Fully convolutional neural networks applied to large-scale marine morphology mapping

In this study we applied for the first time Fully Convolutional Neural Networks (FCNNs) to a marine bathymetric dataset to derive morphological classes over the entire Irish continental shelf. FCNNs are a set of algorithms within Deep Learning that produce pixel-wise classifications in order to create semantically segmented maps. While they have been extensively utilised on imagery for ecological mapping, their application on elevation data is still limited, especially in the marine geomorphology realm. We employed a high-resolution bathymetric dataset to create a set of normalised derivatives commonly utilised in seabed morphology and habitat mapping that include three bathymetric position indexes (BPIs), the vector ruggedness measurement (VRM), the aspect functions and three types of hillshades. The class domains cover ten or twelve semantically distinct surface textures and submarine landforms present on the shelf, with our definitions aiming for simplicity, prevalence and distinctiveness. Sets of 50 or 100 labelled samples for each class were used to train several U-Net architectures with ResNet-50 and VGG-13 encoders. Our results show a maximum model precision of 0.84 and recall of 0.85, with some classes reaching as high as 0.99 in both. A simple majority (modal) voting combining the ten best models produced an excellent map with overall F1 score of 0.96 and class precisions and recalls superior to 0.87. For target classes exhibiting high recall (proportion of positives identified), models also show high precision (proportion of correct identifications) in predictions which confirms that the underlying class boundary has been learnt. Derivative choice plays an important part in the performance of the networks, with hillshades combined with bathymetry providing the best results and aspect functions and VRM leading to an overall deterioration of prediction accuracies. The results show that FCNNs can be successfully applied to the seabed for a morphological exploration of the dataset and as a baseline for more in-depth habitat mapping studies. For example, prediction of semantically distinct classes as “submarine dune” and “bedrock outcrop” can be precise and reliable. Nonetheless, at present state FCNNs are not suitable for tasks that require more refined geomorphological classifications, as for the recognition of detailed morphogenetic processes

Weathering fluxes and sediment provenance on the SW Scottish shelf during the last deglaciation

The reconstruction of past ice sheet dynamics can shed a light on long-term ice stream activity, and in turn provide constraints on the response of modern ice sheets to climate change. The Hebrides Ice Stream (HIS) flowed across part of the western Scottish shelf to the shelf-break during the last glacial cycle and drained a large portion of the northern sector of the British Irish-Ice Sheet. To investigate the deglacial dynamics of the HIS following the Last Glacial Maximum, lead (Pb) isotope records were extracted from the FeMn oxyhydroxide and detrital fractions of recovered laminated glacimarine mud sequences to monitor the changing activity of HIS during its retreat. These provide timing and some source information of glacially weathered inputs to the marine environment. The FeMn oxyhydroxide fraction in the samples is dominated by allochthonous particles (pre-formed) and shows a marked decrease from radiogenic (≤ 20.05 206Pb/204Pb) at ~ 21 cal ka BP to less radiogenic Pb isotope compositions (~ 19.48) towards the Windermere Interstadial (15.4–13 ka). This decrease represents a reduction in the flux of subglacially-derived radiogenic Pb to the continental shelf is interpreted as being associated with the break-up of the ice-stream in western Scotland around that time. The Pb, Sr and Nd isotopic signatures of the detrital fraction indicate a preponderance of Moine-sourced fine sediments (originated from the NW Highlands) in the core locations from ~ 21 to 15 cal ka BP (Dimlington Stadial - Windermere Interstadial), most likely dictated by the orientation of ice flow, tidal and oceanic current directions and sediment delivery. In contrast, ice rafted debris in a ~ 21 cal ka BP old basal diamicton contains volcanic-derived material, suggesting different provenance for different grain sizes. The FeMn oxyhydroxide 208Pb/204Pb ratio shows an unusual inversion relative to the other Pb isotope ratios, and is attributed to the introduction of secondary weathering phases from a source with contrasting 208Pb/204Pb but similar 206Pb/204Pb and 207Pb/204Pb. In the detrital fraction, the inversions are constrained to periodic spikes, which may indicate an increased contribution from a high Th/U source, potentially the neighbouring Archaean amphibolitic Lewisian basement in the Outer Hebrides. This study demonstrates how geochemical investigation on continental shelves can be used to constrain the timing, activity and flow sources of palaeo-ice streams

