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A new method for non-invasive biomass determination based on stereo photogrammetry

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Abstract

A novel, non-destructive method for the biomass estimation of biological samples on culture dishes was developed. To achieve this, a photogrammetric system, which consists of a digital single-lens reflex camera (DSLR), an illuminated platform where the culture dishes are positioned and an Arduino board which controls the capturing process, was constructed. The camera was mounted on a holder which set the camera at different title angles and the platform rotated, to capture images from different directions. A software, based on stereo photogrammetry, was developed for the three-dimensional (3D) reconstruction of the samples. The proof-of-concept was demonstrated in a series of experiments with plant tissue cultures and specifically with calli cultures of Salvia fruticosa and Ocimum basilicum. For a period of 14 days images of these cultures were acquired and 3D-reconstructions and volumetric data were obtained. The volumetric data correlated well with the experimental measurements and made the calculation of the specific growth rate, µ max, possible. The µ max value for S. fruticosa samples was 0.14 day−1 and for O. basilicum 0.16 day−1. The developed method demonstrated the high potential of this photogrammetric approach in the biological sciences.

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References

  1. Kaur G, Sethi P (2012) A novel methodology for automatic bacterial colony counter. Int J Comput Appl 49(15):21–26

    Google Scholar 

  2. Shen W, Zhao J, Wu Y, Zheng H (2010) Experimental study for automatic colony counting system based on image processing. In: IEEE, p V6-612–V6-615. http://ieeexplore.ieee.org/document/5620851/. Accessed 30 Mar 2017

  3. Ates H, Gerek ON (2009) An image-processing based automated bacteria colony counter. In: IEEE, p 18–23. http://ieeexplore.ieee.org/document/5291926/. Accessed 30 Mar 2017

  4. Chiang P-J, Tseng M-J, He Z-S, Li C-H (2015) Automated counting of bacterial colonies by image analysis. J Microbiol Methods 108:74–82

    Article  Google Scholar 

  5. Clarke ML, Burton RL, Hill AN, Litorja M, Nahm MH, Hwang J (2010) Low-cost, high-throughput, automated counting of bacterial colonies. Cytometry A 77A(8):790–797

    Article  Google Scholar 

  6. Geissmann Q (2013) OpenCFU, a new free and open-source software to count cell colonies and other circular objects. PLoS One 8(2):e54072

    Article  CAS  Google Scholar 

  7. Men H, Wu Y, Li X, Kou Z, Shanrang Y (2008) Counting method of heterotrophic bacteria based on image processing. In: IEEE, p 1238–41. http://ieeexplore.ieee.org/document/4670959/. Accessed 30 Mar 2017

  8. Mairhofer S, Zappala S, Tracy SR, Sturrock C, Bennett M, Mooney SJ et al (2012) RooTrak: automated recovery of three-dimensional plant root architecture in soil from x-ray microcomputed tomography images using visual tracking. Plant Physiol 158(2):561–569

    Article  CAS  Google Scholar 

  9. Borisjuk L, Rolletschek H, Neuberger T (2012) Surveying the plant’s world by magnetic resonance imaging: surveying the plant’s world by MRI. Plant J 70(1):129–146

    Article  CAS  Google Scholar 

  10. Jahnke S, Menzel MI, van Dusschoten D, Roeb GW, Bühler J, Minwuyelet S et al (2009) Combined MRI-PET dissects dynamic changes in plant structures and functions. Plant J 59(4):634–644

    Article  CAS  Google Scholar 

  11. Fang S, Yan X, Liao H (2009) 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research: 3D dynamic modeling of root architecture in situ. Plant J 60(6):1096–1108

    Article  CAS  Google Scholar 

  12. Dornbusch T, Lorrain S, Kuznetsov D, Fortier A, Liechti R, Xenarios I et al (2012) Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis—a novel phenotyping approach using laser scanning. Funct Plant Biol 39(11):860

