Georgia Coastal Ecosystems LTER Data Set Details

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GCE-LTER Data Set Summary

Accession:

PLT-GCED-2008

Research Theme:

Plant Ecology (Directed Study)

Contributors:

Steven C. Pennings, Brian Hopkinson

Title:

Estimation of Abundance and Distribution of Salt Marsh Plants from Images Using Deep Learning

Abstract:

Recent advances in computer vision and machine learning, most notably deep convolutional neural networks (CNNs), are exploited to identify and localize various plant species in salt marsh images. Three different approaches are explored that provide estimations of abundance and spatial distribution at varying levels of granularity in terms of spatial resolution. In the coarsest-grained approach, CNNs are tasked with identifying which of six plant species are present/absent in large patches within the salt marsh images. CNNs with diverse topological properties and attention mechanisms are shown capable of providing accurate estimations with > 90% precision and recall in the case of the more abundant plant species whereas the performance of the CNNs is observed to decline in the case of less common plant species. Estimation of percent cover of each plant species is performed at a finer spatial resolution, where smaller image patches are extracted and the CNNs tasked with identifying the plant species or substrate at the center of the image patch. In an ecological setting, several image patches (~100) are extracted and classified using this approach to estimate the percent cover of the various plant species in the image. For the percent cover estimation task, the CNNs are observed to exhibit a performance profile similar to that for the presence/absence estimation task, but with an ~ 5-10% reduction in precision and recall. Finally, estimation of the spatial distribution of the various plant species is performed via semantic segmentation of the input images at the finest level of granularity in terms of spatial resolution. The Deeplab-V3 semantic segmentation architecture is observed to provide very accurate estimations for abundant plant species; however, a significant degradation in performance is observed in the case of less abundant plant species and, in extreme cases, rare plant classes are seen to be ignored entirely. Overall, a clear trade-off is observed between the CNN estimation quality and the spatial resolution of the underlying estimation thereby offering guidance for ecological applications of CNN-based approaches to automated plant identification and localization in salt marsh images.

DOI:

10.6073/pasta/963ef9875283a6e4da18ef0827839b13

Key Words:

Batis maritima, Borrichia frutescens, GCE6, Juncus roemerianus, Limonium carolinianum, marshes, plant cover, Plant Monitoring, remote sensing, Salicornia virginica, Sapelo Island, Spartina alterniflora

LTER Core Area:

Population Studies

Research Themes:

Plant Ecology

Study Period:

14-May-2014 to 15-Jun-2014

Study Sites:

GCE6 -- Dean Creek, Sapelo Island, Georgia, USA

» Download Geographic Coverage: Google Earth

Species References:

Batis maritima, Borrichia frutescens, Juncus roemerianus, Limonium carolinianum, Salicornia virginica, Spartina alterniflora

Publications:

Parashar, J., Bhandarkar, S.M., Simon, J., Hopkinson, B. and Pennings, S.C. 2021. Estimation of Abundance and Distribution of Salt Marsh Plants from Images Using Deep Learning. Proceedings of the 25th International Conference on Pattern Recognition (ICPR). (DOI: 10.1109/ICPR48806.2021.9412264)

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