Application of statistical learning theory to plankton image analysis

Submitted to the Joint Program in Applied Ocean Science and Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy At the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2006A fundamental problem in limnology and oceanography is the inability to quickly identify and map distributions of plankton. This thesis addresses the problem by applying statistical machine learning to video images collected by an optical sampler, the Video Plankton Recorder (VPR). The research is focused on development of a real-time automatic plankton recognition system to estimate plankton abundance. The system includes four major components: pattern representation/feature measurement, feature extraction/selection, classification, and abundance estimation. After an extensive study on a traditional learning vector quantization (LVQ) neural network (NN) classifier built on shape-based features and different pattern representation methods, I developed a classification system combined multi-scale cooccurrence matrices feature with support vector machine classifier. This new method outperforms the traditional shape-based-NN classifier method by 12% in classification accuracy. Subsequent plankton abundance estimates are improved in the regions of low relative abundance by more than 50%. Both the NN and SVM classifiers have no rejection metrics. In this thesis, two rejection metrics were developed. One was based on the Euclidean distance in the feature space for NN classifier. The other used dual classifier (NN and SVM) voting as output. Using the dual-classification method alone yields almost as good abundance estimation as human labeling on a test-bed of real world data. However, the distance rejection metric for NN classifier might be more useful when the training samples are not “good” ie, representative of the field data. In summary, this thesis advances the current state-of-the-art plankton recognition system by demonstrating multi-scale texture-based features are more suitable for classifying field-collected images. The system was verified on a very large realworld dataset in systematic way for the first time. The accomplishments include developing a multi-scale occurrence matrices and support vector machine system, a dual-classification system, automatic correction in abundance estimation, and ability to get accurate abundance estimation from real-time automatic classification. The methods developed are generic and are likely to work on range of other image classification applications.This work was supported by National Science Foundation Grants OCE-9820099 and Woods Hole Oceanographic Institution academic program

Migration of the Antarctic Polar Front through the mid-Pleistocene transition: evidence and climatic implications

The Antarctic Polar Front is an important biogeochemical divider in the Southern Ocean. Laminated diatom mat deposits record episodes of massive flux of the diatom Thalassiothrix antarctica beneath the Antarctic Polar Front and provide a marker for tracking the migration of the Front through time. Ocean Drilling Program Sites 1091, 1093 and 1094 are the only deep piston cored record hitherto sampled from the sediments of the circumpolar biogenic opal belt. Mapping of diatom mat deposits between these sites indicates a glacial-interglacial front migration of up to 6 degrees of latitude in the early / mid Pleistocene. The mid Pleistocene transition marks a stepwise minimum 7 degree northward migration of the locus of the Polar Front sustained for about 450 kyr until an abrupt southward return to a locus similar to its modern position and further south than any mid-Pleistocene locus. This interval from a “900 ka event” that saw major cooling of the oceans and a ?13C minimum through to the 424 ka Mid-Brunhes Event at Termination V is also seemingly characterised by 1) sustained decreased carbonate in the subtropical south Atlantic, 2) reduced strength of Antarctic deep meridional circulation, 3) lower interglacial temperatures and lower interglacial atmospheric CO2 levels (by some 30 per mil) than those of the last 400 kyr, evidencing less complete deglaciation. This evidence is consistent with a prolonged period lasting 450 kyr of only partial ventilation of the deep ocean during interglacials and suggests that the mechanisms highlighted by recent hypotheses linking mid-latitude atmospheric conditions to the extent of deep ocean ventilation and carbon sequestration over glacial-interglacial cycles are likely in operation during the longer time scale characteristic of the Mid-Pleistocene Transition. The cooling that initiated the “900 ka event” may have been driven by minima in insolation amplitude related to eccentricity modulation of precession that also affected low latitude climates as marked by threshold changes in the African monsoon system. The major thresholds in earth system behaviour through the Mid-Pleistocene Transition were likely governed by an interplay of the 100 kyr and 400 kyr eccentricity modulation of precession

Diatom identification including life cycle stages through morphological and texture descriptors

