Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections

  • Jonathan Brecko Royal Belgian Institute of Natural Sciences, Scientific Heritage Service, Vautierstraat 29, B-1000 Brussels. Royal Museum for Central Africa, Biological Collections and Data Management, Leuvensesteenweg 13, B-3080 Tervuren.
  • Aurore Mathys Royal Belgian Institute of Natural Sciences, Scientific Heritage Service, Vautierstraat 29, B-1000 Brussels. Royal Museum for Central Africa, Biological Collections and Data Management, Leuvensesteenweg 13, B-3080 Tervuren.
Keywords: digitisation, handbook, 3D, natural history collections, 2D


Digitising a collection is key to make it last even after the physical objects are no longer available. Almost all of the techniques currently available to digitise a natural history collection in 2D+ and 3D are listed herein. The techniques are explained in a way that even one without any knowledge on the subject may understand their principle. The strong and weak points of the techniques are discussed, and an overview of suitable collections and specimens are given for each one of them. Also, plenty of examples already digitised with each technique are provided together with the links to visualise them in 3D. After explaining all the different digitisation options, the subsequent chapters provide information on how to improve the 2D+ and 3D digital twins of the specimens and techniques are compared to each other by means of test specimens. These give a fast overview of the capabilities of the digitisation techniques. Possible solutions to avoid digitisation errors are equally provided. Lastly, the dissemination of the results and the data management of the 3D models are briefly discussed in the final chapters. Also, a large chapter is provided with several workflows that can be followed to get the best possible results.


Alhwarin F., Ferrein A. & Scholl I. 2014. IR Stereo Kinect: Improving depth images by combining structured light with IR stereo. In: Pham D.N., Park S.B. (eds) Lecture Notes in Computer Science, Vol. 8862: PRICAI 2014: Trends in Artificial Intelligence. Springer, Cham. https://doi.org/10.1007/978-3-319-13560-1_33

Alieva N.O., Konzen K.A., Field S.F., Meleshkevitch E.A., Hunt M.E., Beltran-Ramirez V., Miller D.J., Wiedenmann J., Salih A. & Matz M.V. 2008. Diversity and evolution of coral fluorescent proteins. PLoS ONE 3 (7): e2680. https://doi.org/10.1371/journal.pone.0002680

Anonymous. 2014. Microscope Slide Scanner Manual. Field Museum of Natural history.

Avgousti A., Nikolaidou A. & Georgiou R. 2017. Openumisma: a software platform managing numis-matic collections with a particular focus on reflectance transformation imaging. Code for Libraries Journal 37: 1–14.

Barbero-García I., Lerma J.L., Marqués-Mateu Á., Miranda P. 2017. Low-cost smartphone-based photogrammetry for the analysis of cranial deformation in infants. World Neurosurgery 102: 545–554. https://doi.org/10.1016/j.wneu.2017.03.015

Bay N. 2018. Laowa 25 mm f/2.8 2.5–5× Review: Ultra Macro Lens Comparison with Canon MPE65. Available from https://www.nickybay.com/2018/03/laowa-25mm-f28-25-5x-review-ultra-macro.html [accessed 24 Jul. 2018].

Bell T., Li B. & Zhang S. 2016. Structured light techniques and applications. In: Webster J. (ed.) Wiley Encyclopedia of Electrical and Electronics Engineering: 1–24. https://doi.org/10.1002/047134608X.W8298

Beltran R.S., Ruscher-Hill B., Kirkham A.L. & Burns J.M. 2018. An evaluation of three-dimensional photogrammetric and morphometric techniques for estimating volume and mass in Weddell seals Leptonychotes weddellii. PLoS One 13 (1): e0189865. https://doi.org/10.1371/journal.pone.0189865

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

Boehm J. 2014. Accuracy Investigation for structured-light based consumer 3D sensors. Photogrammetrie - Fernerkundung - Geoinformation 2014 (2): 117–27. https://doi.org/10.1127/1432-8364/2014/0214

Botton-Divet L., Cornette R., Houssaye A., Fabre A.-C. & Herrel A. 2017. Swimming and running: a study of the convergence in long bone morphology among semi-aquatic mustelids (Carnivora: Mustelidae). Biological Journal of the Linnean Society 121 (1): 38–49. https://doi.org/10.1093/biolinnean/blw027

Botton-Divet L., Houssaye A., Herrel A., Fabre A.-C. & Cornette R. 2015. Tools for quantitative form description; an evaluation of different software packages for semi-landmark analysis. PeerJ 3: e1417. https://doi.org/10.7717/peerj.1417

Brecko J., Mathys A., Dekoninck W., De Ceukelaire M., Van den Spiegel D. & Semal P. 2016. Revealing invisible beauty, ultra detailed: the influence of low-cost UV exposure on natural history specimens in 2D+ digitisation. PLoS ONE 11 (8): e0161572. https://doi.org/10.1371/journal.pone.0161572

Brecko J., Mathys A., Dekoninck W., Leponce M., Van den Spiegel D., & Semal P. 2014. Focus stacking: comparing commercial top-end set-ups with a semi-automatic low budget approach. A possible solution for mass digitisation of type specimens. ZooKeys 464: 1–23. https://doi.org/10.3897/zookeys.464.8615

Brunton C. 1998. The evolution of ultraviolet patterns in European Colias butterflies (Lepidoptera, Pieridae): a phylogeny using mitochondrial DNA. Heredity 80: 611–616. https://doi.org/10.1046/j.1365-2540.1998.00336.x

