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Multispectral and colour imaging systems for the detection of small vertebrate fossils: A preliminary study

Xana Delpueyo, Meritxell Vilaseca, Marc Furió, Francisco J. Burgos-Fernández, and Jaume Pujol

Plain Language Abstract

In this study we analyse the usefulness of novel colour and multispectral imaging systems for the identification of fossil remains of small vertebrates to facilitate their subsequent separation from sediments. The analysis is based on the differences of spectral and fluorescence characteristics between bones, teeth and sand-gravel samples. The goal is to improve and accelerate the detection of paleontological samples in sediments. This process, usually carried out manually and based on morphological features, is currently very expensive due to the large amount of time required.

Resumen en Español

Sistemas de imagen multiespectrales y en color para la detección de pequeños fósiles de vertebrados: Un estudio preliminar

El proceso de separación o triado de pequeños fósiles de vertebrados de los sedimentos es un trabajo monótono, generalmente realizado de forma manual y basado principalmente en características morfológicas. La gran cantidad de tiempo empleado por técnicos de laboratorio que requiere esta técnica anticuada implica que los costos económicos sean muy altos. En este estudio probamos el potencial valor práctico de un sistema de imagen multiespectral en color para la detección de pequeños fósiles de vertebrados y así facilitar su separación del sedimento. Esta técnica se basa en el análisis de las características espectrales y de fluorescencia de los fósiles. Específicamente, se utilizó un sistema multiespectral con una cámara de dispositivo de carga acoplada (CCD) unida a un filtro de cristal líquido sintonizable y una cámara digital en color en combinación con fuentes de luz diurna y ultravioleta. Los resultados muestran que la reflectancia de los huesos, los dientes y el sedimento suele ser diferente a longitudes de onda más largas, y que las tasas de fluorescencia también difieren en la región azul-verde. Desafortunadamente, muestras de diferentes sitios paleontológicos presentan patrones diferentes, dificultando la estandarización de un método que discrimine los microfósiles de los sedimentos. Sin embargo, la combinación de sistemas de imagen en color y multiespectrales con avances recientes en fluorescencia estimulada por láser en fósiles podría constituir una solución óptima para un eficiente proceso de triado de pequeños restos de vertebrados en muestras geológicas.

Palabras clave: sistemas multiespectrales; fluorescencia; sistema de triado de fósiles

Traducción: Enrique Peñalver (Sociedad Española de Paleontología)

Résumé en Français

Systèmes d'imagerie multispectrale et couleur pour détecter les fossiles de petits vertébrés : une étude préliminaire

Isoler les fossiles de petits vertébrés dans le sédiment est un exercice monotone, généralement effectué manuellement en se basant principalement sur les caractères morphologiques. La charge importante en termes de temps et de personnel entraine des coûts économiques élevés associés avec cette technique désuète. Dans cette étude, nous testons le potentiel de l'imagerie multispectrale et couleur pour détecter les fossiles de petits vertébrés et faciliter leur séparation du sédiment. Cette technique est basée sur l'analyse des caractéristiques spectrales et de la fluorescence des fossiles. Plus précisément, un système multispectral avec une caméra « charge-coupled device » (CCD) attachée à un filtre accordable à cristaux liquides et une caméra couleur numérique ont été utilisés en combinaison avec des sources de lumière du jour et d'ultraviolets. Les résultats montrent que les réflectivités des os, des dents, et du sédiment sont généralement différentes à des longueurs d'onde plus élevées, et que les taux de fluorescence varient également dans le spectre bleu-vert. Malheureusement, les échantillons de différents sites paléontologiques présentent différents schémas, ce qui empêche la standardisation d'une méthode qui discriminerait les microfossiles des sédiments. Cependant, la combinaison des systèmes d'imagerie multispectrale et couleur avec des avancées récentes en fluorescence induite par laser chez les fossiles pourrait constituer une solution optimale pour un procédé de tri efficace des restes de petits vertébrés dans les échantillons géologiques.

