Skip to main content

Automated Identification of Herbarium Specimens at Different Taxonomic Levels

  • Chapter
  • First Online:
Book cover Multimedia Tools and Applications for Environmental & Biodiversity Informatics

Abstract

The estimated number of flowering plant species on Earth is around 400,000. In order to classify all known species via automated image-based approaches, current datasets of plant images will have to become considerably larger. To achieve this, some authors have explored the possibility of using herbarium sheet images. As the plant datasets grow and start reaching the tens of thousands of classes, unbalanced datasets become a hard problem. This causes models to be inaccurate for certain species due to intra- and inter-specific similarities. Additionally, automatic plant identification is intrinsically hierarchical. In order to tackle this problem of unbalanced datasets, we need ways to classify and calculate the loss of the model by taking into account the taxonomy, for example, by grouping species at higher taxon levels. In this research we compare several architectures for automatic plant identification, taking into account the plant taxonomy to classify not only at the species level, but also at higher levels, such as genus and family.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover + eBook
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
  • Available as EPUB and PDF
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    https://www.idigbio.org/.

References

  1. Matsunaga, A., Thompson, A., Figueiredo, R. J., Germain-Aubrey, C. C., Collins, M., Beaman, R. S., …& Fortes, J. A. (2013, October). A computational-and storage-cloud for integration of biodiversity collections. In eScience (eScience), 2013 IEEE 9th International Conference on (pp. 78–87). IEEE.

    Google Scholar 

  2. Page, L. M., MacFadden, B. J., Fortes, J. A., Soltis, P. S., & Riccardi, G. (2015). Digitization of biodiversity collections reveals biggest data on biodiversity. BioScience, 65(9), 841–842.

    Article  Google Scholar 

  3. E. Mata-Montero and J. Carranza-Rojas, Automated Plant Species Identification: Challenges and Opportunities. Springer International Publishing, 2016, pp. 26–36.

    Chapter  Google Scholar 

  4. J. Carranza-Rojas, H. Goeau, P. Bonnet, E. Mata-Montero, and A. Joly, “Going deeper in the automated identification of herbarium specimens,” BMC Evolutionary Biology, vol. 17, no. 1, p. 181, Aug 2017.

    Google Scholar 

  5. D. P. Bebber, M. A. Carine, J. R. Wood, A. H. Wortley, D. J. Harris, G. T. Prance, G. Davidse, J. Paige, T. D. Pennington, N. K. Robson et al., “Herbaria are a major frontier for species discovery,” Proceedings of the National Academy of Sciences, vol. 107, no. 51, pp. 22 169–22 171, 2010.

    Article  Google Scholar 

  6. A. Joly, H. Goëau, H. Glotin, C. Spampinato, P. Bonnet, W.-P. Vellinga, J. Champ, R. Planqué, S. Palazzo, and H. Müller, LifeCLEF 2016: Multimedia Life Species Identification Challenges. Cham: Springer International Publishing, 2016, pp. 286–310.

    Google Scholar 

  7. N. Kumar, P. N. Belhumeur, A. Biswas, D. W. Jacobs, W. J. Kress, I. C. Lopez, and J. V. Soares, “Leafsnap: A computer vision system for automatic plant species identification,” in Computer Vision–ECCV 2012. Springer, 2012, pp. 502–516.

    Chapter  Google Scholar 

  8. A. Joly, P. Bonnet, H. Goëau, J. Barbe, S. Selmi, J. Champ, S. Dufour-Kowalski, A. Affouard, J. Carré, J.-F. Molino et al., “A look inside the pl@ntnet experience,” Multimedia Systems, vol. 22, no. 6, pp. 751–766, 2016.

    Article  Google Scholar 

  9. C. N. Silla and A. A. Freitas, “A survey of hierarchical classification across different application domains,” Data Min Knowl Disc, vol. 22, pp. 31–72, 2011.

