Micro-computed tomography for natural history specimens: a handbook of best practice protocols

Kleoniki Keklikoglou, Sarah Faulwetter, Eva Chatzinikolaou, Patricia Wils, Jonathan Brecko, Jiří Kvaček, Brian Metscher, Christos Arvanitidis


Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.


micro-CT; microtomography; museum specimens; 3D visualisation; virtual specimens

Full Text:


DOI: https://doi.org/10.5852/ejt.2019.522


Abel R.L., Parfitt S., Ashton N., Lewis S.G., Scott B. & Stringer C. 2011. Digital preservation and dissemination of ancient lithic technology with modern micro-CT. Computers & Graphics 35 (4): 878–884. https://doi.org/10.1016/j.cag.2011.03.001

Abel R.L., Laurini C.R. & Richter M. 2012. A palaeobiologist’s guide to ‘virtual’ micro-CT preparation. Palaeontologia Electronica 15 (2): 6T.

Akkari N., Enghoff H. & Metscher B.D. 2015. A new dimension in documenting new species: high-detail imaging for myriapod taxonomy and first 3D cybertype of a new millipede species (Diplopoda, Julida, Julidae). PLoS ONE 10 (8): e0135243. https://doi.org/10.1371/journal.pone.0135243

Alba-Tercedor J. 2012. Studying the anatomy of wet specimens of mayflies of the genus Baetis (Insecta: Ephemeroptera) by scanning them into a liquid with the Skyscan 1172 high resolution micro-CT. SkyScan microCT 2012 User Meeting, Belgium: 188–191. Skyscan, Brussels.

Alba-Tercedor J. & Sánchez-Tocino L. 2011. The use of the SkyScan 1172 high-resolution micro-CT to elucidate if the spicules of the “sea slugs” (Mollusca: Nudibranchia, Opisthobranchia) have a structural or a defensive function. SkyScan microCT 2011 User Meeting, Belgium: 113–121. Skyscan, Leuven.

Barrett J.F. & Keat N. 2004. Artifacts in CT: recognition and avoidance 1. Radiographics 24 (6): 1679–1691. https://doi.org/10.1148/rg.246045065

Betz O., Wegst U., Weide D., Heethoff M., Helfen L., Lee W.K. & Cloetens P. 2007. Imaging applications

of synchrotron X-ray phase-contrast microtomography in biological morphology and biomaterials science. I. General aspects of the technique and its advantages in the analysis of millimetre-sized arthropod structure. Journal of Microscopy 227 (1): 51–71. https://doi.org/10.1111/j.1365-2818.2007.01785.x

Blagoderov V., Kitching I.J., Livermore L., Simonsen T.J. & Smith V.S. 2012. No specimen left behind: industrial scale digitization of natural history collections. ZooKeys 209: 133–146. https://doi.org/10.3897/zookeys.209.3178

Boas F.E. & Fleischmann D. 2012. CT artifacts: causes and reduction techniques. Imaging in Medicine 4 (2): 229–240.

Boistel R., Swoger J., Kržič U., Fernandez V., Gillet B. & Reynaud E.G. 2011. The future of three-dimensional microscopic imaging in marine biology. Marine Ecology 32 (4): 438–452. https://doi.org/10.1111/j.1439-0485.2011.00442.x

Bribiesca-Contreras F. & Sellers W.I. 2017. Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography. PeerJ 5: e3039. https://doi.org/10.7717/peerj.3039

Briguglio A. & Benedetti A. 2012. X-ray microtomography as a tool to present and discuss new taxa: the example of Risananeiza sp. from the late Chattian of Porto Badisco. Rendiconti Online Società Geologica Italiana 21: 1072–1074.

Brodersen C.R. & Roddy A.B. 2016. New frontiers in the three-dimensional visualization of plant structure and function. American Journal of Botany 103: 1–5. https://doi.org/10.3732/ajb.1500532

Brodersen C.R., McElrone A.J., Choat B., Matthews M.A. & Shackel K.A. 2010. The dynamics of embolism repair in xylem: In vivo visualizations using high-resolution computed tomography. Plant Physiology 154: 1088–1095. https://doi.org/10.1104/pp.110.162396

Brodersen C.R., Lee E.F., Choat B., Jansen S., Phillips R.J., Shackel K.A., McElrone A.J. & Matthews M.A. 2011. Automated analysis of three-dimensional xylem networks using high-resolution computed tomography. The New Phytologist 191: 1168–1179. https://doi.org/10.1111/j.1469-8137.2011.03754.x

Brodersen C.R., McElrone A.J., Choat B., Lee E.F., Shackel K.A. & Matthews M.A. 2013. In vivo visualizations of drought-induced embolism spread in Vitis vinifera. Plant Physiology 161: 1820–1829. https://doi.org/10.1104/pp.112.212712

Burrow C.J., Jones A.S. & Young G.C. 2005. X-ray microtomography of 410 million-year-old optic capsules from placoderm fishes. Micron 36 (6): 551–557. https://doi.org/10.1016/j.micron.2005.05.005