Burkhardt D. 1989. UV vision: a bird's eye view of feathers. Journal of Comparative Physiology 164, 787–796. https://doi.org/10.1007/BF00616750

Busby J. 3D scanning reflective objects with photogrammetry. 3D Scanstore. 2016. Available from http://www.3dscanstore.com/index.php?route=journal2/blog/post&journal_blog_post_id=19 [accessed 5 Sep. 2018]

Carey N., Werfel J. & Nagpal R. 2017. Fast, accurate, small-scale 3D scene capture using a low-cost depth sensor. IEEE Winter Conference on Applications of Computer Vision (WACV): 1268–1276. https://doi.org/10.1109/WACV.2017.146

Carfagni M, Furferi R., Governi L., Servi M., Uccheddu F. & Volpe Y. 2017. On the performance of the Intel SR300 Depth Camera: metrological and critical characterization. IEEE Sensors Journal 17 (14): 4508–4519. https://doi.org/10.1109/JSEN.2017.2703829

Chen F., Brown G.M. & Song M. 2000. Overview of 3-D shape measurement using optical methods. Optical Engineering 39 (1). https://doi.org/10.1117/1.602438

Choe G., Park J., Tai Y.W. & Kweon I.S. 2016. Refining geometry from depth sensors using IR Shading Images. International Journal of Computer Vision 122: 1–16. https://doi.org/10.1007/s11263-016-0937-y

Cosentino A. 2015. Effects of different binders on technical photography and infrared reflectography of 54 historical pigments. International Journal of Conservation Science 6 (3): 287–298.

Courtenay L.A., Maté-González M.Á., Aramendi J., Yravedra J., González-Aguilera D. & Domínguez-Rodrigo M. 2018. Testing accuracy in 2D and 3D geometric morphometric methods for cut mark identification and classification. PeerJ 6: e5133. https://doi.org/10.7717/peerj.5133

Cultural Heritage Imaging. 2018. Available from http://culturalheritageimaging.org/ [accessed 24 Jul. 2018].

Darwish W., Tang S., Li W., & Chen W. 2017. A new calibration method for commercial RGB-D sensors. Sensors 17 (6): 1204. https://doi.org/10.3390/s17061204

Das A.J., Murmann D.C., Cohrn K. & Raskar R. 2017. A method for rapid 3D scanning and replication of large paleontological specimens. PLoS ONE 12 (7): e0179264. https://doi.org/10.1371/journal.pone.0179264

Douglas R. H. and Jeffery G. 2014. The spectral transmission of ocular media suggests ultraviolet sensitivity is widespread among mammals. Proceedings of the Royal Society B 281: 20132995. https://doi.org/10.1098/rspb.2013.2995

Dubreuil L., Savage D., Delgado-Rick S., Plisson H., Stephenson B., De La Torre I. 2015. Current Analytical frameworks for studies of use-wear on ground stone tools. In: Marreiros J.M., Gibaja Bao J.F. & Bicho N. (eds) Use-Wear and Residue Analysis in Archaeology.Manuals in Archaeological Method, Theory and Technique: 105–158. Springer Nature, Cham.

Dupont S., Price B. & Blagoderov V. 2015. Imp: the customizable LEGO Pinned Insect Manipulator. Zookeys 481: 131–138. https://doi.org/10.3897/zookeys.481.8788

Earl G., Basford P.J., Bischoff A.S., Bowman A., Crowther C., Dahl J., Hodgson M., Martinez K., Isaksen L., Pagi H., Piquette K.E. & Kotoula E. 2011. Reflectance transformation imaging systems for ancient documentary artefacts. In: Bowen J.P., Dunn, Stuart & Ng K. (eds) Proceedings of the 2011 International Conference on Electronic Visualisation and the Arts (EVA’11): 147–154. BCS Learning & Development Ltd., Swindon.

Ebrahim M.A. 2015. "3D Laser Scanners' Techniques Overview", International Journal of Science and Research (IJSR) 4 (10): 323–331. Available from: https://www.ijsr.net/search_index_results_paperid.php?id=SUB158346 [accessed 19 Mar. 2020]

Evin A., Souter T., Hulme-Beaman A., Ameen C., Allen R., Viacava P., Larson G., Cucchi T., Dobney K. 2016. The use of close-range photogrammetry in zooarchaeology: creating accurate 3D models of wolf crania to study dog domestication. Journal of Archaeological Science: Reports 9: 87–93. https://doi.org/10.1016/j.jasrep.2016.06.028

Fabre A.-C., Bickford D., Segall M. & Herrel A. 2016. The impact of diet, habitat use, and behaviour on head shape evolution in homalopsid snakes. Biological Journal of the Linnean Society 118 (3): 634–647. https://doi.org/10.1111/bij.12753

Fabre A.-C., Cornette R., Perrard A., Boyer D.M., Prasad G.V.R., Hooker J.J., & Goswami A. 2014. A three-dimensional morphometric analysis of the locomotory ecology of Deccanolestes, a eutherian mammal from the Late Cretaceous of India. Journal of Vertebrate Paleontology 34 (1): 146–156. https://doi.org/10.1080/02724634.2013.789437

Faculteit Letteren - KULeuven. 2016. Leuven Cuneiform Collection. Available from http://www.arts.kuleuven.be/ono/meso/projects/cuneiformcollection [accessed 23 Jul. 2018].

