Efficient identification, localization and quantification of grapevine inflorescences and flowers in unprepared field images using Fully Convolutional Networks

Yield and its prediction is one of the most important tasks in grapevine breeding purposes and vineyard management. Commonly, this trait is estimated manually right before harvest by extrapolation, which mostly is labor-intensive, destructive and inaccurate. In the present study an automated image-based workflow was developed for quantifying inflorescences and single flowers in unprepared field images of grapevines, i.e. no artificial background or light was applied. It is a novel approach for non-invasive, inexpensive and objective phenotyping with high-throughput.First, image regions depicting inflorescences were identified and localized. This was done by segmenting the images into the classes "inflorescence" and "non-inflorescence" using a Fully Convolutional Network (FCN). Efficient image segmentation hereby is the most challenging step regarding the small geometry and dense distribution of single flowers (several hundred single flowers per inflorescence), similar color of all plant organs in the fore- and background as well as the circumstance that only approximately 5 % of an image show inflorescences. The trained FCN achieved a mean Intersection Over Union (IOU) of 87.6 % on the test data set. Finally, single flowers were extracted from the "inflorescence"-areas using Circular Hough Transform. The flower extraction achieved a recall of 80.3 % and a precision of 70.7 % using the segmentation derived by the trained FCN model.Summarized, the presented approach is a promising strategy in order to predict yield potential automatically in the earliest stage of grapevine development which is applicable for objective monitoring and evaluations of breeding material, genetic repositories or commercial vineyards

Mapping the composition of Antarctic ice shelves as a metric for their susceptibility to future climate change

Abstract Antarctic ice shelves control the flow of ice into the ocean, affecting the rate of sea level rise. This flow is regulated by ice-shelf thickness, which depends on tributary flux across the grounding line and the balance between surface accumulation and ocean-induced melting. Consequently, ice shelves that are tributary-sustained will be more susceptible to dynamic changes upstream of the grounding line. In contrast, atmospherically sustained ice shelves will be more susceptible to changing local atmospheric and oceanographic conditions. Our results differentiate between these internal and external regimes by mapping which ice shelves are tributary- and which are atmospherically sustained and we compare these findings with published estimates of local ice-shelf buttressing strength. This approach identifies buttressing relevant areas, particularly near pinning points, in West Antarctica and the Peninsula, which are highly dependent on surface accumulation and therefore vulnerable to the predicted decline of coastal snowfall through the end of the century

Improved optical phenotyping of the grape berry surface using light-separation and automated RGB image analysis

Grape resilience towards Botrytis cinerea (B. cinerea) infections (Botrytis bunch rot) is an important concern of breeders and growers. Beside grape bunch architecture, berry surface characteristics like berry bloom (epicuticular wax) as well as thickness and permeability of the berry cuticle represent further promising physical barriers to increase resilience towards Botrytis bunch rot. In previous studies, two efficient sensor-based phenotyping methods were developed to evaluate both berry surface traits fast and objectively: (1) light-separated RGB (red-green-blue) image analysis to determine the distribution of epicuticular wax on the berry surface; and (2) electrical impedance characteristics of the grape berry cuticle based on point measurements. The present proof-of-concept study aiming at the evaluation of light-separated RGB images for both phenotyping applications, phenotyping wax distribution pattern and berry cuticle impedance values. Within the selected grapevine varieties like \u27Riesling\u27, \u27Sauvignon Blanc\u27 or \u27Calardis Blanc\u27 five contributions were achieved: (1) Both phenotyping approaches were fused into one prototypic unified phenotyping method achieving a wax detection accuracy of 98.6 % and a prediction of electrical impedance with an accuracy of 95 %. (2) Both traits are derived using only light-separated images of the grapevine berries. (3) The improved method allows the detection and quantification of additional surface traits of the grape berry surface such as lenticels (punctual lignification) and the berry stem that are also known as being able to affect the grape susceptibility towards Botrytis. (4) The improved image analysis tools are further integrated into a comprehensive workbench allowing end-users, like breeders to combine phenotyping experiments with transparent data management offering valuable services like visualizations, indexing, etc. (5) Annotation work is supported by a sophisticated annotation tool of the image analysis workbench. The usage of light-separated images enables fast and non-invasive phenotyping of different optical berry surface characteristics, which saves time-consuming labor and additionally allows the reuse of the berry samples for subsequent investigations, e.g. Botrytis infection studies

