Automated species-level identification of planktic foraminifera using convolutional neural networks, with comparison to human performance

Journal Article · 24 January 2019 · Marine Micropaleontology

DOI: https://doi.org/10.1016/j.marmicro.2019.01.005 · OSTI ID:1611377

Mitra, Ritayan ^[1]; Marchitto, Thomas M. ^[2]; Ge, Qian ^[3]; Zhong, Boxuan ^[3]; Kanakiya, Bhargav ^[3]; Cook, Mea S. ^[4]; Fehrenbacher, Jennifer S. ^[5]; Ortiz, Joseph D. ^[6]; Tripati, Aradhna ^[7]; Lobaton, Edgar ^[3]

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1. Univ. of Colorado, Boulder, CO (United States); Indian Inst. of Technology (IIT) Bombay, Mumbai (India); DOE/OSTI
2. Univ. of Colorado, Boulder, CO (United States)
3. North Carolina State University, Raleigh, NC (United States)
4. Williams College, Williamstown, MA (United States)
5. Oregon State Univ., Corvallis, OR (United States)
6. Kent State Univ., Kent, OH (United States)
7. Univ. of California, Los Angeles, CA (United States)

Picking foraminifera from sediment samples is an essential, but repetitive and low-reward task that is well-suited for automation. The first step toward building a picking robot is the development of an automated identification system. We use machine learning techniques to train convolutional neural networks (CNNs) to identify six species of extant planktic foraminifera that are widely used by paleoceanographers, and to distinguish the six species from other taxa. We employ CNNs that were previously built and trained for image classification. Foraminiferal training and identification use reflected light microscope digital images taken at 16 different illumination angles using a light-emitting diode (LED) ring. Overall machine accuracy, as a combination of precision and recall, is better than 80% even with limited training. We compare machine performance to that of human pickers (six experts and five novices) by tasking each with the identification of 540 specimens based on images. Experts achieved comparable precision but poorer recall relative to the machine, with an average accuracy of 63%. Novices scored lower than experts on both precision and recall, for an overall accuracy of 53%. The machine achieved fairly uniform performance across the six species, while participants' scores were strongly species-dependent, commensurate with their past experience and expertise. The machine was also less sensitive to specimen orientation (umbilical versus spiral views) than the humans. Finally, these results demonstrate that our approach can provide a versatile ‘brain’ for an eventual automated robotic picking system.

• Research Organization: Univ. of California, Los Angeles, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC); National Science Foundation (NSF)
• Grant/Contract Number: SC0010288
• OSTI ID: 1611377
• Journal Information: Marine Micropaleontology, Journal Name: Marine Micropaleontology Journal Issue: C Vol. 147; ISSN 0377-8398
• Publisher: ElsevierCopyright Statement
• Country of Publication: United States
• Language: English