Falkingham P.L., Bates K.T., Avanzini M., Bennett M., Bordy E.M., Breithaupt B.H., Castanera D., Citton P., Díaz-Martínez I., Farlow J.O, Fiorillo A.R., Gatesy S.M., Getty P., Hatala K.G., Hornung J.J, Hyatt J.A., Klein H., Lallensack J.N., Martin A.J., Marty D., Matthews N.A., Meyer C.A., Milàn J., Minter N.J., Razzolini N.L., Romilio A., Salisbury S.W., Sciscio L., Tanaka I., Wiseman A.L.A., Xing L.D. & Belvedere M. 2018. A Standard protocol for documenting modern and fossil ichnological data. Palaeontology 61 (4): 469–80. https:/doi.org/10.1111/pala.12373

Feng Q. 2012. Practical application of 3D laser scanning techniques to underground projects, phase 2–3 a part of ISRM-Swedish national task: “A survey of 3D laser scanning techniques for application to rock mechanics”. BeFo Report 114. Stockholm, Sweden.

Fleishman, L., Loew, E. & Leal, M. 1993. Ultraviolet vision in lizards. Nature 365, 397. https://doi.org/10.1038/365397a0

Friess M. 2012. Scratching the surface? The use of surface scanning in physical and paleoanthropology. Journal of Anthropological Sciences 90: 7–31. https://doi.org/10.4436/jass.90004

Fröhlich C. & Mettenleiter M. 2004. Terrestrial laser scanning – new perspectives in 3D surveying. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XXXVI-8/W2: 7–13.

Giacomini G., Scaravelli D., Herrel A., Brown R. & Meloro C. 2017a. Bat skull in three dimensions: Photogrammetry as a portable and reliable scanning solution. 14th European Bat Research Symposium.

Giacomini G., Scaravelli D., Herrel A., Brown R. & Meloro C. 2017b. Echo from the skulls: Is there a trade-off between echolocation and feeding function in bats? 14th European Bat Research Symposium.

Gilblom D.L. & Yoo S.K. 2004. Infrared and ultraviolet imaging with a CMOS having layered photodiodes. In: Sampat N., Blouke M.M. & Motta R.J. (eds) Proceedings of SPIE - The International Society for Optical Engineering 5301, Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications V. https://doi.org/10.1117/12.528427

Gorthi S.S. & Rastogi P. 2010. Fringe projection techniques: whither we are? Optics and Lasers in Engineering 48 (2): 133–140. https://doi.org/10.1016/j.optlaseng.2009.09.001

Goutte S., Mason M.J., Antoniazzi M.M., Jared C., Merle D., Cazes L., Toledo L.F., el-Hafci H., Pallu S., Portier H., Schramm S., Gueriau P. & Thoury M. 2019. Intense bone fluorescence reveals hidden patterns in pumpkin toadlets. Scientific Reports 9, 5388. https://doi.org/10.1038/s41598-019-41959-8

Gruber D.F., Sparks J.S. 2015. First Observation of Fluorescence in Marine Turtles. American Museum Novitates 2015 (3845): 1–8.

Guery J., Hess M. & Mathys A. 2017. Photogrammetry. In: Bentkowska-Kafel A., MacDonald L. (eds) Digital Techniques for Documenting and Preserving Cultural Heritage: 229–235. Kalamazoo and Bradford: Arc Humanities Press, Amsterdam.

Gutiérrez-García J.C., Gutiérrez-García T.A., Mosiño J.F., Vázquez-Domínguez E., Martínez-García A. & Arroyo-Cabrales J. 2015. A novel application of the white light/fringe projection duo: recovering high precision three-dimensional images from fossils for the digital preservation of morphology. Palaeontologia Electronica 18.2.6T: 1–13. https://doi.org/10.26879/516

Hameeuw H. 2014. Portable Light Dome System: from Registration to Online Publication within the Hour. Status Quaestionis Portable Light Dome Project for Cuneiform Documents. KMKG-MRAH, Leuven. Available from https://portablelightdome.files.wordpress.com/2014/12/portable-light-dome-system-from-registration-to-online-publication-within-the-hour_1-1.pdf [accessed 29 Aug. 2018].

Hennen D. 2012. A calm millipede’s UV fluorescence. Normal Biology blogpost available from http://normalbiology.blogspot.be/2012_03_01_archive.html [accessed 28 Aug. 2018].

Hernandez A. & Lemaire E. 2016. A smartphone photogrammetry method for digitising prosthetic socket interiors. Prosthetics and Orthotics International 41 (2): 1–5. https://doi.org/10.1177/0309364616664150

Hess M. & Robson S. 2013. Re-engineering Watt: A case study and best practice recommendations for 3D colour laser scans and 3D printing in museum artefact documentation. In: Saunders D., Strlic M., Kronen C., Birholzerberg K. & Luxford N. (eds) Lasers in the Conservation of Artworks IX: 154–162. Archetype Publications, London. Available from https://discovery.ucl.ac.uk/id/eprint/1411525/ [accessed 30 Mar. 2020].

Hess M. 2017. 3D Laser Scanning. In: Bentkowska A. & MacDonald L. (eds) Digital Techniques for Documenting and Preserving Cultural Heritage: 199–206. Kalamazoo and Bradford: Arc Humanities Press, Amsterdam.

Hess M., Robson S. & Hosseininaveh Ahmadabadian A. 2014. A contest of sensors in close range 3D imaging: Performance evaluation with a new metric test object. The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences 5: 277–284. https://doi.org/10.5194/isprsarchives-XL-5-277-2014

Higgins C. 2015. Applications and challenges of digital pathology and whole slide imaging. Biotechnic & Histochemistry: Official Publication of the Biological Stain Commission 90 (5): 341–347. https://doi.org/10.3109/10520295.2015.1044566

Historic England. 2017. Photogrammetric Applications for Cultural Heritage. Guidance for Good Practice. Historic England, Swindon.