Habitat-based density models of pack-ice seal distribution in the southern Weddell Sea, Antarctica

Climate variability and changes in sea ice dynamics have caused several ice-obligate or krill-dependent populations of marine predators to decline, eliciting concern about their demographic persistence and the indirect ecological consequences that predator depletions may have on marine ecosystems. Pack-ice seals are dominant ice-obligate predators in the Antarctic marine ecosystem, but there is considerable uncertainty about their abundance and population trends. We modelled the density and distribution of pack-ice seals as a function of environmental covariates in the southern Weddell Sea, Antarctica. Our density surface modelling approach used data from aerial surveys of pack-ice seals collected in the 2013/14 austral summer. Crabeater seals Lobo don carcinophaga, the most numerous pack-ice seal we observed, occurred at the highest densities in areas with extensive sea ice near the continental shelf break, but were almost absent in areas of similar sea ice concentration in the southern extent of the Weddell Sea. The highest densities of Weddell seals Leptonychotes weddelli, which were less abundant than crabeater seals within the pack-ice habitat, were predicted to occur over the continental shelf, near the shelf break. The distribution of both seal species broadly corresponded with the distribution and relative abundance of their main prey (Antarctic krill Euphausia superba and Antarctic silverfish Pleuragramma antarctica) obtained from concurrent ecosystem surveys. Ross seals Ommatophoca rossii and leopard seals Hydrurga leptonyx were not detected at all and are apparently rare within the southern Weddell Sea. These results can contribute to biodiversity assessments in the context of marine protected area planning in this region of the Southern Ocean

Antarctic pack ice seals and oceanographic features at the Filchner Outflow System, southern Weddell Sea

The Filchner Outflow System (FOS) in the southern Weddell Sea is one of the most important areas for deep water formation. Here the outflow of Ice Shelf Water (ISW) of the Filchner Ronne Ice Shelf interacts with Warm Deep Water (WDW) of the Weddell Gyre circulation, resulting in Weddell Sea Deep and Bottom Water production (WSDW, WSBW). The interaction around the sill of the Filchner Trough is thought to result in a physical oceanography "hotspot" that may also aggregate primary and secondary producers, leading to increased abundance of top predators. However, data on top predator abundance for the FOS are scarce. Two aerial surveys over ice-covered sea were carried out to estimate density gradients and the regional abundance of pack ice seals in the FOS. A digital imaging survey with fixed wing research aircraft Polar 6 in November 2013 preceded a helicopter survey from aboard RV Polarstern during January 2014. The Polar 6 survey comprised 11 transects summing to a survey effort of 1,148.44 km. 265 seals were counted on transect lines with a higher encounter rate on transects located further to the west. The helicopter survey allowed seal species to be identified. Twenty-five transects (1,367.61 km) were flown in the FOS region and another six transects (425.54 km) further south within the Filchner Trough. Only two seal species, the crabeater seal (Lobodon carcinophaga) (n = 754) and the Weddell seal (Leptonychotes weddellii) (n = 217), were observed. Distance sampling analysis suggested that the density of seals differed strongly between the two survey regions, with very few seals encountered on transects located in the more southerly Filchner Trough region. A longitudinal density gradient increasing from east to west within the FOS region during January 2014 supported the results obtained from the Polar 6 survey, but failed to support the idea of a top predator hotspot at the sill of the Filchner Trough at least for seals