Carlson W.D. & Denison C. 1992. Mechanisms of porphyroblast crystallization: results from high-resolution computed X-ray tomography. Science 257 (5074): 1236–1239. https://doi.org/10.1126/science.257.5074.1236

Carlson W.D., Rowe T., Ketcham R.A. & Colbert M.W. 2003. Applications of high-resolution X-ray computed tomography in petrology, meteoritics and palaeontology. In: Mees F., Swennen R., Van Geet M. & Jacobs P. (eds) Applications of V-ray Computed Tomography in the Geosciences 215 (1): 7–22. Geological Society Special Publications, London. https://doi.org/10.1144/GSL.SP.2003.215.01.02

Chatzinikolaou E., Grigoriou P., Keklikoglou K., Faulwetter S. & Papageorgiou N. 2017. The combined effects of ocean acidification and elevated temperature on the shell density of two gastropod species using micro-CT imaging. ICES Journal of Marine Science 74 (4): 1135–1149. https://doi.org/10.1093/icesjms/fsw219

Cnudde V., Masschaele B., Dierick M., Vlassenbroeck J., Van Hoorebeke L. & Jacobs P. 2006. Recent progress in X-ray CT as a geosciences tool. Applied Geochemistry 21 (5): 826–832.


Cochard H., Delzon S. & Badel E. 2015. X-ray microtomography (micro-CT): A reference technology for high-resolution quantification of xylem embolism in trees. Plant, Cell and Environment 38 (1): 201–206. https://doi.org/10.1111/pce.12391

Crestana S., Cesaero R. & Mascarenhas S. 1986. Using a computer assisted tomography miniscanner in soil science. Soil Science 142: 56–61.

Davies T.G., Rahman I.A., Lautenschlager S., Cunningham J.A., Asher R.J., Barrett P.M., Bates K.T., Bengtson S., Benson R.B., Boyer D.M., Braga J., Bright J.A., Claessens L.P.A.M., Cox P.G., Dong X.-P., Evans A.R., Falkingham P.L., Friedman M., Garwood R.J., Goswami A., Hutchinson J.R., Jeffery N.S., Johanson Z., Lebrun R., Martinez-Pérez C., Marugán-Lobón J., O’Higgins P.M., Metscher B., Orliac M., Rowe T.B., Rücklin M., Sánchez-Villagra M.R., Shubin N.H., Smith S.Y., Starck J.M., Stringer C., Summers A.P., Sutton M.D., Walsh S.A., Weisbecker V., Witmer L.M., Wroe S., Yin Z., Rayfield E.J. & Donoghue P.C.J. 2017. Open data and digital morphology. Proceedings of the Royal Society B 284: 20170194. https://doi.org/10.1098/rspb.2017.0194

Davis G.R. & Elliott J.C. 1997. X-ray microtomography scanner using time-delay integration for elimination of ring artefacts in the reconstructed image. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 394 (1): 157–162. https://doi.org/10.1016/S0168-9002(97)00566-4

Davit Y., Iltis G., Debenest G., Veran-Tissoires S., Wildenschild D., Gérino M. & Quintard M. 2011. Imaging biofilm in porous media using X-ray computed microtomography. Journal of Microscopy 242 (1): 15–25. https://doi.org/10.1111/j.1365-2818.2010.03432.x

de Carlo F., Gürsoy D., Ching D.J., Batenburg K.J., Ludwig W., Mancini L., Marone F., Mokso R., Pelt D.M., Sijbers J. & Rivers M. 2018. TomoBank: a tomographic data repository for computational x-ray science. Measurement Science and Technology 29 (3): 034004. https://doi.org/10.1088/1361-6501/aa9c19

de Man B. 2001. Iterative Reconstruction for Reduction of Metal Artifacts in Computed Tomography. PhD Thesis, KULeuven, Belgium.

Denison C., Carlson W.D. & 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 (1): 29–44. https://doi.org/10.1111/j.1525-1314.1997.00006.x

DeVore M.L., Kenrick P., Pigg K.B. & Ketcham R.A. 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 (12): 1848–1851. https://doi.org/10.3732/ajb.93.12.1848

Dhondt S., Vanhaeren H., Van Loo D., Cnudde V. & Inzé D. 2010. Plant structure visualization by high-resolution X-ray computed tomography. Trends in Plant Science 15: 419–422.