Historic England. 2018. 3D Laser Scanning for Heritage: Advice and Guidance on the Use of Laser Scanning in Archaeology and Architecture. Historic England, Swindon.

Hogg C., Neveu M., Stokkan K-A., Folkow L., Cottrill P., Douglas R., Hunt D.M. & Jeffery G. 2011. Arctic reindeer extend their visual range into the ultraviolet. Journal of Experimental Biology 214 (12), 2014-2019. https://doi.og/10.1242/jeb.053553

Honkavaara J., Koivula M., Korpimäki E., Siitari H. & Viitala J. 2018. Ultraviolet vision and foraging in terrestrial vertebrates. Oikos 98 (3): 505–511.

Information in Images. 2018. Available from https://www.informationinimages.com/auto-scan-micro [accessed 24 Jul. 2018].

Jacobs G. 1992. Ultraviolet Vision in Vertebrates. American Zoologist 32 (4), 544–554.

Jecic S. & Dvar N. 2003. The assessment of structures light and laser scanning methods in 3D shape measurements. 4th International Congress of Croatian Society of Mechanics: 237–244.

Johnston R.A., Barnes K.S., Lovell-Smith T. & Price N. 2013. Use of a hand-held laser scanner in palaeontology: a 3D model of a plesiosaur fossil. Available from: https://www.polhemus.com/_assets/img/Use_of_a_Hand-held_Laser_Scanner_in_Palaeontology.pdf [accessed 19 Mar. 2020]

Keklikoglou K., Faulwetter S., Chatzinikolaou E., Wils P., Brecko J., Kvacek J., Metscher B. & Arvanitidis C. 2019. Micro-computed tomography for natural history specimens: a handbook of best practice protocols. European Journal of Taxonomy 522. https://doi.org/10.5852/ejt.2019.522

Kersten T.P., Przybilla H.-J., Lindstaedt M., Tschirschwitz F. & Misgaiski-Hass M. 2016. Comparative geometrical investigations of hand-held scanning systems. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLI-B5: 507–514. https://doi.org/10.5194/isprsarchives-XLI-B5-507-2016

Kinsman T. 2016. Using Reflectance Transformation Imaging to Shoot Ultra-Detailed Macro. Available from https://petapixel.com/2016/04/21/shoot-super-detailed-macro-photographs-rti-camera-rig/ [accessed 25 Jul. 2018].

Koch R., May S. & Nüchter A. 2017. Detection and purging of specular reflective and transparent object influences in 3D range measurements. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, XLII-2/W3: 377–384. https://doi.org/10.5194/isprs-archives-XLII-2-W3-377-2017

Kohler A.M., Olson E.R., Martin J.G. & Spaeth Anich P. 2019. Ultraviolet fluorescence discovered in New World flying squirrels (Glaucomys). Journal of Mammalogy 100 (1): 21-30. https://doi.org/10.1093/jmammal/gyy177

Kontogianni G., Chliverou R., Koutsoudis A., Pavlidis G. & Georgopoulos A. 2017. Enhancing close-up image based 3d digitisation with focus stacking. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-2/W5: 421–425. https://doi.org/10.5194/isprs-archives-XLII-2-W5-421-2017

Kotoula E. & Earl G. 2014. Integrated RTI approaches for the study of painted surfaces. Computer Applications and Quantitative methods in Archaeology 45911. Available from http://caa2014.sciencesconf.org/45911/ [accessed 10 Jan. 2020].

Kotoula E. 2012. Infrared RTI: experimentation towards the development of multispectral RTI. Available from http://acrg.soton.ac.uk/blog/1569/ [accessed 28 Aug. 2018].

Kotoula E. 2015. Ultraviolet RTI. Available from http://acrg.soton.ac.uk/blog/4175/ [accessed 31 Aug. 2018].

Kreij A., Scriffignano J., Rosendahl D., Nagel T. & Ulm S. 2018. Aboriginal stone-walled intertidal fishtrap morphology, function and chronology investigated with high-resolution close-range Unmanned Aerial Vehicle photogrammetry. Journal of Archaeological Science 96: 148–161. https://doi.org/10.1016/j.jas.2018.05.012

Kühsel S., Brückner A., Schmelzle S., Heethoff M. & Blüthgen N. 2017. Surface area-volume ratios in insects. Insect Science 24: 829–841. https://doi.org/10.1111/1744-7917.12362

Lachat E., Macher H., Mittet M.A., Landes T. & Grussenmeyer P. 2015. First experiences with Kinect V2 Sensor for close range 3D modelling. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XL-5/W4: 93–100. https://doi.org/10.5194/isprsarchives-XL-5-W4-93-2015

Lallensack J.N., van Heteren A.H. & Wings O. 2016. Geometric morphometric analysis of intratrackway variability: a case study on theropod and ornithopod dinosaur trackways from Münchehagen (Lower Cretaceous, Germany). PeerJ 4: e2059. https://doi.org/10.7717/peerj.2059

Lautenschlager S. 2016. Reconstructing the past: methods and techniques for the digital restoration of fossils. Royal Society Open Science 3 (10): 160342. https://doi.org/10.1098/rsos.160342

Leong, F. J. & McGee J. O. 2001. Automated complete slide digitisation: a medium for simultaneous viewing by multiple pathologists. The Journal of Pathology, 195 (4): 508–514. https://doi.org/10.1002/path.972

Luhmann T., Robson S., Kyle S. & Böhm J. 2013. Close-Range Photogrammetry and 3D Imaging. De Gruyter, Berlin. https://doi.org/10.1515/9783110302783

MacDonald L.W. 2011. Visualising an egyptian artefact in 3D: comparing RTI with laser scanning. In: Bowen J.P., Dunn, Stuart & Ng K. (eds) Proceedings of the 2011 International Conference on Electronic Visualisation and the Arts (EVA’11): 155–162. BCS Learning & Development Ltd., Swindon.