Mots-clés: systèmes multispectraux ; fluorescence ; système de séparation des fossiles

Translator: Antoine Souron

Deutsche Zusammenfassung

Multispektrale und farbige Abbildungssysteme zur Erkennung kleiner Wirbeltierfossilien: eine Vorstudie

Kleine Wirbeltierfossilien aus dem Sediment herauszutrennen ist eine monotone Aufgabe, die üblicherweise per Hand durchgeführt wird und auf morphologischen Merkmalen basiert. Der große Zeit-und Personalaufwand dieser antiquierten Technik resultiert in hohen ökonomischen Kosten. In dieser Studie testen wir das Potential von farbiger und multispektraler Bildgebung zur Erkennung kleiner Wirbeltierfossilien und wie man sie besser aus dem Sediment trennen kann. Diese Technik basiert auf Untersuchungen zu den spektralen und fluoreszierenden Eigenschaften von Fossilien. In diesem Fall wurde ein multispektrales System mit einer ladungsgekoppelten Kamera (CCD) verbunden mit einem regelbaren Flüssigkristallfilter und einer digitalen Farbkamera eingesetzt in Kombination mit Tageslicht und Lichtquellen mit ultraviolettem Licht. Die Ergebnisse zeigen, dass die Reflexion von Knochen, Zähnen und Sedimenten bei längeren Wellenlängen normalerweise unterschiedlich ist und dass Fluoreszenz-Raten im blau-grünen Bereich ebenso unterschiedlich sind. Bedauerlicherweise zeigen Proben aus verschiedenen paläontologischen Fundstellen unterschiedliche Muster, was die Standardisierung einer Methode zur Trennung von Mikrofossilien vom Sediment behindert. Eine Kombination farbiger und multispektraler Bildgebung mit den neuesten Ergebnissen der laserstimulierten Fluoreszenz könnte jedoch eine optimale Lösung für einen effizienten Sortierungsprozess kleiner Vertebratenüberreste innerhalb geologischer Proben darstellen.

Schlüsselwörter: multispektrale Systeme; Fluoreszenz; Trennungssystem für Fossilen

Translator: Eva Gebauer

Arabic

Translator: Ashraf M.T. Elewa

 

 

FIGURE 1. 1, Wet sieving process of palaeontological samples using Freudenthal’s technique. 2, Visual recognition and separation of teeth and bones using a binocular microscope and pincers.

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FIGURE 2. Experimental multispectral imaging system.

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FIGURE 3.1, Reflectance spectra of sediment (sand and gravel) and fossils (bones and teeth) of Sample 1. 2, Fluorescence spectra (radiance in W/sr·cm 2) of sediment (sand and gravel) and fossils (bones and teeth) of Sample 1.

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FIGURE 4. Examples of spectral images of Sample 1 through spectral bands (420, 520, 620, 670, and 720 nm) taken under daylight. An RGB image computed using the sRGB - standard RGB colour space is also provided.

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FIGURE 5. Mixture of bones-teeth and sand-gravel from Sample 1. 1, RGB image under daylight (D65). 2, RGB image under UV light. 3, Blue channel image under UV light. 4, Green channel image (grayscale) under UV light. 5, Black and white image after segmentation of the green channel image.

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FIGURE 6.1, Reflectance spectra of sediment (sand and gravel), fossils (bones and teeth) and ferrous sediment of Sample 2. 2 , Fluorescence spectra (radiance in W/sr*cm 2) of sediment (sand and gravel), fossils (bones and teeth) and ferrous sediment of Sample 2.

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FIGURE 7. Examples of spectral images of Sample 2 through spectral bands (420, 520, 620, 670 and 720 nm) taken under daylight. An RGB computed using the sRGB - standard RGB colour space image is also provided.

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FIGURE 8. RGB images of Sample 2 with ferrous particles, bones-teeth, sand-gravel and a mixture of bones-teeth and sand-gravel. 1, Under daylight (D65). 2, Under UV Light.

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FIGURE 9. 1, Reflectance spectra of sediment (sand and gravel) and fossils (bones and teeth) of Sample 3. 2, Fluorescence spectra (radiance in W/sr*cm 2) of sediment (sand and gravel) and fossils (bones and teeth) of Sample 3.

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FIGURE 10. Examples of spectral images of Sample 3 through spectral bands (420, 520, 620, 670, and 720 nm) taken under daylight. An RGB computed using the sRGB - standard RGB colour space image is also provided.

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FIGURE 11. Fossils (bones and teeth) and a mixture of fossils and sediment (sand and gravel) from Sample 3. 1, RGB image under daylight (D65). 2, RGB image under UV light. 3, Blue channel image (grayscale) under UV light. 4, Black and white image after segmentation of the blue channel image.