Simultaneous two-photon imaging of intracellular chloride concentration and pH in mouse pyramidal neurons in vivo

Intracellular chloride ([Cl-](i)) andpH(pH(i)) are fundamental regulators of neuronal excitability. They exert wide-ranging effects on synaptic signaling and plasticity and on development and disorders of the brain. The ideal technique to elucidate the underlying ionic mechanisms is quantitative and combined two-photon imaging of [Cl-](i) and pH(i), but this has never been performed at the cellular level in vivo. Here, by using a genetically encoded fluorescent sensor that includes a spectroscopic reference (an element insensitive to Cl-and pH), we show that ratiometric imaging is strongly affected by the optical properties of the brain. We have designed a method that fully corrects for this source of error. Parallel measurements of [Cl-](i) and pH(i) at the single-cell level in the mouse cortex showed the in vivo presence of the widely discussed developmental fall in [Cl-](i) and the role of the K-Cl cotransporter KCC2 in this process. Then, we introduce a dynamic two-photon excitation protocol to simultaneously determine the changes of pHi and [Cl-](i) in response to hypercapnia and seizure activity.Peer reviewe

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe

Lateglacial to Holocene palaeoenvironmental change in the Muck Deep, offshore western Scotland

Seismic unit classification in the Muck Deep, summary of the Muck Core Units described, core photos showing details of the sedimentary structures in cores 729 and 731 and Correlation between core 731 and MD6

Seismic Noise Measurements on Unstable Rock Blocks: The Case of Bismantova Rock Cliff

In this work, we tested the use of passive seismic for the characterization of potentially unstable rock blocks in the Pietra di Bismantova site, a wide slab of calcareous sandstone located in the Northern Apennines of Italy. Ambient vibrations recordings with broad-band 3-component seismometers were carried out on potentially unstable areas such as 5 rock blocks and 1 rock column located close to the top of the 100 m-high cliff. The rock blocks are also monitored by means of crackmeters. Seismic noise recordings were processed with a standard sequence and noise spectra and spectral ratios have been evaluated. Preliminary results are promising since in some cases a significant frequency peak can be observed, indicating resonance effects due to the vibration of the rock pillars. In addition, for the most favorable case, noise polarization analysis presents vibration direction values at given frequency in a limited angle range, reasonably corresponding to the direction of maximum displacement. Future investigations could address additional noise measurements and their correlation with the crackmeter datasets in order to understand possible relationship between change in resonance frequency or signal polarization and crackmeter hysteresis path. Moreover, new ambient noise surveys could be planned as a pilot investigation campaign, with the aim of designing extensometer monitoring network tuned on the most critical situations

Crowdsourcing experiment and fully convolutional neural networks for coastal remote sensing of seagrass and macro-algae

Recently, convolutional neural networks (CNNs) and fully convolutional neural networks (FCNs) have been successfully used for monitoring coastal marine ecosystems, in particular vegetation. However, even with recent advances in computational modelling and data acquisition, deep learning models require substantial amounts of good quality reference data to effectively self-learn internal representations of input imagery. The classical approach for coastal mapping requires experts to transcribe insitu records and delineate polygons from high-resolution imagery such that FCNs can self-learn. However, labelling by a single individual limits the training data, whereas crowdsourcing labels can increase the volume of training data, but may compromise label quality and consistency. In this paper we assessed the reliability of crowdsourced labels on a complex multi-class problem domain for estuarine vegetation and unvegetated sediment. An inter-observer variability experiment was conducted in order to assess the statistical differences in crowdsourced annotations for plant species and sediment. The participants were grouped based on their discipline and level of expertise, and the statistical differences were evaluated using the Cochran's Q-test and the annotation accuracy of each group to determine for observation biases. Given the crowdsourced labels, FCNs were trained with majority-vote annotations from each group to check whether observation biases were propagated to FCN performance. Two scenarios were examined: first, a direct comparison of FCNs trained with transcribed in-situ labels and crowdsourced labels from each group was established. Then, transcribed in-situ labels were supplemented with crowdsourced labels to investigate the feasibility of training FCNs with crowdsourced labels in coastal mapping applications. We show that annotations sourced from discipline experts (ecologists and geomorphologists) familiar with the study site were more accurate than experts wi..

