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Automated plankton image analysis using convolutional neural networks
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Luo, Jessica Y., Irisson, Jean-Olivier, Graham, Benjamin, Guigand, Cedric, Sarafraz, Amin, Mader, Christopher and Cowen, Robert K. (2018) Automated plankton image analysis using convolutional neural networks. Limnology and Oceanography: Methods, 16 (12). doi:10.1002/lom3.10285 ISSN 1541-5856.
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Official URL: https://doi.org/10.1002/lom3.10285
Abstract
The rise of in situ plankton imaging systems, particularly high-volume imagers such as the In Situ Ichthyoplankton Imaging System, has increased the need for fast processing and accurate classification tools that can identify a high diversity of organisms and nonliving particles of biological origin. Previous methods for automated classification have yielded moderate results that either can resolve few groups at high accuracy or many groups at relatively low accuracy. However, with the advent of new deep learning tools such as convolutional neural networks (CNNs), the automated identification of plankton images can be vastly improved. Here, we describe an image processing procedure that includes preprocessing, segmentation, classification, and postprocessing for the accurate identification of 108 classes of plankton using spatially sparse CNNs. Following a filtering process to remove images with low classification scores, a fully random evaluation of the classification showed that average precision was 84% and recall was 40% for all groups. Reliably classifying rare biological classes was difficult, so after excluding the 12 rarest taxa, classification accuracy for the remaining biological groups became > 90%. This method provides proof of concept for the effectiveness of an automated classification scheme using deep-learning methods, which can be applied to a range of plankton or biological imaging systems, with the eventual application in a variety of ecological monitoring and fisheries management contexts.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history T Technology > TA Engineering (General). Civil engineering (General) |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Statistics | |||||||||
| SWORD Depositor: | Library Publications Router | |||||||||
| Library of Congress Subject Headings (LCSH): | Plankton, Plankton -- Classification -- Molecular aspects, Imaging systems in biology, Image processing | |||||||||
| Journal or Publication Title: | Limnology and Oceanography: Methods | |||||||||
| Publisher: | Wiley | |||||||||
| ISSN: | 1541-5856 | |||||||||
| Official Date: | 7 December 2018 | |||||||||
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| Volume: | 16 | |||||||||
| Number: | 12 | |||||||||
| DOI: | 10.1002/lom3.10285 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Restricted or Subscription Access | |||||||||
| RIOXX Funder/Project Grant: |
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