Phytoplankton Community Composition in the Surface Ocean: Methods for Detection using Optical Measurements, Pigment Concentrations, and Flow Cytometry

Phytoplankton are microscopic photoautotrophs living in the surface ocean waters and help support all life on earth via photosynthetic production of oxygen. Thousands of species make up the bulk phytoplankton community, and the spatial and temporal distribution of different types of phytoplankton has relevance for many ocean ecosystem questions including marine food web dynamics, and carbon flux and sequestration. Methods to detect phytoplankton community composition (PCC) on the vast scale of the global ocean require estimates of PCC from remote platforms, namely earth-observing satellites. The use of satellite data to observe and interpret PCC in the surface ocean requires significant effort to develop and evaluate algorithms based on measurements made in situ; the work of this thesis contributes to that effort. Information from both global and regional (North Atlantic Ocean) datasets is applied to develop methods to estimate phytoplankton pigment concentrations, phytoplankton size classes, and diatom carbon concentrations. Optical spectra, specifically hyperspectral remote-sensing reflectance, are used in the algorithm for estimating phytoplankton pigments, which resolves the concentrations of three pigments and one pigment group (chlorophylls a, b, c, and photoprotective carotenoids). This result has implications for use with hyperspectral ocean color data measured by satellite. A novel dataset of open-ocean image-in-flow cytometry is used to evaluate and improve a commonly applied phytoplankton size class algorithm, as well as to calculate diatom carbon and develop a model to map diatom carbon using environmental parameters as model input. Biases and uncertainties in the size class algorithm are reduced by our method relative to previously published work for all three size classes (pico-, nano-, and microplankton). Diatom carbon measurements from quantitative cell imagery elucidate the variability of diatom biomass as function of chlorophyll a concentration, and this novel information enables improved methods to detect diatoms from space. The findings of this thesis are relevant to large-scale studies of ocean ecosystems and are critical for algorithm development using both current and upcoming earth-observing satellite data. Additionally, the results presented here provide tools that will benefit oceanographic research on spatial scales relevant to a changing ocean climate

Two Supervised Neural Networks for Classification ofSedimentary Organic Matter Images fromPalynological Preparations

An improvement in the supervised artificial neural network classification of sedimentary organic matter images from palynological preparations is presented. Sedimentary organic matter encompasses the entire acid-resistant organic micro-particles (typically with a diameter of 5-500μm) recovered from a sediment or sedimentary rock. Supervised neural networks are trained to recognize patterns within databases for which the correct classifications are already known. Once trained, they are verified on pre-classified samples not seen by the network, and then used for classification of samples whose class is not known. Such networks have an input, hidden and output layer. Typically, these networks determine what the output class is by adjusting weights associated with the layer interconnects, and by modifying the signals that propagate through the hidden layer by a non-linear transfer function. In this example, the inputs in each network are the salient features selected from an available set of 194, while the outputs are the sedimentary organic matter classifications which were formerly developed with the rationalization of descriptive terms from previous classification schemes. The author's past work tested the supervised back propagation neural network for the classification of sedimentary organic matter images. This gave an overall correct classification rate of 87%. However, because the back propagation network underperformed on two of the four classes, the radial basis function neural network was tested on the same databases initially used in an attempt to improve the recognition rate of these two classes. The difference between the back propagation and radial basis function networks lies in the non-linear transfer function applied in the hidden layer, which was modified by a Gaussian function in the latter. In the best-case scenario, this improved the recognition rate by 4% to just over 91%. This has also determined that a series of different supervised neural networks may be better for classification of sedimentary organic matter images. These results are encouraging enough to prompt further research that may result in a commercially viable syste

Automatic Detection of Freshwater Phytoplankton Specimens in Conventional Microscopy Images

[Abstract] Water safety and quality can be compromised by the proliferation of toxin-producing phytoplankton species, requiring continuous monitoring of water sources. This analysis involves the identification and counting of these species which requires broad experience and knowledge. The automatization of these tasks is highly desirable as it would release the experts from tedious work, eliminate subjective factors, and improve repeatability. Thus, in this preliminary work, we propose to advance towards an automatic methodology for phytoplankton analysis in digital images of water samples acquired using regular microscopes. In particular, we propose a novel and fully automatic method to detect and segment the existent phytoplankton specimens in these images using classical computer vision algorithms. The proposed method is able to correctly detect sparse colonies as single phytoplankton candidates, thanks to a novel fusion algorithm, and is able to differentiate phytoplankton specimens from other image objects in the microscope samples (like minerals, bubbles or detritus) using a machine learning based approach that exploits texture and colour features. Our preliminary experiments demonstrate that the proposed method provides satisfactory and accurate results.This work is supported by the European Regional Development Fund (ERDF) of the European Union and Xunta de Galicia through Centro de Investigación del Sistema Universitario de Galicia, ref. ED431G 2019/01Xunta de Galicia; ED431G 2019/0

Phytoplankton functional types from Space.