Diatoms are unicellular algae present almost wherever there is water. Diatom identification has many applications in different fields of study, such as ecology, forensic science, etc. In environmental studies, algae can be used as a natural water quality indicator. The diatom life cycle consists of the set of stages that pass through the successive generations of each species from the initial to the senescent cells. Life cycle modeling is a complex process since in general the distribution of the parameter vectors that represent the variations that occur in this process is non-linear and of high dimensionality. In this paper, we propose to characterize the diatom life cycle by the main features that change during the algae life cycle, mainly the contour shape and the texture. Elliptical Fourier Descriptors (EFD) are used to describe the diatom contour while phase congruency and Gabor filters describe the inner ornamentation of the algae. The proposed method has been tested with a small algae dataset (eight different classes and more than 50 samples per type) using supervised and non-supervised classification techniques obtaining accuracy results up to 99% and 98% respectively

Self-Supervised Discovery of Anatomical Shape Landmarks

Statistical shape analysis is a very useful tool in a wide range of medical and biological applications. However, it typically relies on the ability to produce a relatively small number of features that can capture the relevant variability in a population. State-of-the-art methods for obtaining such anatomical features rely on either extensive preprocessing or segmentation and/or significant tuning and post-processing. These shortcomings limit the widespread use of shape statistics. We propose that effective shape representations should provide sufficient information to align/register images. Using this assumption we propose a self-supervised, neural network approach for automatically positioning and detecting landmarks in images that can be used for subsequent analysis. The network discovers the landmarks corresponding to anatomical shape features that promote good image registration in the context of a particular class of transformations. In addition, we also propose a regularization for the proposed network which allows for a uniform distribution of these discovered landmarks. In this paper, we present a complete framework, which only takes a set of input images and produces landmarks that are immediately usable for statistical shape analysis. We evaluate the performance on a phantom dataset as well as 2D and 3D images.Comment: Early accept at MICCAI 202

Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber

<p>Abstract</p> <p>Background</p> <p>Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Pyritization is the most important and extensive mode of preservation of animals and especially of plants. Entrapping in amber, a fossilized resin, is considered an alternative mode of biological preservation. For the first time, the internal organization of 114-million-year-old microfossils entrapped in Lower Cretaceous amber is described and analyzed, using adapted scanning electron microscopy in backscattered electron mode in association with energy dispersive X-ray spectroscopy microanalysis. Double fossilization of several protists included in diverse taxonomical groups and some vegetal debris is described and analyzed.</p> <p>Results</p> <p>In protists without an exoskeleton or shell (ciliates, naked amoebae, flagellates), determinate structures, including the nuclei, surface envelopes (cortex or cytoplasmic membrane) and hyaloplasm are the main sites of pyritization. In protists with a biomineralized skeleton (diatoms), silicon was replaced by pyrite. Permineralization was the main mode of pyritization. Framboidal, subhedral and microcrystalline are the predominant pyrite textures detected in the cells. Abundant pyritized vegetal debris have also been found inside the amber nuggets and the surrounding sediments. This vegetal debris usually contained numerous pyrite framboids and very densely packed polycrystalline pyrite formations infilled with different elements of the secondary xylem.</p> <p>Conclusion</p> <p>Embedding in amber and pyritization are not always alternative modes of biological preservation during geological times, but double fossilization is possible under certain environmental conditions. Pyritization in protists shows a quite different pattern with regard to plants, due to the different composition and cellular architecture in these microorganisms and organisms. Anaerobic sulphate-reducing bacteria could play a crucial role in this microbial fossilization.</p

Sedimentary processes at the base of a West Antarctic ice stream: Constraints from textural and compositional properties of subglacial debris

Samples of sediments from beneath Ice Stream B (at camp UpB), West Antarctica, provide the first opportunity to study the relationship between sediment properties and physical conditions in a sub-ice-stream environment. Piston coring in holes bored by hot-water drilling yielded five 1-3 m long, undisturbed subglacial sediment cores. We analyzed granulometry, composition, and particle morphology in these cores. The UpB cores are composed of a clay-rich, unsorted diamicton containing rare marine diatoms. Sedimentary particles in these cores bear no evidence of the recent crushing or abrasion that is common in other subglacial sedimentary environments. The presence of reworked diatoms and their state of preservation, as well as the relative spatial homogeneity of this diamicton, suggest that the UpB cores sampled a several-meter-thick till layer and not in situ glacimarine sediments. The till does incorporate material recycled from the subjacent poorly indurated Tertiary glacimarine sediments of the Ross Sea sedimentary basin, which extends beneath this part of the West Antarctic Ice Sheet. We propose that the lack of significant comminution in the UpB till is ultimately due to its setting over these easily erodible, clay-rich source sediments. The resulting fine-grained till matrix inhibits glacial comminution, because it facilitates buildup of high pore-water pressures and hinders interparticle stress concentrations. Our observations are consistent with the conjecture that subglacial deformation of weak, fine-grained tills does not produce significant comminution of till debris (Elson 1988). Based on our findings, we hypothesize that extensive layers of weak till may develop preferentially where ice overrides preexisting, poorly indurated, fine-grained sediments. Since such weak till layers create a permissive condition for ice streaming, sub-glacial geology may have an indirect but strong control over the location, extent, and basal mechanics of ice streams

High-Resolution Correlation of a Time-Bounded Unit of the Pisco Formation, Peru

Correlation of beds in the Pisco Basin across significant distances is problematic and has not yet been effectively achieved. I chose to examine an interval bounded by two time markers, an 40Ar/39Ar-dated white tuff at the base and an 40Ar/39Ar-dated tuff couplet at the top. This interval was chosen because of the continuity and excellent exposure of the tuff beds at six distinct locations in a linear transect 30 km long. Correlation of units was achieved through 40Ar/39Ar dating, lithology, sedimentary structures, and magnetic susceptibility. The vertical and lateral variability in lithology, fossil assemblages, structures, and sequences was examined in detail and used to develop a paleoenvironmental model of the time-bounded sequence. Six distinct facies from the Pisco Formation were defined and used toward developing the paleoenvironmental model. Sedimentary structures associated with the facies, such as hummocky cross-stratification and ripple laminations, suggest wave reworking in a nearshore environment. The presence of clastics and coarse-grained sediments decrease from the northern outcrops to the southern outcrops, suggesting a decrease in energy levels and an increase of water depth away from the shore. This study provides the first secure correlation across a significant distance and a more comprehensive stratigraphy and paleoenvironmental interpretation of the Upper Pisco Formation

Laser Surface Texturing To Create Biomimetic Surface Topographies For Marine Antifouling Efficacy Testing

Biofouling is the unwanted colonisation of organisms on a living or artificial surface. Convergent evolution has led to the development of antifouling textures on many marine species. This thesis provides novel investigation into creating biomimetic antifouling surface directly onto marine grade stainless steel using laser micro machining. The investigation was split into three main research questions: (1) can laser surface texturing be used to create antifouling surfaces, and their effects on surface parameters (roughness / contact angle); (2) can biomimetic antifouling surfaces be created using laser surface texturing?; (3) can features of those successful surfaces be combined to create enhanced biomimetic antifouling surface?. All three experiments had similar methods, as laser processing was used to transfer the selected biomimetic micro-topography patterns onto marine grade stainless steel (316L). Samples were deployed in the field (Liverpool South Docks, UK) for 7 days. Abundance of biofilm was assessed using random systematic sampling. For the biomimetic surfaces, a fringe projection microscope (GFM) was used to investigate 3D scans of the surface topography of shells of bivalve and crab species, to provide bio-inspiration for the design of the surfaces created in this research. It was found that the micro-topography pattern limits the attachment of the biofilm to the surface. This thesis shows that (1) laser surface texturing can be used to create antifouling surfaces; (2) biomimetic antifouling surfaces can be created and enhance antifouling efficacy, and (3) that combining biomimetic features into multi-scale and multi-feature patterns have enhanced antifouling effects. This reinforces that biomimetic surfaces have the potential to be a non-toxic, eco-friendly antifouling technology that work directly on marine metal structures without the need for further coatings or chemicals