    Article  Google Scholar 

  13. Calders K, Newnham G, Burt A, Murphy S, Raumonen P, Herold M et al (2015) Nondestructive estimates of above-ground biomass using terrestrial laser scanning. Methods Ecol Evol 6(2):198–208

    Article  Google Scholar 

  14. Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil J-L et al (2010) Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat Methods 7(7):547–553

    Article  CAS  Google Scholar 

  15. Biskup B, Scharr H, Schurr U, Rascher U (2007) A stereo imaging system for measuring structural parameters of plant canopies. Plant Cell Environ 30(10):1299–1308

    Article  Google Scholar 

  16. Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ et al (2011) Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 156(2):455–465

    Article  CAS  Google Scholar 

  17. Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J et al (2010) Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems. Plant Physiol 152(3):1148–1157

    Article  CAS  Google Scholar 

  18. Lati RN, Filin S, Eizenberg H (2013) Estimating plant growth parameters using an energy minimization-based stereovision model. Comput Electron Agric 98:260–271

    Article  Google Scholar 

  19. Nguyen C, Lovell D, Oberprieler R, Jennings D, Adcock M, Gates-Stuart E et al (2013) Virtual 3D models of insects for accelerated quarantine control. In: IEEE, p. 161–7. http://ieeexplore.ieee.org/document/6755892/. Accessed 30 Mar 2017

  20. Nguyen CV, Lovell DR, Adcock M, La Salle J (2014) Capturing natural-colour 3D models of insects for species discovery and diagnostics. PLoS One 9(4):e94346

    Article  Google Scholar 

  21. Galantucci LM, Pesce M, Lavecchia F (2016) A powerful scanning methodology for 3D measurements of small parts with complex surfaces and sub millimeter-sized features, based on close range photogrammetry. Precis Eng 43:211–219

    Article  Google Scholar 

  22. Galantucci LM, Pesce M, Lavecchia F (2015) A stereo photogrammetry scanning methodology, for precise and accurate 3D digitization of small parts with sub-millimeter sized features. CIRP Ann Manuf Technol 64(1):507–510

    Article  Google Scholar 

  23. Lenk F, Sürmann A, Oberthür P, Schneider M, Steingroewer J, Bley T (2014) Modeling hairy root tissue growth in in vitro environments using an agent-based, structured growth model. Bioprocess Biosyst Eng 37(6):1173–1184

    Article  CAS  Google Scholar 

  24. Andújar D, Fernández-Quintanilla C, Dorado J (2015) Matching the best viewing angle in depth cameras for biomass estimation based on poplar seedling geometry. Sensors 15(6):12999–13011

    Article  Google Scholar 

  25. Nguyen TT, Townsley SDavidC, Brad T, Carriedo, Leonela, Maloof JN, Sinha N (2016) In-field plant phenotyping using multi-view reconstruction: an investigation in eggplant. In: ResearchGate [Internet]. St. Louis, Missouri, USA. https://www.researchgate.net/publication/306959617_In-field_Plant_Phenotyping_using_Multi-view_Reconstruction_An_Investigation_in_Eggplant. Accessed 31 Mar 2017

  26. Haas C, Hengelhaupt K-C, Kümmritz S, Bley T, Pavlov A, Steingroewer J (2014) Salvia suspension cultures as production systems for oleanolic and ursolic acid. Acta Physiol Plant 36(8):2137–2147

    Article  CAS  Google Scholar 

  27. Linsmaier EM, Skoog F (1965) Organic growth factor requirements of tobacco tissue cultures. Physiol Plant 18(1):100–127

    Article  CAS  Google Scholar 

  28. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15(3):473–497

    Article  CAS  Google Scholar 

  29. Elnima EE (2015) A solution for exterior and relative orientation in photogrammetry, a genetic evolution approach. J King Saud Univ Eng Sci 27(1):108–113

    Google Scholar 

  30. Bradski G The OpenCV library [Internet]. Dr. Dobb’s. http://www.drdobbs.com/open-source/the-opencv-library/184404319. Accessed 30 Mar 2017