Dierick M., Cnudde V., Masschaele B., Vlassenbroeck J., Van Hoorebeke L. & Jacobs P. 2007. Micro-CT of fossils preserved in amber. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 580 (1): 641–643. https://doi.org/10.1016/j.nima.2007.05.030

Dixon L.E., Bencivenga S. & Boden S.A. 2018. A new opening for wheat seed production. Journal of Experimental Botany 69 (3): 341–343. https://doi.org/10.1093/jxb/erx430

Faraj K.A., Cuijpers V.M., Wismans R.G., Walboomers X.F., Jansen J.A., van Kuppevelt T.H. & Daamen W.F. 2009. Micro-computed tomographical imaging of soft biological materials using contrast techniques. Tissue Engineering Part C: Methods 15 (3): 493–499. https://doi.org/10.1089/ten.tec.2008.0436

Faulwetter S., Vasileiadou A., Kouratoras M., Dailianis T. & Arvanitidis C. 2013a. Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1–45. https://doi.org/10.3897/zookeys.263.4261

Faulwetter S., Dailianis T., Vasileiadou A. & Arvanitidis C. 2013b. Contrast enhancing techniques for the application of micro-CT in marine biodiversity studies. Microscopy and Analysis 27 (2): S4–S7.

Faulwetter S., Minadakis N., Keklikoglou K., Doerr M. & Arvanitidis C. 2015. First steps towards the development of an integrated metadata management system for biodiversity-related micro-CT datasets. Bruker microCT 2015 user meeting, Belgium: 149–159. Bruker, Bruges.

Fernández R., Kvist S., Lenihan J., Giribet G. & Ziegler A. 2014. Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography. PloS ONE 9 (5): e96617. https://doi.org/10.1371/journal.pone.0096617

Franzen J.L., Gingerich P.D., Habersetzer J., Hurum J.H., von Koenigswald W. & Smith B.H. 2009. Complete primate skeleton from the middle Eocene of Messel in Germany: morphology and paleobiology. PLoS ONE 4 (5): e5723. https://doi.org/10.1371/journal.pone.0005723

Gamisch A., Staedler Y.M., Schönenberger J., Fischer G.A. & Comes H.P. 2013. Histological and micro-CT evidence of stigmatic rostellum receptivity promoting auto-pollination in the Madagascan orchid Bulbophyllum bicoloratum. PLoS ONE 8 (8): e72688. https://doi.org/10.1371/journal.pone.0072688

Garwood R.J., Sharma P.P., Dunlop J.A. & Giribet G. 2014. A Paleozoic stem group to mite harvestmen revealed through integration of phylogenetics and development. Current Biology 24 (9): 1017–1023. https://doi.org/10.1016/j.cub.2014.03.039

Gee C.T. 2013. Applying microCT and 3D visualization to Jurassic silicified conifer seed cones: a virtual advantage over thin-sectioning. Applications in Plant Sciences 1 (11): 1300039. https://doi.org/10.3732/apps.1300039

Gignac P.M. & Kley N.J. 2014. Iodine-enhanced micro-CT imaging: Methodological refinements for the study of the soft-tissue anatomy of post-embryonic vertebrates. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (3): 166–176. https://doi.org/10.1002/jez.b.22561

Gignac P.M., Kley N.J., Clarke J.A., Colbert M.W., Morhardt A.C., Cerio D., Cost I.N., Cox P.G., Daza J.D., Early C.M., Echolsm M.S., Henkelman R.M., Herdina A.N., Holliday C.M., Li Z., Mahlow K., Merchant S., Müller J., Orsbon C.P., Paluh D.J., Thies M.L., Tsai H.P. & Witmer L.M. 2016. Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues. Journal of Anatomy 228 (6): 889–909. https://doi.org/10.1111/joa.12449

Godfray H.C.J. 2007. Linnaeus in the information age. Nature 446: 259–260. https://doi.org/10.1038/446259a

Golding R.E. & Jones A.S. 2007. Micro-CT as a novel technique for 3D reconstruction of molluscan anatomy. Molluscan Research 27: 123–128.

Görög Á., Szinger B., Tóth E. & Viszkok J. 2012. Methodology of the micro-computer tomography on Foraminifera. Palaeontologia Electronica 15 (1): 1–15.

Greco M.K., Welz P.M., Siegrist M., Ferguson S.J., Gallmann P., Roubik D.W. & Engel M.S. 2011. Description of an ancient social bee trapped in amber using diagnostic radioentomology. Insectes Sociaux 58 (4): 487–494. https://doi.org/10.1007/s00040-011-0168-8

Green O.R. 2001. A Manual of Practical Laboratory and Field Techniques in Palaeobiology. Springer Science & Business Media, Berlin.

