Automated plankton image analysis using convolutional neural networks

Jessica Y. Luo, Jean Olivier Irisson, Benjamin Graham, Cedric Guigand, Amin Sarafraz, Christopher Mader, Robert K. Cowen

Research output: Contribution to journalArticlepeer-review

42 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)814-827
Number of pages14
JournalLimnology and Oceanography: Methods
Issue number12
StatePublished - Dec 2018
Externally publishedYes

ASJC Scopus subject areas

  • Ocean Engineering


Dive into the research topics of 'Automated plankton image analysis using convolutional neural networks'. Together they form a unique fingerprint.

Cite this