Abstract
In this report, we present a 3D simulator for the numerical validation of segmentation algorithms for seedling in soil from X-ray or MRI. A 3D simulator of root in elongation is coupled to a simulator of the image acquisition to generate images of simulated seedling associated with a known synthetic ground truth. We detail how acquisition parameters of the seedling and parameters of the imaging systems are estimated and combined to produce realistic images. The resulting simulator is available on line to open the possibility of segmentation challenges with in silico validation based on unlimited number of seedling.
Chapter PDF
References
Mairhofer, S., Zappala, S., Tracy, S., Sturrock, C., Bennett, M., Mooney, S., Pridemore, T.: Rootrak: automated recovery of 3D plant root architecture in soil with X-Ray micro computed tomography using visual tracking. Plant Physiology 158, 561–569 (2012)
Zappala, S., Mairhofer, S., Tracy, S., Sturrock, C., Bennett, M., Pridemore, T., Mooney, S.: Quantifying the effect of soil moisture content on segmenting root system architecture in X-Ray micro-Computed Tomography. Plant and Soil (2013)
Mairhofer, S., Zappala, S., Sturrock, C., Bennett, M., Mooney, S., Pridemore, T. Recovering complete plant root system architectures from soil via X-Ray Micro-Computed Tomography. Plant Physiology 359 (2013)
Schultz, H., Postma, J., Dusschoten, D., Scharr, H., Behnke, S.: Plant root system from MRI images. Computer Vision, Imaging and Computer Graphics 359, 411–425 (2013)
Glatard, T., Lartizien, C., Gibaud, B.: Ferreira da Silva, G., Cervenansky, F., Alessandrini, M., Benoit Cattin, H., Bernard, O., Camarasu Pop, S.: A virtual imaging platform for multi-modality medical image simulation. IEEE Transactions on Medical Imaging 32, 110–118 (2013)
Benoit, L., Rousseau, D., Belin, E., Demilly, D., Chapeau-Blondeau, F.: Simulation of image acquisition in machine vision dedicated to seedling elongation to validate image processing root segmentation algorithms. Computers and Electronics in Agriculture 104, 84–92 (2014)
Popova, L., Russino, A., Ascrizzi, A., Mazzolai, B.: Analysis of movement in primary maize roots. Biologia 67, 517–524 (2012)
Leitner, D., Klepsch, S., Bodner, G., Schnepf, A.: A dynamic root system growth model based on L-systems. Plant Soil 332, 177–192 (2010)
http://lisabiblio.univ-angers.fr/PHENOTIC/telechargements.html
Jahnke, S., Menzel, M.I., Van Dusschoten, D., Roeb, G.W., Bühler, J., Minwuyelet, S., Blümler, P., Temperton, V.M., Hombach, T., Streun, M., Beer, S., Khodaverdi, M., Ziemons, K., Coenen, H.H., Schurr, U.: Combined MRI-PET dissects dynamic changes in plant structures and functions. Plant Journal 59, 634–644 (2009)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Benoit, L. et al. (2015). 3D Multimodal Simulation of Image Acquisition by X-Ray and MRI for Validation of Seedling Measurements with Segmentation Algorithms. In: Agapito, L., Bronstein, M., Rother, C. (eds) Computer Vision - ECCV 2014 Workshops. ECCV 2014. Lecture Notes in Computer Science(), vol 8928. Springer, Cham. https://doi.org/10.1007/978-3-319-16220-1_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-16220-1_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-16219-5
Online ISBN: 978-3-319-16220-1
eBook Packages: Computer ScienceComputer Science (R0)