  31. Rusu RB, Cousins S (2011) 3D is here: point cloud library (PCL). In: IEEE, p 1–4. http://ieeexplore.ieee.org/document/5980567/. Accessed 30 Mar 2017

  32. Hirschmuller H (2005) Accurate and efficient stereo processing by semi-global matching and mutual information. In: IEEE [cited 2017 Mar 30], p 807–14. http://ieeexplore.ieee.org/document/1467526/

  33. Bradski GR, Kaehler A (2011) Learning OpenCV: [computer vision with the OpenCV library], 1st edn., [Nachdr.]. O’Reilly, Beijing, (Software that sees)

    Google Scholar 

  34. Szeliski R (2011) Computer Vision [Internet]. Springer, London. (Texts in Computer Science). http://link.springer.com/10.1007/978-1-84882-935-0. Accessed 30 Mar 2017

  35. Point Cloud Library (PCL) (2017) PCL API Documentation [Internet]. http://docs.pointclouds.org/trunk/. Accessed 30 Mar 2017

  36. Hussein S, Halmi MIE, Kiong ALP (2016) Modelling the growth kinetics of callus cultures from the seedling of Jatropha curcas L. according to the modified Gompertz model. J Biochem Microbiol Biotechnol 4(1):20–23

    Google Scholar 

  37. Werner S, Greulich J, Geipel K, Steingroewer J, Bley T, Eibl D (2014) Mass propagation of Helianthus annuus suspension cells in orbitally shaken bioreactors: improved growth rate in single-use bag bioreactors: xxx. Eng Life Sci 14(6):676–684

    Article  CAS  Google Scholar 

  38. Dalton CC (1983) Chlorophyll production in fed-batch cultures of Ocimum basilicum (sweet basil). Plant Sci Lett 32(3):263–270

    Article  CAS  Google Scholar 

  39. Caplin SM (1963) Effect of initial size on growth of plant tissue cultures. Am J Bot 50(1):91

    Article  Google Scholar 

  40. Heo SW, Ryu BG, Nam K, Kim W, Yang JW (2015) Simultaneous treatment of food-waste recycling wastewater and cultivation of Tetraselmis suecica for biodiesel production. Bioprocess Biosyst Eng 38(7):1393–1398

    Article  CAS  Google Scholar 

  41. Vogel M, Boschke E, Bley T, Lenk F (2015) PetriJet platform technology: an automated platform for culture dish handling and monitoring of the contents. J Lab Autom 20(4):447–456

    Article  Google Scholar 

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Acknowledgements

We would like to thank the research group Plant- and Algaebiotechnology of the Chair of Bioprocess Engineering at the Technische Universität Dresden for the provision of the plant tissue cultures of S. fruticosa and O. basilicum. Funding was provided by The Saxon Ministry of Science and the Fine Arts (Grant no.: 100239260).

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Authors and Affiliations

  1. Chair of Bioprocess Engineering, Faculty of Mechanical Science and Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, Dresden, Germany

    Maria Syngelaki, Patrick Oberthuer, Thomas Bley & Felix Lenk

  2. Chair of Photogrammetry, Department of Geosciences, Faculty of Environmental Sciences, Institute of Photogrammetry and Remote Sensing, Technische Universität Dresden, Dresden, Germany

    Matthias Hardner & Danilo Schneider

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  1. Maria Syngelaki
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  2. Matthias Hardner
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  3. Patrick Oberthuer
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  4. Thomas Bley
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  5. Danilo Schneider
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  6. Felix Lenk
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Correspondence to Felix Lenk.

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Syngelaki, M., Hardner, M., Oberthuer, P. et al. A new method for non-invasive biomass determination based on stereo photogrammetry. Bioprocess Biosyst Eng 41, 369–380 (2018). https://doi.org/10.1007/s00449-017-1871-2

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