MacDonald L.W. 2014. Colour and directionality in surface reflectance. 40th Annual Convention of the Society for the Study of Artificial Intelligence and the Simulation of Behaviour (AISB 2014): 223–229.

Mallison H. & Wings O. 2014. Photogrammetry in paleontology. A practical guide. Journal of Paleontological Techniques 12: 1–31.

Mallison H. 2011. Digitising methods for paleontology – applications, benefits and limitations. In: Elewa AMT (ed.) Computational Paleontology: 7–44. Springer, Berlin.

Mallison H., Hohloch A. & Pfretzschner H.-U. 2009. Mechanical digitising for paleontology – new and improved techniques. Palaeontologia Electronica. 12 (2): 4T.: 1–41. http://palaeo-electronica.org/2009_2/185/index.html

Malzbender T., Gelb D. & Wolters H.J. 2001. Polynomial texture maps. Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques (SIGGRAPH 2001): 519–528. ACM, Los Angeles.

Manfredi M., Bearman G. H., Williamson G., Kronkright D., Doehne E., Jacobs M. & Marengo E. 2014. A new quantitative method for the non-invasive documentation of morphological damage in paintings using RTI surface normals. Sensors 14 (7): 12271–12284. https://doi.org/10.3390/s140712271

Manfredi M., Williamson G., Kronkright D., Doehne E., Jacobs M., Marengo E. & Bearman G. 2013. Measuring Changes in Cultural Heritage Objects with Reflectance Transformation Imaging. In: Addison A.C., De Luca L., Guidi G., Pescarin S. (eds) 2013 Digital Heritage International Congress (DigitalHeritage): 189–192. IEEE, Marseilles. https://doi.org/10.1109/DigitalHeritage.2013.6743730

Marcy A.E., Fruciano C., Phillips M.J., Mardon K. & Weisbecker V. 2018. Low resolution scans can provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for 3D shape analyses. PeerJ 6: e5032. https://doi.org/10.7717/peerj.5032

Martin M., Meylan S., Gomez D. & Le Galliard J.F. 2013. Ultraviolet and carotenoid-based colouration in the common lizard Zootoca vivipara (Squamata: Lacertidae) in relation to age, sex, and morphology. Biological Journal of the Linnean Society 110:128–141. https://doi.org/10.1111/bij.12104

Marziali S. & Dionisio G. 2017. Photogrammetry and macro photography. The experience of the MUSINT II Project in the 3D digitising process of small size archaeological artifacts. Studies in Digital Heritage 1 (2): 298–309. https://doi.org/10.14434/sdh.v1i2.23250

Maté González M.A., Aramendi J., González-Aguilera D. & Yravedra J. 2017. Statistical Comparison between low-cost methods for 3D characterization of cut-marks on bones. Remote Sensing 9 (9): 873. https://doi.org/10.3390/rs9090873

Maté González M.Á., González M.Á.M., Yravedra J., González-Aguilera D., Palomeque-González J.F. & Domínguez-Rodrigo M. 2015. Micro-photogrammetric characterization of cut marks on bones. Journal of Archaeological Science 62: 128–142. https://doi.org/10.1016/j.jas.2015.08.006

Mathys A., Brecko J. & Semal P. 2013a. Comparing 3D digitising technologies: what are the differences? In: Addison A.C., De Luca L., Guidi G., Pescarin S. (eds) Digital Heritage International Congress: 201–204. CNRS, Marseilles. https://doi.org/10.1109/DigitalHeritage.2013.6743733

Mathys A., Brecko J. & Semal P. 2014. Cost evaluation of 3D digitisation techniques. In: Ioannides M., Magnenat-Thalmann N., Fink E., Zarnic R., Yen A. & Quak E. (eds) EUROMED 2014 Proceedings: 17–25. Multi-Science Publishing Co., Hockley.

Mathys A., Brecko J., Di Modica K., Abrams G., Bonjean D. & Semal P. 2013b. Low cost 3D imaging: a first look for field archaeology. Notae Praehistoricae 33: 33–42.

Mathys A., Brecko J., Van den Spiegel D. & Semal P. 2015. 3D and challenging materials: guidelines for different 3D digitisation methods for museum collections with varying material optical properties. Proceedings of the 2nd International Congress on Digital Heritage. https://doi.org/10.1109/DigitalHeritage.2015.7413827

Mathys A., Semal P., Brecko J. & Van den Spiegel D. 2019. Improving 3D photogrammetry models through spectral imaging: Tooth enamel as a case study. PLoS ONE 14 (8): e0220949. https://doi.org/10.1371/journal.pone.0220949

Mathys A., Semal P., Brecko J., Bello S.M., Van den Spiegel D. & Abrams G. In preparation. An overview of the advantages and limitations of 9 different methods to analyse bone retouchers.

