Palaeobotanical Tools /
Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)
Preparation and Conservation
Managing Fossil Collections
Palynological Preparation Techniques
Cellulose Peel Technique
Photography and Scanning
Scanning- (SEM) and Environmental Scanning Electron Microscopy (ESEM)
Digital Cameras on the Microscope
Cameras With Focus Bracketing or Built-In Focus Stacking
Focus Stacking (Photography, Extended Depth of Field)
High Dynamic Range Imaging (HDR)
Imaging Fossils Using UV-Light (Black-Light Photography)
Transmission Electron Microscopy (TEM)
Writing, Translating and Drawing
Glossaries, Dictionaries and Encyclopedias: Microscopy@
! 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:
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. Kevin Boyce et al. (2003): CHEMICAL EVIDENCE FOR CELL WALL LIGNIFICATION AND THE EVOLUTION OF TRACHEIDS IN EARLY DEVONIAN PLANTS. Int. J. Plant Sci., 164: 691-702.
A. Brayard et al. (2019): Glow in the dark: Use of synchrotron µXRF trace elemental mapping and multispectral macro-imaging on fossils from the Paris Biota (Bear Lake County, Idaho, USA). Geobios, 54: 1-79. See also here (in PDF).
! C.R. Brodersen and A.B. Roddy (2016): New frontiers in the three-dimensional visualization of plant structure and function. Open access, 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, Botany, 94. See also here (in PDF).
! 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).
D. Coty et al. (2014): The First Ant-Termite Syninclusion in Amber with CT-Scan Analysis of Taphonomy. Open access, PLoS ONE 9.
J.A. Cunningham et al. (2014):
virtual world of paleontology. In PDF,
Trends in Ecology & Evolution, 29: 347-357. See also
"... in recent years the discipline has been revolutionized by the emergence of powerful methods for the digital visualization and analysis of fossil material. This has included improvements in both computer technology and its availability, and in tomographic techniques, which have made it possible to image a series of 2D sections or slices through a fossil and to use these to make a 3D reconstruction of the specimen".
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. Open access, 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.
! S. Faulwetter et al. (2013): Micro-computed tomography: Introducing new dimensions to taxonomy. Open access, Zookeys, 2013; (263): 1–45.
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. (2019):
Early Cretaceous Mesofossil Flora of Torres Vedras (Ne of Forte Da Forca), Portugal:
A Palaeofloristic Analysis of an Early Angiosperm Community. Open access,
Fossil Imprint, 75: 153–257. See also
"... the oldest mesofossil flora containing angiosperm remains to be described in detail based on well-preserved flower, fruit and seed remains. It provides the most detailed information currently available on the structural diversity of angiosperms at this early stage in their evolution, the range of angiosperm species present, and their relationships to extant angiosperm lineages. ..."
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).
E.M. Friis et al. (2013):
Diversity among Chlamydospermous Seeds from the Early Cretaceous of Portugal and
North America. Free accesss,
International Journal of Plant Sciences, 174: 530–558.
"... The material is based on numerous charcoalified and lignitic specimens recovered from Early Cretaceous mesofossil floras [...]
! Attenuation-based synchrotron-radiation x-ray tomographic microscopy (SRXTM) and phase-contrast x-ray tomographic microscopy (PCXTM) were carried out [...]
! Volume rendering (voltex), which provides transparent reconstructions, was also used for the virtual sections ..."
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):
Fossil Fruits from the Paleocene
of Patagonia, Argentina. In PDF,
The Botanical Review, 78: 205–234.
See also here.
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.P. Gueriau and L. Bertrand (2015): Deciphering Exceptional Preservation of Fossils Through Trace Elemental Imaging. In PDF, Microscopy Today. See also here.
T. Hegna et al. (2013): Not Quite Frozen in Time: Windows into the Internal Taphonomy of Fossils in Amber via MicroCT-scan Technology. Abstract.
F. Herrera et al. (2022):
permineralized Early Cretaceous lycopsid from China and the evolution of crown clubmosses. In PDF,
New Phytologist, 233: 2310-2322.
See also here.
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.
K. Keklikoglou et al. (2019):
tomography for natural history specimens: a handbook of best practice protocols.
European Journal of Taxonomy, 522: 1–55.
Worth checking out: Chapter 3.1.3. Palaeontological samples.
S. Kiel et al. (2012): Fossilized digestive systems in 23 million-year-old wood-boring bivalves. In PDF, Journal of Molluscan Studies, 78: 349–356.
R. Kundrata et al. (2020): X-ray micro-computed tomography reveals a unique morphology in a new click-beetle (Coleoptera, Elateridae) from the Eocene Baltic amber. Open access, Scientific Reports, 10.