Submarine deglacial sediment and geomorphological record of southwestern Scotland after the Last Glacial Maximum

Understanding the style and pattern of retreat of the offshore sectors of the last British-Irish Ice Sheet (BIIS) is critical to any attempt to reconstruct its history following the Last Glacial Maximum (LGM). This paper presents a new seismo-stratigraphic analysis of Quaternary deposits on the inner continental shelf offshore of southwestern Scotland. It correlates these data with new high resolution seafloor bathymetry and sediment cores to reconstruct the post-LGM retreat dynamics of the Hebrides Ice Stream, a major outlet of the last BIIS which drained across the continental shelf offshore of northwest Britain. Two primary glacigenic units (Units III and IV) are observed in seismic sequences from the region. Unit III partly corresponds to the previously defined Barra Formation, but is re-interpreted here as a time-transgressive subglacial to ice-proximal deposit. On the mid-shelf, this unit comprises grounding-zone wedges (GZWs). Within inshore waters and sea lochs Unit III can be found at or near seabed, where it is associated with retreat moraines, as well as with proglacial outwash sediments near the Kintyre coast (RSL ~10 m OD). The younger Unit IV (equivalent to the Jura Formation) represents ice-proximal to hemipelagic conditions. Bathymetric data imaged streamlined subglacial landforms recording ice sheet flow onto the inner shelf and a variety of transverse landforms collectively interpreted as moraines recording episodic retreat. These new data indicate that during the last deglaciation of the shelf offshore of southwestern Scotland the retreat dynamics of the Hebrides Ice Stream followed three main stages: i) tidewater margin retreat punctuated by stillstands on the inner shelf, ii) topography-controlled fjordic retreat, with evolution from a coherent ice-sheet to separate tidewater glaciers, and iii) stabilisation at the transition from a tidewater to land-based ice margin

Submarine glacial landforms record Late Pleistocene ice-sheet dynamics, Inner Hebrides, Scotland

We use ∼7000km2 of high-resolution swath bathymetry data to describe and map the submarine glacial geomorphology, and reconstruct Late Pleistocene ice sheet flow configurations and retreat dynamics within the Inner Hebrides, western Scotland. Frequently dominated by outcrops of structurally complex bedrock, the seabed also comprises numerous assemblages of well-preserved glacigenic landforms typical of grounded ice sheet flow and punctuated ice-margin retreat. The occurrence and character of the glacially streamlined landforms is controlled in part by the shallow geology and topography, however these factors alone cannot account for the location, orientation, and configuration of the observed landforms. We attribute the distribution of these elongate streamlined landforms to the onset zone of the former Hebrides Ice Stream (HIS) – part of a major ice stream system that drained 5–10% of the last British–Irish Ice Sheet (BIIS). We suggest this geomorphic signature represents the transition from slow ‘sheet flow’ to ‘streaming flow’ as ice accelerated out from an environment characterized by numerous bedrock obstacles (e.g. islands, headlands), towards the smooth, sediment dominated shelf. The majority of streamlined landforms associated with the HIS indicate ice sheet flow to the southwest, with regional-scale topography clearly playing a major role in governing the configuration of flow. During maximal glacial conditions (∼29–23ka) we infer that the HIS merged with the North Channel-Malin Shelf Ice Stream to form a composite ice stream system that ultimately reached the continental shelf edge at the Barra-Donegal Trough-Mouth Fan. Taken collectively however, the pattern of landforms now preserved at seabed (e.g. convergent flow indicators, cross-cutting flow sets) is more indicative of a thinning ice mass, undergoing reorganization during overall ice sheet retreat (during latter stages of Late Weischselian glaciation). Suites of moraines overprinting the streamlined landforms suggest partial stabilization of the HIS prior to the ice sheet retreating to more isolated, topographically confined troughs and basins. Retreat from the shelf towards, and back into the Inner Hebrides may have been rapid due the prevalence of overdeepened troughs. Within the near-shore fjord-like troughs and deeps, basin-aligned streamlined landforms indicate the subsequent flow of thinner topographically partitioned ice masses, and overprinted moraines record further ice margin retreat, potentially along tide-water margins. This work provides the first geomorphological constraints for this large marine-influenced sector of the former BIIS. We also shed new light on the glacial geomorphic record found at the transition from terrestrial to marine continental-shelf settings, and examine the interplay between substrate geology, bed topography/bathymetry, and grounding-line positions – relationships which are important for characterizing contemporary marine ice sheet margins