Spectral mixture analysis for surveillance of harmful algal blooms (SMASH): A field-, laboratory-, and satellite-based approach to identifying cyanobacteria genera from remotely sensed data

Remote Sensing of Environment
By: , and 



Algal blooms around the world are increasing in frequency and severity, often with the possibility of adverse effects on human and ecosystem health. The health and economic impacts associated with harmful algal blooms, or HABs, provide compelling rationale for developing new methods for monitoring these events via remote sensing. Although concentrations of chlorophyll-a and key pigments like phycocyanin are routinely estimated from satellite images and used to infer algal or cyanobacterial cell counts, current methods are unable to provide information on the taxonomic composition of a bloom. This study introduced a new approach capable of differentiating among genera based on their reflectance characteristics: Spectral Mixture Analysis for Surveillance of HABs, or SMASH. The foundation of SMASH is a multiple endmember spectral mixture analysis (MESMA) algorithm that takes a library of cyanobacteria endmembers and a hyperspectral image as input and estimates the fractional abundance of each genus, plus water, on a per-pixel basis. Importantly, we assume that the water column consists of only pure water and cyanobacteria, implying that our linear spectral unmixing models do not account for other optically active constituents such as suspended sediment and colored dissolved organic matter (CDOM). We used reflectance spectra for 12 genera measured under a microscope to populate an algal spectral library and applied the SMASH workflow to satellite images from four waterbodies across the United States. Normalized spectral separability scores indicated that the 12 genera were distinct from one another and the MESMA algorithm reproduced known input fractions for simulated mixtures that included all pairwise combinations of genera and water. We used Upper Klamath Lake as an example to illustrate data products generated via SMASH: maps of the normalized difference chlorophyll index and cyanobacterial index, a MESMA-based classification of algal genera, fraction images for each endmember, and a root mean square error (RMSE) image that summarizes uncertainty. For Upper Klamath Lake, these outputs highlighted a complex algal bloom featuring several genera, primarily Aphanizomenon, and intricate spatial patterns associated with gyres. The maximum RMSE constraint imposed on the MESMA algorithm provided a means of avoiding false positive detection of genera not present in a waterbody but must not be set so low as to leave much of an image unclassified in cases where genera included in the library are present. Comparison of endmember fractions with relative biovolumes calculated from field samples indicated that taxonomic information from SMASH was consistent with field observations. For example, the algorithm successfully identified Microcystis in Owasco Lake but avoided misclassifying Asterionella, a genus not yet included in our library, in Detroit Lake. This proof-of-concept investigation demonstrates the potential of SMASH to enhance our understanding of algal blooms, particularly with respect to their spatial and temporal dynamics.

Study Area

Publication type Article
Publication Subtype Journal Article
Title Spectral mixture analysis for surveillance of harmful algal blooms (SMASH): A field-, laboratory-, and satellite-based approach to identifying cyanobacteria genera from remotely sensed data
Series title Remote Sensing of Environment
DOI 10.1016/j.rse.2022.113089
Volume 279
Year Published 2022
Language English
Publisher Elsevier
Contributing office(s) Idaho Water Science Center, National Research Program - Eastern Branch, New York Water Science Center, Oregon Water Science Center, Texas Water Science Center, National Civil Applications Center, WMA - Integrated Modeling and Prediction Division, Florence Bascom Geoscience Center
Description 113089, 19 p.
Country United States
State New York, Oregon, Texas
City Dallas, Forth Worth
Other Geospatial Detroit Lake, Finger Lakes, Grapevine Lake, Owasco Lake, Santiam River, Trinity River Basin, Upper Klamath Lake
Google Analytic Metrics Metrics page
Additional publication details