    Article  MathSciNet  Google Scholar 

  10. F. Wu, J. Zhang, and V. Honavar, “Learning classifiers using hierarchically structured class taxonomies,” in Proceedings of the 6th International Conference on Abstraction, Reformulation and Approximation, ser. SARA’05. Berlin, Heidelberg: Springer-Verlag, 2005, pp. 313–320. [Online]. Available: http://dx.doi.org/10.1007/11527862_24

    Google Scholar 

  11. B. Shahbaba and R. M. Neal, “Improving classification when a class hierarchy is available using a hierarchy-based prior,” Bayesian Anal., vol. 2, no. 1, pp. 221–237, 03 2007. [Online]. Available: http://dx.doi.org/10.1214/07-BA209

  12. Z. Yan, H. Zhang, R. Piramuthu, V. Jagadeesh, D. DeCoste, W. Di, and Y. Yu, “Hd-cnn: Hierarchical deep convolutional neural network for large scale visual recognition,” in ICCV’15: Proc. IEEE 15th International Conf. on Computer Vision, 2015.

    Google Scholar 

  13. J. Carranza-Rojas, A. A.J.Joly, P. Bonnet, H.H.G. Goëau, and E. Mata-Montero, “Automated herbarium specimen identification using deep learning,” Biodiversity Information Science and Standards, vol. 1, p. e20302, 2017.

    Article  Google Scholar 

  14. H. Goëau, P. Bonnet, and A. Joly, “LifeCLEF Plant Identification Task 2015,” in CLEF: Conference and Labs of the Evaluation forum, ser. CLEF2015 Working notes, CEUR-WS, Ed., vol. 1391, Toulouse, France, Sep. 2015. [Online]. Available: https://hal.inria.fr/hal-01182795

  15. O. Russakovsky, J. Deng, H. Su, J. Krause, S. Satheesh, S. Ma, Z. Huang, A. Karpathy, A. Khosla, M. Bernstein, A. C. Berg, and L. Fei-Fei, “ImageNet Large Scale Visual Recognition Challenge,” International Journal of Computer Vision (IJCV), vol. 115, no. 3, pp. 211–252, 2015.

    Article  MathSciNet  Google Scholar 

  16. S. Ioffe and C. Szegedy, “Batch normalization: Accelerating deep network training by reducing internal covariate shift,” CoRR, vol. abs/1502.03167, 2015. [Online]. Available: http://arxiv.org/abs/1502.03167

  17. S. Dieleman, J. Schlüter, C. Raffel, E. Olson, S. K. Sønderby, D. Nouri et al., “Lasagne: First release.” Aug. 2015. [Online]. Available: http://dx.doi.org/10.5281/zenodo.27878

  18. Theano Development Team, “Theano: A Python framework for fast computation of mathematical expressions,” arXiv e-prints, vol. abs/1605.02688, May 2016. [Online]. Available: http://arxiv.org/abs/1605.02688

  19. C. Szegedy, W. Liu, Y. Jia, P. Sermanet, S. Reed, D. Anguelov, D. Erhan, V. Vanhoucke, and A. Rabinovich, “Going deeper with convolutions,” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 07-12-June, pp. 1–9, 2015.

    Google Scholar 

  20. I. J. Goodfellow, Y. Bulatov, J. Ibarz, S. Arnoud, and V. Shet, “Multi-digit number recognition from street view imagery using deep convolutional neural networks,” 2014. [Online]. Available: https://arxiv.org/pdf/1312.6082.pdf

Download references

Acknowledgements

Special thanks to the Colaboratorio Nacional de Computación Avanzada (CCNA) in Costa Rica for sharing their Tesla K40-based cluster and providing technical support for this research. We also thank the Costa Rica Institute of Technology for the financial support for this research.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jose Carranza-Rojas .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Carranza-Rojas, J., Joly, A., Goëau, H., Mata-Montero, E., Bonnet, P. (2018). Automated Identification of Herbarium Specimens at Different Taxonomic Levels. In: Joly, A., Vrochidis, S., Karatzas, K., Karppinen, A., Bonnet, P. (eds) Multimedia Tools and Applications for Environmental & Biodiversity Informatics. Multimedia Systems and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-76445-0_9

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-76445-0_9

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-76444-3

  • Online ISBN: 978-3-319-76445-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics