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High Dynamic Range Imaging (HDR)
Image Processing
Transmission Electron Microscopy (TEM)
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! Chemotaxonomy and Chemometric Palaeobotany@
Glossaries, Dictionaries and Encyclopedias: Microscopy@

Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)

! R.L. Abel et al. (2012): A palaeobiologist´s guide to "virtual" micro-CT preparation. In PDF, Palaeontologia Electronica, 15.

Department of Geological Sciences (High-Resolution X-ray Computed Tomography (CT) Facility), University of Texas, Austin: Image Folio. Snapshot taken by the Internet Archive´s Wayback Machine.
High-resolution X-ray CT (Computed Tomography) is a completely nondestructive technique for visualizing features in the interior of opaque solid objects, and for obtaining digital information on their 3-D geometries and properties.
What is X-ray CT? Eexcerpted and adapted from: Denison, C., Carlson, W.D., and Ketcham, R.A. 1997. Three-dimensional quantitative textural analysis of metamorphic rocks using high-resolution computed X-ray tomography: Part I. Methods and techniques. Journal of Metamorphic Geology, 15: 29-44.

J.C. Benedict (2015): A new technique to prepare hard fruits and seeds for anatomical studies. In PDF, Appl. Plant Sci., 3.

! L. Bertrand et al. (2012): Development and trends in synchrotron studies of ancient and historical materials. In PDF, Physics Reports, 519: 51-96.

! L. Bertrand et al. (2011): European research platform IPANEMA at the SOLEIL synchrotron for ancient and historical materials. In PDF, Journal of Synchrotron Radiation.

M.I. Bird et al. (2008): X-ray microtomographic imaging of charcoal. Abstract, Journal of Archaeological Science, 35: 2698-2706.

B. Blonder et al. (2012): X-ray imaging of leaf venation networks. In PDF, New Phytologist.


! C.R. Brodersen and A.B. Roddy (2016): New frontiers in the three-dimensional visualization of plant structure and function. American journal of botany, 103: 184-188.

! C.R. Brodersen et al. (2011): Automated analysis of three-dimensional xylem networks using high-resolution computed tomography. In PDF, New Phytologist, 191: 1168-1179.

William D. Carlson (2006): Three-dimensional imaging of earth and planetary materials. In PDF, Earth and Planetary Science Letters, 249: 133-147. Provided by the Internet Archive´s Wayback Machine.

! M.E. Collinson et al. (2016): X-ray micro-computed tomography (micro-CT) of pyrite-permineralized fruits and seeds from the London Clay Formation (Ypresian) conserved in silicone oil: a critical evaluation. Abstract.

! M.E. Collinson et al. (2012): The value of X-ray approaches in the study of the Messel fruit and seed flora. In PDF, Palaeobiodiversity and Palaeoenvironments, 92: 403-416. See also here (abstract).

! J.A. Cunningham et al. (2014): A virtual world of paleontology. Trends in Ecology & Evolution, 29: 347-357.

Charles Daghlian (Dartmouth College, Hannover, NH) and Jennifer Svitko, Paleobotanical Holdings at the Liberty Hyde Bailey Hortorium at Cornell University: Paleoclusia 3D Reconstructions. Movies from CT scans done on the Turonian fossils. Provided by the Internet Archive´s Wayback Machine. See also here (W.L. Crepet and K.C. Nixon 1998, abstract and photos).

M.L. DeVore et al. (2006): Utility of high resolution x-ray computed tomography (HRXCT) for paleobotanical studies: An example using london clay fruits and seeds. American journal of botany, 93: 1848-1851.

The Digital Morphology (part of the National Science Foundation). The Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.

J.A. Dunlop et al. (2012): A minute fossil phoretic mite recovered by phasecontrast X-ray computed tomography. In PDF, Biol. Lett., 8: 457-460.

A.M.T. Elewa (2011): Computational Paleontology. Provided by Google books.

Aaron G. Filler, Department of Neurosurgery, Institute for Nerve Medicine, Santa Monica, California: The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI (PDF file). About Magnetic Resonance Imaging, Diffusion Tensor Imaging, etc.

E.M. Friis et al. (2014): Arcellites punctatus sp. nov.: a new megaspore from the Early Cretaceous of Portugal studied using high resolution synchrotron radiation X-ray tomographic microscopy (SRXTM). In PDF, Grana, 53: 91-102. See also here.

! E.M. Friis et al. (2014): Three-dimensional visualization of fossil flowers, fruits, seeds, and other plant remains using synchrotron radiation X-ray tomographic microscopy (SRXTM): new insights into Cretaceous plant diversity. In PDF, Journal of Paleontology, 88: 684–701. See also here (abstract).