Griffin L.D., Elangovan P., Mundell A. & Hezel D.C. 2012. Improved segmentation of meteorite micro-CT images using local histograms. Computers & Geosciences 39: 129-134. https://doi.org/10.1016/j.cageo.2011.07.002

Hagedorn G., Mietchen D., Agosti D., Penev L., Berendsohn W. & Hobern D. 2011. Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information. ZooKeys 150: 127–149. https://doi.org/10.3897/zookeys.150.2189

Hamba H., Nikaido T., Sadr A., Nakashima S. & Tagami J. 2012. Enamel lesion parameter correlations between polychromatic micro-CT and TMR. Journal of Dental Research 91 (6): 586–591. https://doi.org/10.1177/0022034512444127

Heřmanová Z., Dašková J., Ekrt B. & Kvaček J. 2017. Zlivifructus gen. nov., a new member of the Normapolles complex. Review of Palaeobotany and Palynology 246: 177–184. https://doi.org/10.1016/j.revpalbo.2017.06.012

Hezel D.C., Elangovan P., Viehmann S., Howard L., Abel R.L. & Armstrong R. 2013. Visualisation and quantification of CV chondrite petrography using micro-tomography. Geochimica et Cosmochimica Acta 116: 33–40. https://doi.org/10.1016/j.gca.2012.03.015

Hsieh J. 2009. Computed Tomography: Principles, Design, Artifacts, and Recent Advances. SPIE Press, Bellingham, Washington. https://doi.org/10.1117/3.817303

Holliday C.M., Tsai H.P., Skiljan R.J., George I.D. & Pathan S. 2013. A 3D interactive model and atlas of the jaw musculature of Alligator mississippiensis. PloS ONE 8 (6): e62806. https://doi.org/10.1371/journal.pone.0062806

Jeppsson L., Anehus R. & Fredholm D. 1999. The optimal acetate buffered acetic acid technique for extracting phosphatic fossils. Journal of Paleontology 73 (5): 964–972. https://doi.org/10.1017/S0022336000040798

Johnson E., Dwarte D. & Jones A. 2011. Specimen preparation for X-ray micro-computed tomography of plants. Microscopy and Microanalysis 17: 2010–2011. https://doi.org/10.1017/S1431927611002091

Kachelrieß M. 2008. Micro-CT. In: Semmler W. & Schwaiger M. (eds) Molecular Imaging I. Handbook of Experimental Pharmacology 185/1: 23–52. Springer, Berlin / Heidelberg.

Kamenz C. & Weidemann G. 2009. Heavy metal—A contrasting substance for micro-tomographical visualization of scorpion book lungs. Micron 40 (8): 911–917. https://doi.org/10.1016/j.micron.2009.05.007

Kędzierski M., Uchman A., Sawlowicz Z. & Briguglio A. 2015. Fossilized bioelectric wire – the trace fossil Trichichnus. Biogeosciences (Online) 12 (8): 2301–2309. https://doi.org/10.5194/bg-12-2301-2015

Kehlmaier C., Dierick M. & Skevington J.H. 2014. Micro-CT studies of amber inclusions reveal internal genitalic features of big-headed flies, enabling a systematic placement of Metanephrocerus Aczél, 1948 (Insecta: Diptera: Pipunculidae). Arthopod Systematics & Phylogeny 72 (1): 23–36.

Keklikoglou K., Chatzinikolaou E., Faulwetter S., Grigoriou P., Papageorgiou N., Queirós A., Rühl S. & Schmidbaur H. 2015. Revealing effects of ocean acidification on the calcified structures of marine invertebrates through micro-computed tomography (micro-CT). Bruker microCT 2015 user meeting, Belgium: 21–31. Bruker, Bruges.

Keklikoglou K., Faulwetter S., Chatzinikolaou E., Michalakis N., Filiopoulou I., Minadakis N., Panteri E., Perantinos G., Gougousis A. & Arvanitidis C. 2016. MicroCTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (microCT). Biodiversity Data Journal 4: e8740. https://doi.org/10.3897/BDJ.4.e8740

Ketcham R.A. & Carlson W.D. 2001. Acquisition, optimization and interpretation of X-ray computed tomographic imagery: applications to the geosciences. Computers & Geosciences 27 (4): 381–400. https://doi.org/10.1016/S0098-3004(00)00116-3

Kim J.S., Min J., Recknagel A.K., Riccio M. & Butcher J.T. 2011. Quantitative three-dimensional analysis of embryonic chick morphogenesis via microcomputed tomography. The Anatomical Record 294 (1): 1–10. https://doi.org/10.1002/ar.21276

Kim S.J., Xu W., Ahmad M.W., Baeck J.S., Chang Y., Bae J.E., Chae K.S., Jeong T.K., Park J.A. & Lee G.H. 2015. Synthesis of nanoparticle CT contrast agents: in vitro and in vivo studies. Science and Technology of Advanced Materials 16: 055003. https://doi.org/10.1088/1468-6996/16/5/055003

Knipfer T., Eustis A., Brodersen C., Walker A.M. & McElrone A.J. 2015. Grapevine species from varied native habitats exhibit differences in embolism formation/repair associated with leaf gas exchange and root pressure. Plant, Cell & Environment 38 (8): 1503–1513. https://doi.org/10.1111/pce.12497

Kniss J., Kindlmann G. & Hansen C. 2002. Multidimensional transfer functions for interactive volume rendering. IEEE Transactions on Visualization and Computer Graphics 8 (3): 270–285. https://doi.org/10.1109/TVCG.2002.1021579

Koenigswald W.V., Habersetzer J. & Gingerich P.D. 2011. Morphology and evolution of the distal phalanges in primates. In: Lehmann T. & Schaal S.F.K (eds) The World at the Time of Messel: Puzzles in Palaeobiology, Palaeoenvironment, and the History of Early Primates: 91–94. 22nd International Senckenberg Conference, Frankfurt am Main.

