCT), and synchrotron radiation X-ray tomographic microscopy (SRXTM). Of these, HRCT and SRXTM are the most useful methods to visualize both internal and external morphology and anatomy in a noninvasive and nondestructive manner, and are useable for a range of specimen sizes. HRCT has been used in plant sciences to examine structure and morphology of extant flowers and fruits (1; see also the Digital Morphology digital library of the University of Texas at Austin, www.digimorph.org), density of extant woods (2, 3), spatial distribution of root systems (4-6), and light interception of the tree canopy (7,8). In paleobotany, CT has been used in a few cases to reveal internal structures, including in Paleozoic charophytes (9), silicified Cycadeoidea stems and Araucaria mirabilis cones from the Jurassic (10), an undescribed Cretaceous gymnosperm fructification (11, 12), a Paleogene hymenophyllaceous fern rhizome (13), and Eocene myrtaceous fruits (14).Recently, SRXTM has become increasingly used in biology, especially in paleontology (e.g., 15-20; see ref. 19 for comparative review of the various methods mentioned...

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“…MRI has been considered to be poorly suited to geological material 16 and at present does not compete with µXCT or NCT. MRI machines are not easily accessible to palaeontological researchers, scans are very expensive and scan times are long compared with those of XCT.…”

Section: Research Articlementioning

confidence: 99%

Finding fossils in Malapa breccia – medical CT scanning or micro-CT scanning?

Smilg¹

2017

S. Afr. J. Sci.

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Computed tomography (CT) imaging of fossils has revolutionised the field of palaeontology, allowing researchers to gain a better understanding of fossil anatomy, preservation and conservation. Micro focus X-ray computed tomography (μXCT) has been far more extensively used for these purposes than medical CT (XCT) – mostly because of the exquisite detail that the μXCT scanning modality, using slices of micron thicknesses, can produce. High energy X-rays can potentially penetrate breccia more effectively than lower energy beams. This study demonstrates that lower energy beams produce superior images for prioritising breccia for preparation. Additionally, XCT scanners are numerous, accessible, fast and relatively cost-effective when compared to μXCT scanners – the latter are not freely available, scanning times are much longer and there are significant limitations on the size and weight of scannable objects. Breccia blocks from Malapa were scanned at high and lower energy and images were analysed for image quality, artifact and certainty of diagnosis. Results show that lower energy images are deemed superior to higher energy images for this particular application. This finding, taken together with the limitations associated with the use of μXCT for the imaging of the large breccia from Malapa, shows that XCT is the better modality for this specific application. The ability to choose fossil-bearing breccia, ahead of manual mechanical preparation by laboratory technicians, would allow for the optimal use of limited resources, manual preparatory skills as well as the curtailment of costs.

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Tomographic techniques for the study of exceptionally preserved fossils

Cited by 162 publications

References 53 publications

BoneJ: Free and extensible bone image analysis in ImageJ

BoneJ: Free and extensible bone image analysis in ImageJ

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

Finding fossils in Malapa breccia – medical CT scanning or micro-CT scanning?

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