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 (2016): Reconstructing the past: methods and techniques for the digital restoration of fossils. Abstract, R. Soc. sci., 3. See also here (in PDF).
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.
D. Lewis (2019):
fight for control over virtual fossils. Palaeontologists have been urged to share 3D scans of fossils online, but a
Nature analysis finds that few researchers do so.
Nature News Feature.
! 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.S.R. Manchester and B. Balmaki (2018): Spiny fruits revealed by nano-CT scanning: Pseudoanacardium peruvianum (Berry) gen. et comb. nov. from the early Oligocene Belén flora of Peru. In PDF, Acta Palaeobotanica 2018 58(1): 41–48.
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.
C. Mays et al. (2017):
the limits of neutron tomography in palaeontology: Three-dimensional modelling
of in situ resin within fossil plants.
Palaeontologia Electronica, 20.3.57A: 1-12. See also
Please note figure 3: Artist´s reconstruction of ovuliferous cone and fertile shoot of Austrosequoia novae-zeelandiae.
! S. McLoughlin et al. (2021): Neutron tomography, fluorescence and transmitted light microscopy reveal new insect damage, fungi and plant organ associations in the Late Cretaceous floras of Sweden. Open access, GFF, 143: 248-276.
! 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. (2017): 100-million-year-old conifer tissues from the mid-Cretaceous amber of Charente (western France) revealed by synchrotron microtomography. Free access, Annals of Botany, 119: 117–128.
J.D. Moreau et al. (2015):
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.
MorphoSource (by Duke University): This is a project-based data archive that allows researchers to store and organize, share, and distribute their own 3d data.
National Center for X-ray Tomography (NXCT)
N. Nestle et al. (2018):
but functional – Tomographic insights into
nature’s most resilient actuators. In PDF,
Micro-CT User Meeting.
See also here (P. Gaupels, Geohorizon; in German).
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. Free access, Rivista italiana di Paleontologia e Stratigrafia.
! I.A. Rahman et al. (2012): Virtual Fossils: a New Resource for Science Communication in Paleontology. In PDF, Evolution: Education and Outreach, 5: 635–641.
Palaeontology: What´s It All About?
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.
T. Särkinen et al. (2018): A new commelinid monocot seed fossil from the early Eocene previously identified as Solanaceae. In PDF, American Journal of Botany, 105: 95–107. See also here.
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.
A.C. Scott et al. (2009):
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.
See figure 4, SEM of charcoalified pteridosperm ovule from the mid-Mississippian (Carboniferous). See also here.
! A.C. Scott and M.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):
(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.
See also here.
! 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. (2017):
insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae
seeds from the Jurassic Oxford Clay biota. PeerJ 5.
Description of a new genus of anatomically preserved gymnosperm seed from the Callovian–Oxfordian (Jurassic) Oxford Clay Formation (UK), using a combination of traditional sectioning and synchrotron radiation X-ray micro-tomography (SRXMT).
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):
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.
Now recovered from the Internet Archive´s Wayback Machine.
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.
S.R. Stock (2019):
Methodology and Applications, Second Edition. Abstracts available. 389 pages,
Taylor & Francis.
All about computed tomography (CT).
C. Strullu-Derrien et al. (2019): The Rhynie chert. Open access, Current Biology 29: R1211–R1223.
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. Free access, NRC Research Press.
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):
techniques for the study of exceptionally preserved fossils.
PDF file, Proc. R. Soc. B, 275: 1587-1593.
See also here.
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.
Thomas van de Kamp et al. (2018):
biology preserved in mineralized fossils. Open access,
Nature Communications, 9.
Using high-throughput synchrotron X-ray microtomography 55 parasitation events by four wasp species were identified from the Paleogene of France.
T. van der Niet et al. (2010): Three-dimensional geometric morphometrics for studying floral shape variation. In PDF, Trends in Plant Science, 15.
M.A. Vicente et al. (2017): The Use of Computed Tomography to Explore the Microstructure of Materials in Civil Engineering: From Rocks to Concrete. Open access.
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. Frere access, Am. J. Bot., 104: 127-149.
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):
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:
! Synchrotron X-ray Tomographic Microscopy.
Category:X-ray computed tomography.
Tomografie (in German).
Computertomographie (in German).
Kategorie:Tomografie (in German).
P.J. Withers et al. (2021):
computed tomography. In PDF,
Nature Reviews Methods Primers, 1.
See also here.
! A. Ziegler et al. (2010): Opportunities and challenges for digital morphology. In PDF, Biology Direct.
M. Zuber et al. (2017):
laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils.
Sci. Rep., 7: 41413.
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