Konietzko-Meier D. & Schmitt A. 2013. A histological study of a femur of Plagiosuchus, a Middle Triassic temnospondyl amphibian from southern Germany, using thin sections and micro-CT scanning. Netherlands Journal of Geosciences 92 (2–3): 97–108. https://doi.org/10.1017/S0016774600000020

Korte N. & Porembski S. 2011. Anatomical analysis of turgescent and semi-dry resurrection plants: the effect of sample preparation on the sample, resolution, and image quality of X-ray micro-computed tomography (μCT). Microscopy Research and Technique 74 (4): 364–369. https://doi.org/10.1002/jemt.20917

Krings M., Müller H., Heneka M.J. & Rödder D. 2017. Modern morphological methods for tadpole studies. A comparison of micro-CT, and clearing and staining protocols modified for frog larvae. Biotechnic & Histochemistry 92 (8): 595–605. https://doi.org/10.1080/10520295.2017.1369162

Kuebler K.E., McSween H.Y., Carlson W.D. & Hirsch D. 1999. Sizes and masses of chondrules and metal–troilite grains in ordinary chondrites: possible implications for nebular sorting. Icarus 141 (1): 96–106. https://doi.org/10.1006/icar.1999.6161

Kuva J., Sammaljärvi J., Parkkonen J., Siitari-Kauppi M., Lehtonen M., Turpeinen T., Timonen J. & Voutilainen M. 2018. Imaging connected porosity of crystalline rock by contrast agent-aided X-ray microtomography and scanning electron microscopy. Journal of Microscopy 270 (1): 98–109. https://doi.org/10.1111/jmi.12661

Kvaček J. & Heřmanová Z. 2017. Fossil angiosperm fruit Allericarpus parvivalvis (Ericales) from the Coniacian of the Bohemian Cretaceous Basin. Journal of the National Museum (Prague), Natural History Series 186: 117–124.

Kvaček J., Doyle J.A., Endress P.K., Daviero-Gomez V., Gomez B. & Tekleva M. 2016. Pseudoasterophyllites cretaceus from the Cenomanian (Cretaceous) of the Czech Republic – a possible link between Chloranthaceae and Ceratophyllum. Taxon 65 (6): 1345–1373. https://doi.org/10.12705/656.8

Kvaček J., Barrón E., Heřmanová Z., Mendes M.M., Karch J., Žemlička J. & Dudák J. 2018a. Araucarian conifer from late Albian amber of northern Spain. Papers in Palaeontology 4 (3): 1–14. https://doi.org/10.1002/spp2.1223

Kvaček J., Heřmanová Z., Bruthansová J.M.M., Karch J., Žemlička J. & Dudák J. 2018b. Stutzeliastrobus bohemicus - basal Curessaceae conifer from the Cenomanian of the Bohemian Cretaceous Basin, Central Europe. Fossil Imprint 74: 179–188.

Leroux O., Leroux F., Bellefroid E., Claeys M., Couvreur M., Borgonie G., Van Hoorebeke L., Masschaele B. & Viane R. 2009. A new preparation method to study fresh plant structures with X-ray computed tomography. Journal of Microscopy 233 (1): 1–4. https://doi.org/10.1111/j.1365-2818.2008.03088.x

Li X., Pan Z., Upadhyaya S.K., Atungulu G.G. & Delwiche M. 2011. Three-dimensional geometric modeling of processing tomatoes. Transactions of the American Society of Agricultural and Biological Engineers 54 (6): 2287–2296. https://doi.org/10.13031/2013.40642

Li Z., Clarke J.A., Ketcham R.A., Colbert M.W. & Yan F. 2015. An investigation of the efficacy and mechanism of contrast-enhanced X-ray computed tomography utilizing iodine for large specimens through experimental and simulation approaches. BMC Physiology 15: 5. https://doi.org/10.1186/s12899-015-0019-3

Liu Y., Scholtz G. & Hou X. 2015. When a 520 million-year-old Chengjiang fossil meets a modern micro-CT–a case study. Scientific Reports 5: 12802. https://doi.org/10.1038/srep12802

Lorensen W.E. & Cline H.E. 1987. Marching cubes: a high resolution 3D surface construction algorithm. ACM Siggraph Computer Graphics 21 (4): 163–169.