Mathys, A., Brecko J. & Semal P. 2014. Cost evaluation of 3D digitisation techniques. In: Ioannides M., Magnenat-Thalmann N., Fink E., Zarnic R., Yen A. & Quak E. (eds) EUROMED 2014 Proceedings. MultiScience Ltd, Essex.

McPherron S.P., Gernat T. & Hublin J.-J. 2009. Structured light scanning for high-resolution documentation of in-situ archaeological finds. Journal of Archaeological Science 36 (1): 19–24. https://doi.org/10.1016/j.jas.2008.06.028

Medina J.M., Díaz J.A & Vukusic P. 2015. Classification of peacock feather reflectance using principal component analysis similarity factors from multispectral imaging data. Optics Express 23, 10198–10212. https://doi.org/10.1364/OE.23.010198

Micheletti N., Chandler J.H. & Lane S.N. 2014. Investigating the geomorphological potential of freely available and accessible structure-from-motion photogrammetry using a smartphone. Earth Surface Processes and Landforms 40 (4):473–486. https://doi.org/10.1002/esp.3648

Micheletti N., Chandler J.H. & Lane S.N. 2015. Structure from Motion (SfM) Photogrammetry. In: Clarke, L.E. & Nield, J.M. (eds) Geomorphological Techniques (Online Edition). British Society for Geomorphology, London.

Minidome. SD. Minidome Webpage. Available from http://www.minidome.be/v01/home.php [accessed 23 Jul. 2018].

Moran Z.R. & Parker A.G. 2016. Near infrared imaging as a method of studying tsetse fly (Diptera: Glossinidae) pupal development. Journal of Insect Science 16 (1): 72, 1–9. https://doi.org/10.1093/jisesa/iew047

Mudge M., Malzbender T., Schroer C. & Lum, M. 2006. New Reflection Transformation imaging methods for rock art and multiple-viewpoint display. The 7th International Symposium on Virtual Reality, Archaeology and Cultural Heritage (VAST2006): 195–200.

Muñoz-Muñoz F., Quinto-Sánchez M. & González-José R. 2016. Photogrammetry: a useful tool for three-dimensional morphometric analysis of small mammals. Journal of zoological systematics and evolutionary research 54 (4): 318–325. https://doi.org/10.1111/jzs.12137

Nguyen C.V., Lovell D.R., Adcock M. & La Salle J. 2014. Capturing natural-colour 3D models of insects for species discovery and diagnostics. PLoS ONE 9 (4): 1–11. https://doi.org/10.1371/journal.pone.0094346

Nguyen D.D. 2012. Water body extraction from multispectral image by spectral pattern analysis. International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XXXIX-B8: 181–186. https://doi.org/10.5194/isprsarchives-XXXIX-B8-181-2012

Nowogrodzki A. 2017. First fluorescent frog found. Nature 543 (7645).

Objective Imaging. 2009. Objective Imaging Surveyor Turboscan System with Slide Loader. Available from https://www.youtube.com/watch?v=RoHejrt-w9Q [accessed 24 Nov. 2019].

Ohta J. 2017. Smart CMOS Image Sensors and Applications. CRC Press, Boca Raton.

Padfield J. & Saunders D. 2005. Polynomial texture mapping: a new tool for examining the surface of paintings. ICOM-CC Preprints, the Hague (1): 504–510.

Pavlidis G., Koutsoudis A., Arnaoutoglou F., Tsioukas V. & Chamzas C. 2007. Methods for 3D digitisation of Cultural Heritage. Journal of Cultural Heritage 8 (1): 93–98. https://doi.org/10.1016/j.culher.2006.10.007

Pawlowicz L. 2016. Affordable Reflectance Transformation Imaging Dome. Available from https://hackaday.io/project/11951-affordable-reflectance-transformation-imaging-dome [accessed 25 Jul. 2018].

Pearson G. 2013. Luminous beauty: the secret world of fluorescent arthropods. Wired. Available from http://www.wired.com/2013/11/arthropods-are-having-a-secret-rave/ [accessed 28 Aug. 2018].

Pecháček P., Stella D. & Kleisner K. 2019. A morphometric analysis of environmental dependences between ultraviolet patches and wing venation patterns in Gonepteryx butterflies (Lepidoptera, Pieridae). Evol Ecol 33, 89–110. https://doi.org/10.1007/s10682-019-09969-0

Piquette K. 2011. Reflectance transformation imaging (RTI) and ancient egyptian material culture. Damqatum: The CEHAO Newsletter - El boletín de Noticias del CEHAO 7: 16–22.

Plisson H. 2015. Digital photography and traceology, from 2D to 3D. In: Lozovskaya O.V., Lozovski V.M. & Girya E. (eds) Traces in the history. Dedicated to 75 anniversary of Viacheslav E. Shchelinsky. IIMKRAN, Saint Petersbourg.

Plisson H. et Zotkina L. V. 2015. From 2D to 3D at macro- and microscopic scale in rock art studies. Digital Applications in Archaeology and Cultural Heritage 2 (2–3): 102–119. https://doi.org/10.1016/j.daach.2015.06.002

Pöhlmann S.T.L., Harkness E.F., Taylor C.J. & Astley S.M. 2016. Evaluation of Kinect 3D Sensor for healthcare imaging. Journal of Medical and Biological Engineering 36 (6): 857–870. https://doi.org/10.1007/s40846-016-0184-2

Polo M.-E. & Felicísimo Á. M. 2012. Analysis of uncertainty and repeatability of a low-cost 3D laser scanner. Sensors 12 (7): 9046–9054. https://doi.org/10.3390/s120709046

Portable Light Dome. 2017. Portable Light Dome, Relighting Cultural Heritage. Available from https://portablelightdome.wordpress.com/ [accessed 23 Jul. 2018].