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delpueyoXana Delpueyo. Centre for Sensors, Instruments and Systems Development (CD6), Universitat Politècnica de Catalunya (UPC) (Rambla Sant Nebridi 10, 08222-Terrassa, Barcelona, Spain). This email address is being protected from spambots. You need JavaScript enabled to view it.

She completed her BSc degree in Optics and Optometry in 2011 and the MSc in Optometry and Vision Sciences in 2013 at the Technical University of Catalonia (UPC). She is currently a predoctoral researcher at the Centre for Sensors, Instruments and Systems Development (CD6) of the UPC where she enrolled the doctorate program in Optical Engineering. Her main research interests are multiespectral and hyperspectral imaging systems and colour measurement.

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Meritxell Vilaseca. Centre for Sensors, Instruments and Systems Development (CD6), Universitat Politècnica de Catalunya (UPC) (Rambla Sant Nebridi 10, 08222-Terrassa, Barcelona, Spain) This email address is being protected from spambots. You need JavaScript enabled to view it.

Meritxell Vilaseca completed her BSc Degree in Physics at the Autonomous University of
Barcelona in 2000 and received a PhD in Optical Engineering from the UPC in 2005. She completed her Degree in Optics and Optometry at the UPC in 1996. She is currently an Associate Professor at the UPC and a researcher at the Centre for Sensors, Instruments and Systems Development (CD6). Her work focuses on optical engineering, especially in colour and spectral imaging, industrial colorimetry, visual optics and biophotonics. She has authored more than 40 papers, more than 100 communications in international and national conferences and 4 patents. She has been involved in more than 60 research projects from public agencies and private companies, 4 of them as a leader.

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furioMarc Furió. Institut Català de Paleontologia M. Crusafont, Universitat Autònoma de Barcelona (UAB) (Edifici ICP, c/ de les Columnes s/n, Campus de la UAB, 08193-Cerdanyola del Vallès, Barcelona, Spain) This email address is being protected from spambots. You need JavaScript enabled to view it.

Marc Furió graduated in Geology and completed his PhD in Palaeontology at the Autonomous University of Barcelona. He is researcher at the Catalan Institute of Palaeontology since 2007. His main topics are the palaeobiology, biostratigraphy and taxonomy of Neogene and Quaternary insectivores, to which he has dedicated all his scientific life. Apart from this strict field of research, he organizes and participates in several activities addressed to all kind of audiences to popularize palaeontology.

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burgosFrancisco J. Burgos-Fernández. Centre for Sensors, Instruments and Systems Development (CD6), Universitat Politècnica de Catalunya (UPC) (Rambla Sant Nebridi 10, 08222-Terrassa, Barcelona, Spain) This email address is being protected from spambots. You need JavaScript enabled to view it.

He is a PhD student in Optical Engineering at the Centre for Sensors, Instruments and Systems Development (CD6) of the Technical University of Catalonia (UPC). He received his degree in Optics and Optometry (2008) and his MSc in Photonics (2011) from the Technical University of Catalonia. He has worked in research projects related to the ocular optical quality, radiometry, photometry and colorimetric and spectral analysis. His PhD is focused on LED-based hyperspectral systems.

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pujolJaume Pujol. Centre for Sensors, Instruments and Systems Development (CD6), Universitat Politècnica de Catalunya (UPC) (Rambla Sant Nebridi 10, 08222-Terrassa, Barcelona, Spain) This email address is being protected from spambots. You need JavaScript enabled to view it.

He received his BSc and PhD degrees in Physics from the Autonomous University of Barcelona in 1981 and 1990, respectively. Since 1984 he teaches vision sciences and colour at the Technical University of Catalonia (UPC). He is the author of more than 80 papers, more than 175 communications in international and national conferences, 4 books in physiological optics and color, holds 11 patents and has supervised 10 PhD theses. His main current research interests are the colour and spectral imaging technology and visual optics and biophotonics. He has been responsible for more than 50 research projects for public agencies and private companies, and organizer of several scientific conferences. He has been director of the Optics and Optometry Department (1994-2000) and Center for Sensors, Instruments, and Systems Development (CD6) (1997-2009), president of the Spanish Color Committee (2007-2010) and the main entrepreneur of the spin-off company VISIOMETRICS S.L. Presently, he is the scientific director of the Davalor Research Center (DRC) since its creation.

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