Mancini L., Kourousias G., Billè F., De Carlo F. & Fidler A. 2018. About a method for compressing x-ray computed microtomography data. Measurement Science and Technology 29 (4): 044002. https://doi.org/10.1088/1361-6501/aaa0fa

McElrone A.J., Choat B., Parkinson D.Y., MacDowell A.A. & Brodersen C.R. 2013. Using high resolution computed tomography to visualize the three dimensional structure and function of plant vasculature. Journal of Visualized Experiments 74: e50162. https://doi.org/10.3791/50162

Meganck J.A., Kozloff K.M., Thornton M.M., Broski S.M. & Goldstein S.A. 2009. Beam hardening artifacts in micro-computed tomography scanning can be reduced by X-ray beam filtration and the resulting images can be used to accurately measure BMD. Bone 45 (6): 1104–1116. https://doi.org/10.1016/j.bone.2009.07.078

Metscher B.D. 2009a. MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC Physiology 9: 11. https://doi.org/10.1186/1472-6793-9-11

Metscher B.D. 2009b. MicroCT for developmental biology: A versatile tool for high-contrast 3D imaging at histological resolutions. Developmental Dynamics 238 (3): 632–640. https://doi.org/10.1002/dvdy.21857

Metscher B.D. 2011. X-ray microtomographic imaging of intact vertebrate embryos. Cold Spring Harbor Protocols 12: 1462–1471. https://doi.org/10.1101/pdb.prot067033

Meyer M., Elliott D., Wood A.D., Polys N.F., Colbert M., Maisano J.A., Vickers-Rich P., Hall M., Hoffman K.H., Schneider G. & Xiao S. 2014. Three-dimensional microCT analysis of the Ediacara fossil Pteridinium simplex sheds new light on its ecology and phylogenetic affinity. Precambrian Research 249: 79–87. https://doi.org/10.1016/j.precamres.2014.04.013

Miller J.S. & Venable D.L. 2003. Floral morphometrics and the evolution of sexual dimorphism in Lycium (Solanaceae). Evolution 57 (1): 74–86. https://doi.org/10.1111/j.0014-3820.2003.tb00217.x

Mizutani R. & Suzuki Y. 2012. X-ray microtomography in biology. Micron 43 (2–3): 104–115. https://doi.org/10.1016/j.micron.2011.10.002

Mizutani R., Takeuchi A., Hara T., Uesugi K. & Suzuki Y. 2007. Computed tomography imaging of the neuronal structure of Drosophila brain. Journal of Synchrotron Radiation 14 (3): 282–287. https://doi.org/10.1107/S0909049507009004

Mizutani R., Takeuchi A., Akamatsu G., Uesugi K. & Suzuki Y. 2008a. Element-specific microtomo-graphic imaging of Drosophila brain stained with high-Z probes. Journal of Synchrotron Radiation 15 (4): 374–377. https://doi.org/10.1107/S0909049508003725

Mizutani R., Takeuchi A., Uesugi K., Takekoshi S., Osamura R.Y. & Suzuki Y. 2008b. X-ray micro-tomographic imaging of three-dimensional structure of soft tissues. Tissue Engineering Part C: Methods 14 (4): 359–363. https://doi.org/10.1089/ten.tec.2008.0274

Mizutani R., Takeuchi A., Uesugi K., Takekoshi S., Osamura R.Y. & Suzuki Y. 2009. Three-dimensional microstructural analysis of human brain tissue by using synchrotron radiation microtomographs. In: Westland T.B. & Calton R.N. (eds) Handbook on White Matter: 247–277. Nova Science Publishers, New York.

Mooney S.J., Pridmore T.P., Helliwell J. & Bennett M.J. 2012. Developing X-ray computed tomography to non-invasively image 3-D root systems architecture in soil. Plant and Soil 352: 1–22. https://doi.org/10.1007/s11104-011-1039-9

Needham A.W., Abel R.L., Tomkinson T. & Grady M.M. 2013. Martian subsurface fluid pathways and 3D mineralogy of the Nakhla meteorite.Geochimica et Cosmochimica Acta 116: 96-110. https://doi.org/10.1016/j.gca.2012.07.004

Pajor R., Fleming A., Osborne C.P., Rolfe S.A., Sturrock C.J. & Mooney S.J. 2013. Seeing space: visualization and quantification of plant leaf structure using X-ray micro-computed tomography: View Point. Journal of Experimental Botany 64 (2): 385–390. https://doi.org/10.1093/jxb/ers392

Paquit V.C., Gleason S.S. & Kalluri U.C. 2011. Monitoring plant growth using high resolution micro-CT images. Proceedings of SPIE-IS&T Electronic Imaging 7877: 78770W. https://doi.org/10.1117/12.876719

Paredes U.M., Prys-Jones R., Adams M., Groombridge J., Kundu S., Agapow P.M. & Abel R.L. 2012. Micro-CT X-rays do not fragment DNA in preserved bird skins. Journal of Zoological Systematics and Evolutionary Research 50 (3): 247–250. https://doi.org/10.1111/j.1439-0469.2012.00657.x

Paterson G.L., Sykes D., Faulwetter S., Merk R., Ahmed F., Hawkins L.E., Dinley J., Bal A.D. & Arvanitidis C. 2014. The pros and cons of using micro-computed tomography in gross and micro-anatomical assessments of polychaetous annelids. Memoirs of Museum Victoria 71: 237–46.