Porter S.T, Missal K. & Pawlowicz L. 2016. A comparison of methods for creating 3D models of obsidian artifacts. Computer Applications and Quantitative Methods in Archaeology (CAA). Oslo, Norway, 29 Mar –2 Apr. 2016. Presentation. Available from https://www.researchgate.net/publication/299820517_A_Comparison_of_Methods_for_Creating_3D_Models_of_Obsidian_Artifacts [accessed 9 Jul. 2018].

Pronti L., Felici A.C., Ménager M., Vieillescazes C. & Piacentini, M. 2017. Spectral behavior of white pigment mixtures using reflectance, ultraviolet—fluorescence spectroscopy, and multispectral imaging. Applied Spectroscopy 71 (12): 2616–2625. https://doi.org/10.1177/0003702817717969

Prötzel D., Heβ M., Scherz M. D., Schwager M., va not Padje A. & Glaw F. 2018. Widespread bone-based fluorescence in chameleons. Scientific Reports 8: 698.

Randall T. 2013. Client guide to 3D scanning and data capture. Building information modelling (BIM) task group. Available from http://bim-level2.org/globalassets/pdfs/clients-guide-to-3d-scanning-and-data-capture.pdf [accessed 30 Aug. 2018]

Remondino F. 2011. Heritage Recording and 3D Modeling with Photogrammetry and 3D Scanning. Remote Sensing 3: 1104–1138. https://doi.org/10.3390/rs3061104

Remondino F., Rizzi A., Girardi S., Petti F.M. & Avanzini M. 2010. 3D Ichnology-recovering digital 3D models of dinosaur footprints. The Photogrammetric Record 25: 266–282. https://doi.org/10.1111/j.1477-9730.2010.00587.x

Richards A. 2005. Infrared spectral selection; it begins with the Detector. Photonics Handbook 2005. Available from https://www.photonics.com/a25132/Infrared_Spectral_Selection_It_Begins_with_the [accessed 28 Aug. 2018].

Rieke-Zapp D. & Royo S. 2017. Structured light 3D scanning. In: Bentkowska-Kafel A., MacDonald L. (eds) Digital Techniques for Documenting and Preserving Cultural Heritage: 247–251. Kalamazoo and Bradford: Arc Humanities Press. Amsterdam.

Rojo M.G., García G.B., Mateos C.P., García J.G. & Vicente M.C. 2006. Critical comparison of 31 commercially available digital slide systems in pathology. International Journal of Surgical Pathology 14 (4): 285–305. https://doi.org/10.1177/1066896906292274

Salih A., Larkum A., Cox G., Kuhl M. & Hoegh-Guldberg O. 2000. Fluorescent pigments in corals are photoprotective. Nature 408: 850–853. https://doi.org/10.1038/35048564

Salvant J., Walton M., Kronkright D., Yeh C-K., Li F., Cossairt O. & Katsaggelo A.K. 2017. Photometric Stereo by UV-Induced Fluorescence to Detect Protrusions on Georgia O’Keeffe’s Paintings. Computing Research Repository Graphics (cs.GR) abs/1711.08103. https://arxiv.org/abs/1711.08103

San José Alonso J.I., Martínez-Rubio J., Fernandez J. & Garcia Fernandez J. 2011. Comparing time-of and phase-shift the survey of the Royal Pantheon in the Basilica of San Isidoro (LEÓN). ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XXXVIII-5/W16: 377–385. https://doi.org/10.5194/isprsarchives-XXXVIII-5-W16-377-2011

Sansoni G., Trebeschi M. & Docchio F. 2009. State-of-the-art and applications of 3D imaging sensors in industry, cultural heritage, medicine, and criminal investigation. Sensors 9 (1): 568–601. https://doi.org/10.3390/s90100568

Santella M. & Milner A.R.C. 2017. Coupling focus stacking with photogrammetry to illustrate small fossil teeth. Journal of Paleontological Techniques 18: 1–17.

Schmidt S., Balke M. & Lafogler S. 2012. DScan – a high-performance digital scanning system for entomological collections. ZooKeys 209: 183–191. https://doi.org/10.3897/zookeys.209.3115

Segall M., Cornette R., Fabre A.-C., Godoy-Diana R. & Herrel A. 2016. Does aquatic foraging impact head shape evolution in snakes? Proceedings of the Royal Society B: Biological Sciences 283 (1837): 20161645. https://doi.org/10.1098/rspb.2016.1645

Shan J. & Toth C.K. 2008. Topographic Laser Ranging and Scanning: Principles and Processing, Second Edition. CRC Press, Boca Raton. https://doi.org/10.1201/9781420051438

Siebeck U.E., Parker A.N., Sprenger D., Mäthger L.M. & Wallis G. 2010. A species of reef fish that uses ultraviolet patterns for covert face recognition. Current Biology 20 (5): 407–410. https://doi.org/10.1016/j.cub.2009.12.047

Slizewski A., Friess M. & Semal P. 2010. Surface scanning of anthropological specimens: nominal-actual comparison with low-cost laser scanning and high-end fringe light projection surface scanning systems. Quartär 57: 179–187.