Else Marie Friis et al. (2007): Phase-contrast X-ray microtomography links Cretaceous seeds with Gnetales and Bennettitales. Abstract, Nature 450: 549-552.
! See also here and there (in PDF).

M.K. Futey et al. (2012): Arecaceae Fossil Fruits from the Paleocene of Patagonia, Argentina. In PDF, Bot. Rev.

R. Garwood and M. Sutton (2010): X-ray micro-tomography of Carboniferous stem-Dictyoptera: new insights into early insects. In PDF, Biology Letters.

R. Garwood et al. (2009): High-fidelity X-ray microtomography reconstruction of siderite-hosted Carboniferous arachnids. In PDF, Biol. Lett., 5: 841-844.

! C.T. Gee (2013): Applying microCT and 3D Visualization to Jurassic Silicified Conifer Seed Cones: a virtual advantage over thin-sectioning. In PDF, Applications in plant sciences. See also here.

C.T. Gee et al. (2003): A Miocene rodent nut cache in coastal dunes of the Lower Rhine Embayment, Germany. In PDF, Palaeontology, 46. See also here (abstract). One of the first CT applications to solve a palaeobotanical problem.

Ann Gibbons (2007): Paleontologists Get X-ray Vision. Science Vol. 318: 1546-1547.

Larry Greenemeier, Scientific American: Megavoltage CT Imaging Unlocks Fossil Mysteries. The proficiency of cancer-care computerized tomography on geologic finds.

T. Hegna et al. (2013): Not Quite Frozen in Time: Windows into the Internal Taphonomy of Fossils in Amber via MicroCT-scan Technology. Abstract.

Anette E.S. Högström et al. (2009): A pyritized lepidocoleid machaeridian (Annelida) from the Lower Devonian Hunsrück Slate, Germany. PDF file, Proc. R. Soc. B, 276: 1981-1986. This paper is exemplary in its combination of X-ray and CT of animal body fossils.

Y. Huang et al. (2012): New fossil endocarps of Sambucus (Adoxaceae) from the upper Pliocene in SW China. In PDF, Review of Palaeobotany and Palynology, 171: 152-163. Snapshot taken by the Internet Archive´s Wayback Machine.

S. Kiel et al. (2012): Fossilized digestive systems in 23 million-year-old wood-boring bivalves. In PDF.

M. Lak et al. (2008): Phase contrast X-ray synchrotron imaging: opening access to fossil inclusions in opaque amber. In PDF, Microsc. Microanal., 14, 251-259.

S. Lautenschlager, Software Sustainability Institute: A Digital (R)evolution in Palaeontology.

Karen Lee et al. (2006): Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography. Abstract, Plant Cell, 8(9): 2145-2156.

! A. Lukeneder (2012): Computed 3D visualisation of an extinct cephalopod using computer tomographs. In PDF, Computers & Geosciences, 45: 68-74.

! H. Mallison (2012): Digitizing Methods for Paleontology: Applications, Benefits and Limitations. In PDF.

P. Matysová (2016): Study of fossil wood by modern analytical methods: case studies. Doctoral Thesis, Charles University in Prague, Faculty of Science, Institute of Geology and Palaeontology.
Please take notice: Fig. (PDF page 37): Artistic reconstruction of wood deposition and silicification in river sediments. Fig. 7 (PDF page 37): Artistic reconstruction of plant burial by volcanic fall-out.

! D. Mietchen et al. (2008): Three-dimensional Magnetic Resonance Imaging of fossils across taxa. PDF file, Biogeosciences, 5: 25-41. Fossil cones of the conifer Pararaucaria patagonica. Magnetic Resonance Imaging (MRI). See also here.

! J.D. Moreau et al. (2015): Study of the Histology of Leafy Axes and Male Cones of Glenrosa carentonensis sp. nov. (Cenomanian Flints of Charente-Maritime, France) Using Synchrotron Microtomography Linked with Palaeoecology. PloS one, 10.
Plant fossils embedded inside flint nodules.

National Center for X-ray Tomography (NXCT)

Paul Scherrer Institut, Villigen (the largest research institute for natural and engineering sciences in Switzerland): TOMCAT - X02DA: Tomographic Microscopy. The beamline for TOmographic Microscopy and Coherent rAdiology experimentTs (TOMCAT) offers cutting-edge technology and scientific expertise for exploiting the distinctive peculiarities of synchrotron radiation for fast, non-destructive, high resolution, quantitative investigations on a large variety of samples.

K.B. Pigg et al. (2006): VALUE OF HRXCT FOR SYSTEMATIC STUDIES OF PYRITIZED FOSSIL FRUITS. Abstract, 2006 Philadelphia Annual Meeting, Geological Society of America.