The concept of phytoplankton functional types has emerged as a useful approach to classifying phytoplankton. It finds many applications in addressing some serious contemporary issues facing science and society. Its use is not without challenges, however. As noted earlier, there is no universally-accepted set of functional types, and the types used have to be carefully selected to suit the particular problem being addressed. It is important that the sum total of all functional types matches all phytoplankton under consideration. For example, if in a biogeochemical study, we classify phytoplankton as silicifiers, calcifiers, DMS-producers and nitrogen fix- ers, then there is danger that the study may neglect phytoplankton that do not contribute in any significant way to those functions, but may nevertheless be a significant contributor to, say primary production. Such considerations often lead to the adoption of a category of “other phytoplankton” in models, with no clear defining traits assigned them, but that are nevertheless necessary to close budgets on phytoplankton processes. Since this group is a collection of all phytoplankton that defy classification according to a set of traits, it is difficult to model their physi- ological processes. Our understanding of the diverse functions of phytoplankton is still growing, and as we recognize more functions, there will be a need to balance the desire to incorporate the increasing number of functional types in models against observational challenges of identifying and mapping them adequately. Modelling approaches to dealing with increasing functional diversity have been proposed, for example, using the complex adaptive systems theory and system of infinite diversity, as in the work of Bruggemann and Kooijman (2007). But it is unlikely that remote-sensing approaches might be able to deal with anything but a few prominent functional types. As long as these challenges are explicitly addressed, the functional- type concept should continue to fill a real need to capture, in an economic fashion, the diversity in phytoplankton, and remote sensing should continue to be a useful tool to map them. Remote sensing of phytoplankton functional types is an emerging field, whose potential is not fully realised, nor its limitations clearly established. In this report, we provide an overview of progress to date, examine the advantages and limitations of various methods, and outline suggestions for further development. The overview provided in this chapter is intended to set the stage for detailed considerations of remote-sensing applications in later chapters. In the next chapter, we examine various in situ methods that exist for observing phytoplankton functional types, and how they relate to remote-sensing techniques. In the subsequent chapters, we review the theoretical and empirical bases for the existing and emerging remote-sensing approaches; assess knowledge about the limitations, assumptions, and likely accuracy or predictive skill of the approaches; provide some preliminary comparative analyses; and look towards future prospects with respect to algorithm development, validation studies, and new satellite mis- sions

Machine learning in marine ecology: an overview of techniques and applications

Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.Machine learning in marine ecology: an overview of techniques and applicationspublishedVersio

Automatic Identification of Algae using Low-cost Multispectral Fluorescence Digital Microscopy, Hierarchical Classification & Deep Learning

Harmful algae blooms (HABs) can produce lethal toxins and are a rising global concern. In response to this threat, many organizations are monitoring algae populations to determine if a water body might be contaminated. However, identifying algae types in a water sample requires a human expert, a taxonomist, to manually identify organisms using an optical microscope. This is a tedious, time-consuming process that is prone to human error and bias. Since many facilities lack on-site taxonomists, they must ship their water samples off site, further adding to the analysis time. Given the urgency of this problem, this thesis hypothesizes that multispectral fluorescence microscopy with a deep learning hierarchical classification structure is the optimal method to automatically identify algae in water on-site. To test this hypothesis, a low-cost system was designed and built which was able generate one brightfield image and four fluorescence images. Each of the four fluorescence images was designed to target a different pigment in algae, resulting in a unique autofluorescence spectral fingerprint for different phyla groups. To complement this hardware system, a software framework was designed and developed. This framework used the prior taxonomic structure of algae to create a hierarchical classification structure. This hierarchical classifier divided the classification task into three steps which were phylum, genus, and species level classification. Deep learning models were used at each branch of this hierarchical classifier allowing the optimal set of features to be implicitly learned from the input data. In order to test the efficacy of the proposed hardware system and corresponding software framework, a dataset of nine algae from 4 different phyla groups was created. A number of preprocessing steps were required to prepare the data for analysis. These steps were flat field correction, thresholding and cropping. With this multispectral imaging data, a number of spatial and spectral features were extracted for use in the feature-extraction-based models. This dataset was used to determine the relative performance of 12 different model architectures, and the proposed multispectral hierarchical deep learning approach achieved the top classification accuracy of 97% to the species level. Further inspection revealed that a traditional feature extraction method was able to achieve 95% to the phyla level when only using the multispectral fluorescence data. These observations strongly support that: (1) the proposed low-cost multispectral fluorescence imaging system, and (2) the proposed hierarchical structure based on the taxonomy prior, in combination with (3) deep learning methods for feature learning, is an effective method to automatically classify algae