Pauwels E., Van Loo D., Cornillie P., Brabant L. & Van Hoorebeke L. 2013. An exploratory study of contrast agents for soft tissue visualization by means of high resolution X-ray computed tomography imaging. Journal of Microscopy 250 (1): 21–31. https://doi.org/10.1111/jmi.12013

Penney D., Dierick M., Cnudde V., Masschaele B., Vlassenbroeck J., Van Hoorebeke L. & Jacobs P. 2007. First fossil Micropholcommatidae (Araneae), imaged in Eocene Paris amber using X-ray computed tomography. Zootaxa 1623: 47–53. https://doi.org/10.5281/zenodo.179249

Plougonven E., Srichamnong W., Srzednicki G. & Léonard A. 2012. Characterisation of macadamia nuts using X-ray microtomography. SkyScan MicroCT User Meeting 2012, Belgium: 1–5. Skyscan, Brussels.

Presnell J.K. & Schreibman M.P. 1997. Humason’s Animal Tissue Techniques. Fifth edition. Johns Hopkins University Press, Baltimore / London.

Rahman I.A. & Smith S.Y. 2014. Virtual paleontology: computer-aided analysis of fossil form and function. Journal of Paleontology 88 (4): 633–635. https://doi.org/10.1666/13-001I

Rivers M.L., Sutton S.R. & Eng P.J. 1999. Geoscience applications of X-ray computed microtomography. In: Developments in X-Ray Tomography II (Vol. 3772): 78–86. SPIE’s International Symposium on Optical Science, Engineering, and Instrumentation, Denver, CO, United States. https://doi.org/10.1117/12.363741

Roche R.C., Abel R.A., Johnson K.G. & Perry C.T. 2010. Quantification of porosity in Acropora pulchra (Brook 1891) using X-ray micro-computed tomography techniques. Journal of Experimental Marine Biology and Ecology 396 (1): 1–9. https://doi.org/10.1016/j.jembe.2010.10.006

Rossi M., Casali F., Romani D., Bondioli L., Macchiarelli R. & Rook L. 2004. MicroCT scan in paleobiology: application to the study of dental tissues. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 213: 747–750. https://doi.org/10.1016/S0168-583X(03)01697-5

Ruthensteiner B., Baeumler N. & Barnes D.G. 2010. Interactive 3D volume rendering in biomedical publications. Micron 41 (7): 886-e1. https://doi.org/10.1016/j.micron.2010.03.010

Salmon P.L., Liu X. & Sasov A. 2009. A post-scan method for correcting artefacts of slow geometry changes during micro-tomographic scans. Journal of X-Ray Science and Technology 17 (2): 161–174.

Sansone S., Rocca-Serra P., Field D., Maguire E., Taylor C., Hofmann O., Fang H., Neumann S., Tong W., Amaral-Zettler L., Begley K., Booth T., Bougueleret L., Burns G., Chapman B., Clark T., Coleman L., Copeland J., Das S., de Daruvar A., de Matos P., Dix I., Edmunds S., Evelo C.T., Forster M.J., Gaudet P., Gilbert J., Goble C., Griffin J.L., Jacob D., Kleinjans J., Harland L., Haug K., Hermjakob H., Sui S.J.H., Laederach A., Liang S., Marshall S., McGrath A., Merrill E., Reilly D., Roux M., Shamu C.E., Shang C.A., Steinbeck C., Trefethen A., Williams-Jones B., Wolstencroft K., Xenarios I. & Hide W. 2012. Toward interoperable bioscience data. Nature Genetics 44 (2): 121–126. https://doi.org/10.1038/ng.1054

Schambach S.J., Bag S., Schilling L., Groden C. & Brockmann M.A. 2010. Application of micro-CT in small animal imaging. Methods 50 (1): 2–13. https://doi.org/10.1016/j.ymeth.2009.08.007

Schmidbaur H., Keklikoglou K., Metscher B.D. & Faulwetter S. 2015. Exploring methods to remove iodine and phosphotungstic acid stains from zoological specimens. Micro-CT User Meeting, Belgium: 116–123. Bruker, Bruges.

Simons F.J., Verhelst F. & Swennen R. 1997. Quantitative characterization of coal by means of microfocal X-ray computed microtomography (CMT) and color image analysis (CIA). International Journal of Coal Geology 34 (1): 69–88. https://doi.org/10.1016/S0166-5162(97)00011-6

Staedler Y.M., Masson D. & Schönenberger J. 2013. Plant tissues in 3D via X-ray tomography: simple contrasting methods allow high resolution imaging. PLoS ONE 8 (9): e75295. https://doi.org/10.1371/journal.pone.0075295

Staedler Y.M., Kreisberger T., Manafzadeh S., Chartier M., Handschuh S., Pamperl S., Sontag S., Paun O. & Schönenberger J. 2018. Novel computed tomography-based tools reliably quantify plant reproductive investment. Journal of Experimental Botany 69 (3): 525–535. https://doi.org/10.1093/jxb/erx405

Stanley S.M. 1992. Exploring Earth and Life Through Time. W H Freeman & Co, New York.