Stella D., Pecháček P., Meyer-Rochow V.B. & Kleisner K. 2018. UV reflectance is associated with environmental conditions in Palaearctic Pieris napi (Lepidoptera: Pieridae). Insect Science 25: 508–518. https://doi.org/10.1111/1744-7917.12429

Ströbel B., Schmelzle S., Bluethgen N. & Heethoff M. 2018. An automated device for the digitisation and 3D modelling of insects combining extended-depth-of-field and all-side multi-view imaging. ZooKeys 759: 1–27. https://doi.org/10.3897/zookeys.759.24584

Taboada C., Brunetti A.E., Pedron F.N., Neto F.C., Estrin D.A., Bari S.E., Chemes L.B., Peporine Lopes N., Lagorio M.G., & Faivovich J. 2017. Proceedings of the National Academy of Sciences. 114 (14) 3672–3677. https://doi.org/10.1073/pnas.1701053114

Taylor C.R. 2011. From microscopy to whole slide digital images: a century and a half of image analysis. Applied Immunohistochemistry & Molecular Morphology. 19 (6):491–493.

Thiel K.H. & Wehr A. 2004. Performance capabilities of laser scanners—an overview & measurement principle analysis. Proceedings of ISPRS International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XXXVI-8/WG2: 14–18.

Thompson M.E., Saporito R.A., Ruiz-Valderrama D.H., G.F. Medina-Rangel & Donnelly M.A. 2019. A field-based survey of fluorescence in tropical tree frogs using an LED UV-B flashlight. Herpetology Notes 12: 987–990.

Trucco E, Fisher R.B. & Fitzgibbon A.W. 1994. Direct calibration and data consistency in 3-D Laser Scanning. Proceedings of the Conference on British Machine Vision 2: 489–498. https://doi.org/10.5244/C.8.48

Valinasab B., Rukosuyev M., Lee J. & Jun M.B.G. 2015. Atomization-based spray coating for improved 3D scanning. Journal of The Korean Society of Manufacturing Technology Engineers 24: 23–30. https://doi.org/10.7735/ksmte.2015.24.1.023

Van der Perre A. & Hameeuw H. 2015. La création d’images multi-spectrales: les portraits romains du Fayoum. In: Delvaux L., Therasse I. (eds) Sarcophages: Sous les étoiles de Nout: 164–165. Éditions Racine, Brussels.

Van der Perre A., Hameeuw H., Boschloos V., Delvaux L. Proesmans M., Vandermeulen B., Van Gool L. & Watteeuw L. 2016. Towards a combined use of IR, UV and 3D-imaging for the study of small inscribed and illuminated artefacts. In: Homom P.M. (ed.) Lights On … Cultural Heritage and Museums!: 163–192. FLUP, University of Porto, Porto.

Venus lens. 2018. Laowa 25 mm f/2.8 2.5–5× Ultra Macro. Available from https://www.venuslens.net/product/laowa-25mm-f-2-8-2-5-5x-ultra-macro-2/ [accessed 24 Jul. 2018].

Villena-Martínez V., Fuster-Guilló A., Azorín-López J., Saval-Calvo M., Mora-Pascual J., Garcia-Rodriguez J. & Garcia-Garcia A. 2017. A Quantitative comparison of calibration methods for RGB-D sensors using different technologies. Sensors 17 (2): 243. https://doi.org/10.3390/s17020243

Wachowiak M.J. & Karas B.V. 2009. 3D scanning and replication for museum and cultural heritage applications. Journal of the American Institute for Conservation 48 (2): 141–158. https://doi.org/10.1179/019713609804516992

Watteeuw L., Vandermeulen B., Van der Stock J., Delsaerdt P., Gradmann S. & Truyen F. 2017. Illuminare, Centre for study of Medieval Art. RICH Project. Available from http://ec2-34-244-170-214.eu-west-1.compute.amazonaws.com/accordion-item/rich/ [accessed 23 Jul. 2018].

Willems G., Verbiest F., Moreau W., Hameeuw H., Van Lerberghe K. & Van Gool L. 2005. Easy and cost-effective cuneiform digitising. The 6th International Symposium on Virtual Reality, Archaeology and Cultural Heritage VAST. http://hdl.handle.net/1854/LU-8572126

Wizen G. 2018. Review: Laowa 25 mm f/2.8 2.5–5× Ultra Macro lens. Available from http://gilwizen.com/laowa-25mm-ultra-macro-lens-review/ [accessed 24 Jul. 2018].

Zachar J., Hornak M. & Novakovic P. 2017. 3D digital recording of archaeological, architectural and artistic heritage. CONPRA series I. https://doi.org/10.4312/9789610603061

Ze-Lin W., Ngan-Kee N., Teo S.L.M. & Parra-Velandia F.J. 2012. Fluorescent patterns in some portunus species (Crustacea: Brachyura: Portunidae). Contributions to Marine Science 2012: 135–143. Available from https://www.yumpu.com/en/document/read/38378257/wong-ze-lin-serena-teo-lay-ming-tropical-marine-science-institute [accesed 30 Mar. 2020]

Zennaro S., Munaro M., Milani S., Zanuttigh P., Bernardi A., Ghidoni S. & Menegatti E. 2015. Performance evaluation of the 1st and 2nd generation Kinect for multimedia applications. IEEE International Conference on Multimedia and Expo (ICME). https://doi.org/10.1109/icme.2015.7177380

Zerene Systems. 2017. Available from http://zerenesystems.com/cms/stacker [accessed 24 Jul. 2018].

ZooSphere. 2018. Available from http://www.zoosphere.net/ [accessed 02 Jul. 2018].

How to Cite
Brecko, J., & Mathys, A. (2020). Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections. European Journal of Taxonomy, (623). https://doi.org/10.5852/ejt.2020.623