M. Pika-Biolzi et al. (2000): Industrial X-ray computed tomography applied to paleobotanical research. In PDF Rivista italiana di Paleontologia e Stratigrafia.

I. Rahman, WordPress: Virtual Palaeontology: What´s It All About?
Virtual Palaeontology.

A.R. Rees (2013): On the 3-D reconstruction of Paleozoic and Mesozoic paleobotanical problematica. Abstract.

F. Riquelme et al. (2009): Palaeometry: Non-destructive analysis of fossil materials. In PDF.

D. Schwarz et al. (2005): Neutron Tomography of Internal Structures of Vertebrate Remains: A Comparison with X-Ray Computed Tomography. Palaeontologica Electronica Volume 8, Issue 2.

! Andrew C. Scott et al. (2009): Scanning Electron Microscopy and Synchrotron Radiation X-Ray Tomographic Microscopy of 330 Million Year Old Charcoalified Seed Fern Fertile Organs. PDF file, Microsc. Microanal., 15: 166-173.

! Andrew C. Scott and Margaret E. Collinson (2003): Non-destructive multiple approaches to interpret the preservation of plant fossils: implications for calcium-rich permineralisations. PDF file, Journal of the Geological Society, 160: 857-862. See also here.

! B.J. Slater et al. (2011): Guadalupian (Middle Permian) megaspores from a permineralised peat in the Bainmedart Coal Measures, Prince Charles Mountains, Antarctica. In PDF, Review of Palaeobotany and Palynology, 167: 140-155.

! Selena Y. Smith et al. (2009): Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants. Abstract and free PDF (4.5 MB), PNAS, 106: 12013-12018. Excellent!

A.R.T. Spencer et al. (2013): Combined methodologies for three-dimensional reconstruction of fossil plants preserved in siderite nodules: Stephanospermum braidwoodensis nov. sp. (Medullosales) from the Mazon Creek lagerstätte. In PDF, Review of Palaeobotany and Palynology, 188: 1-17. See also here (abstract).

M. Speranza et al. (2010): Traditional and new microscopy techniques applied to the study of microscopic fungi included in amber. PDF file, In: A. Méndez-Vilas and J. Díaz (eds.): Microscopy: Science, Technology, Applications and Education. Scanning electron microscopy in backscattered electron mode, with energy dispersive X-ray spectroscopy microanalysis.

D.C. Steart et al. (2014): X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov. In PDF, see also here.

C. Strullu-Derrien (2014): The earliest wood and its hydraulic properties documented in c. 407-million-year-old fossils using synchrotron microtomography. Abstract, Botanical Journal of the Linnean Society, 175: 423-437.

! G.W. Stull et al. (2016): Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT. In PDF (26 MB), NRC Research Press. See also here

Wolfgang H. Stuppy et al. (2003): Three-dimensional analysis of plant structure using high-resolution X-ray computed tomography. PDF file, Trends in Plant Science, 8.

! M.D. Sutton et al. (2012): SPIERS and VAXML; A software toolkit for tomographic visualisation and a format for virtual specimen interchange. In PDF, Palaeontologia Electronica, 15.

! M.D. Sutton (2008): Tomographic techniques for the study of exceptionally preserved fossils. PDF file, Proc. R. Soc. B, 275: 1587-1593.

P. Tafforeau et al. (2007): Nature of laminations and mineralization in rhinoceros enamel using histology and X-ray synchrotron microtomography: Potential implications for palaeoenvironmental isotopic studies. Abstract, Palaeogeography, Palaeoclimatology, Palaeoecology, 246: 206-227.

T. van der Niet et al. (2010): Three-dimensional geometric morphometrics for studying floral shape variation. In PDF, Trends in Plant Science, 15.

S.-J. Wang et al. (2017): Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities. In PDF, Am. J. Bot., 104: 127-149.

Geophysical Laboratory, Washington, DC: micro-XANES. Synchrotron Based Scanning Transmission X-ray Microscopy and Microspectroscopy (C-, N-, O-XANES).
Snapshot provided by the Internet Archive´s Wayback Machine.

! M.W. Westneat (2008): Advances in biological structure, function, and physiology using synchrotron X-ray imaging. In PDF, Annu. Rev. Physiol., 70: 119-142.
This expired link is available through the Internet Archive´s Wayback Machine.

Wikipedia, the free encyclopedia:
! Tomography.
! Synchrotron X-ray Tomographic Microscopy.
Category:X-ray computed tomography.
Tomografie (in German).
Computertomographie (in German).
Kategorie:Tomografie (in German).

! A. Ziegler et al. (2010): Opportunities and challenges for digital morphology. In PDF, Biology Direct.

M. Zuber et al. (2017): Augmented laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils. Sci. Rep., 7: 41413.

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Last updated June 08, 2017

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