Stoev P., Komerički A., Akkari N., Liu S., Zhou X., Weigand A.M., Hostens J., Porco D.& Penev L. 2013. Transcriptomic, DNA barcoding, and micro-CT imaging data from an advanced taxonomic description of a novel centipede species (Eupolybothrus cavernicolus Komerički & Stoev, sp. n.). GigaScience. https://doi.org/10.5524/100063

Stuppy W.H., Maisano J.A., Colbert M.W., Rudall P.J. & Rowe T.B. 2003. Three-dimensional analysis of plant structure using high-resolution X-ray computed tomography. Trends in Plant Science 8 (1): 2–6. https://doi.org/10.1016/S1360-1385(02)00004-3

Sutton M.D. 2008. Tomographic techniques for the study of exceptionally preserved fossils. Proceedings of the Royal Society of London B 275 (1643): 1587–1593. https://doi.org/10.1098/rspb.2008.0263

Sutton M.D., Briggs D.E., Siveter D.J. & Siveter D.J. 2001. Methodologies for the visualization and reconstruction of three-dimensional fossils from the Silurian Herefordshire Lagerstätte. Palaeontologia Electronica 4 (1): 1–17.

Sutton M., Rahman I. & Garwood R. 2014. Techniques for Virtual Palaeontology. John Wiley & Sons, New York.

Vågberg W., Larsson J.C. & Hertz H.M. 2017. Removal of ring artifacts in microtomography by characterization of scintillator variations. Optics Express 25 (19): 23191–23198. https://doi.org/10.1364/OE.25.023191

van der Niet T., Zollikofer C.P.E., de León M.S.P., Johnson S.D. & Linder H.P. 2010. Three-dimensional geometric morphometrics for studying floral shape variation. Trends in Plant Science 15 (8): 423–426. https://doi.org/10.1016/j.tplants.2010.05.005

van Soldt B.J., Metscher B.D., Poelmann R.E., Vervust B., Vonk F.J., Muller G.B. & Richardson M.K. 2015. Heterochrony and early left-right asymmetry in the development of the cardiorespiratory system of snakes. PLoS ONE 10 (1): e116416. https://doi.org/10.1371/journal.pone.0116416

Vodrážka R. 2009. A new method for the extraction of macrofossils from calcareous rocks using sulphuric acid. Palaeontology 52 (1): 187–192. https://doi.org/10.1111/j.1475-4983.2008.00829.x

Walter T., Shattuck D.W., Baldock R., Bastin M.E., Carpenter A.E., Duce S., Ellenberg J., Fraser A., Hamilton N., Pieper S., Ragan M.A., Schneider J.E., Tomancak P. & Hériché J.-K. 2010. Visualization of image data from cells to organisms. Nature Methods 7: S26–S41. https://doi.org/10.1038/nmeth.1431

Wan B., Xiao S., Yuan X., Chen Z., Pang K., Tang Q., Guan C. & Maisano J.A. 2014. Orbisiana linearis from the early Ediacaran Lantian Formation of South China and its taphonomic and ecological implications. Precambrian Research 255: 266–275. https://doi.org/10.1016/j.precamres.2014.09.028

Wang C.N., Hsu H.C., Wang C.C., Lee T.K. & Kuo Y.F. 2015. Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers. Frontiers in Plant Science 6: 724. https://doi.org/10.3389/fpls.2015.00724

Wellington S.L. & Vinegar H.J. 1987. X-ray computerized tomography. Journal of Petroleum Technology 39: 885–898.

Wellman C. & Axe L. 1999. Extracting plant mesofossils and megafossils by bulk acid maceration. In: Jones T.P. & Rowe N.P. (eds) Fossil Plants and Spores: Modern Techniques: 11–14. Geological Society, London.

Yakami M., Ishizu K., Kubo T., Okada T. & Togashi K. 2011. Development and evaluation of a low-cost and high-capacity DICOM image data storage system for research. Journal of Digital Imaging 24 (2): 190–195. https://doi.org/10.1007/s10278-009-9267-8

Yang H., Chen Z.Q., Wang Y., Ou W., Liao W. & Mei X. 2015. Palaeoecology of microconchids from microbialites near the Permian–Triassic boundary in South China. Lethaia 48 (4): 497–508. https://doi.org/10.1111/let.12122

Zinsmeister W.J. & De Nooyer C. 1996. Computed tomography; non-destructive techniques for visualizing internal morphology of invertebrates. Geological Society of America, Abstracts with Programs 28 (7): 294.


  • There are currently no refbacks.

License URL: https://creativecommons.org/licenses/by/4.0/