Stagnant ice and age modelling in the Dome C region, Antarctica

The European Beyond EPICA project aims to extract a continuous ice core of up to 1.5 Ma, with a maximum age density of 20 kyr m-1 at Little Dome C (LDC). We present a 1D numerical model which calculates the age of the ice around Dome C. The model inverts for basal conditions and accounts either for melting or for a layer of stagnant ice above the bedrock. It is constrained by internal reflecting horizons traced in radargrams and dated using the EPICA Dome C (EDC) ice core age profile. We used three different radar datasets ranging from a 10 000 km2 airborne survey down to 5 km long ground-based radar transects over LDC. We find that stagnant ice exists in many places, including above the LDC relief where the new Beyond EPICA drill site (BELDC) is located. The modelled thickness of this layer of stagnant ice roughly corresponds to the thickness of the basal unit observed in one of the radar surveys and in the autonomous phase-sensitive radio-echo sounder (ApRES) dataset. At BELDC, the modelled stagnant ice thickness is 198±44 m and the modelled oldest age of ice is 1.45±0.16 Ma at a depth of 2494±30 m. This is very similar to all sites situated on the LDC relief, including that of the Million Year Ice Core project being conducted by the Australian Antarctic Division. The model was also applied to radar data in the area 10-15 km north of EDC (North Patch), where we find either a thin layer of stagnant ice (generally <60 m) or a negligible melt rate (<0.1 mm yr-1). The modelled maximum age at North Patch is over 2 Ma in most places, with ice at 1.5 Ma having a resolution of 9-12 kyr m-1, making it an exciting prospect for a future Oldest Ice drill site

Extreme melting at Greenland's largest floating ice tongue

The 79° North Glacier (Nioghalvfjerdsbrae, 79NG) is one of three remaining glaciers with a floating tongue in Greenland. Although the glacier has been considered exceptionally stable in the past, earlier studies have shown that the ice tongue has thinned in recent decades. By conducting high-resolution ground-based and airborne radar measurements in conjunction with satellite remote-sensing observations, we find significant changes in the geometry of 79NG. In the vicinity of the grounding line, a 500 m high subglacial channel has grown since ∼ 2010 and has caused surface lowering of up to 7.6 m a−1. Our results show extreme basal melt rates exceeding 150 m a−1 over a period of 17 d within a distance of 5 km from the grounding line, where the ice has thinned by 32 % since 1998. We find a heterogeneous distribution of melt rates, likely due to variability in water column thickness and channelization of the ice base. Time series of melt rates show a decrease in basal melting since 2018, indicating an inflow of colder water into the cavity below 79NG. We discuss the processes that have led to the changes in geometry and conclude that the inflow of warm ocean currents has led to the extensive thinning of 79NG's floating ice tongue near the grounding line over the last 2 decades. In contrast, we hypothesize that the growth of the channel results from increased subglacial discharge due to a considerably enlarged area of summer surface melt due to the warming of the atmosphere.</p

High resolution boundary conditions of an old ice target near Dome C, Antarctica

A high resolution (1 km line spacing) aerogeophysical survey was conducted over a region near the East Antarctic Ice Sheet's Dome C that may hold a 1.5 million year old climate record. New ice thickness data derived from an airborne coherent radar sounder was combined with unpublished data that was unavailable for earlier compilations. We find under the primary candidate region elevated rough topography, near a number of subglacial lakes, but also regions of smoother bed. The high resolution of this ice thickness dataset also allows us to explore the nature of ice thickness uncertainties in the context of radar geometry and processing

Bedmap2: improved ice bed, surface and thickness datasets for Antarctica

We present Bedmap2, a new suite of gridded products describing surface elevation, ice-thickness and the seafloor and subglacial bed elevation of the Antarctic south of 60° S. We derived these products using data from a variety of sources, including many substantial surveys completed since the original Bedmap compilation (Bedmap1) in 2001. In particular, the Bedmap2 ice thickness grid is made from 25 million measurements, over two orders of magnitude more than were used in Bedmap1. In most parts of Antarctica the subglacial landscape is visible in much greater detail than was previously available and the improved data-coverage has in many areas revealed the full scale of mountain ranges, valleys, basins and troughs, only fragments of which were previously indicated in local surveys. The derived statistics for Bedmap2 show that the volume of ice contained in the Antarctic ice sheet (27 million km3) and its potential contribution to sea-level rise (58 m) are similar to those of Bedmap1, but the mean thickness of the ice sheet is 4.6% greater, the mean depth of the bed beneath the grounded ice sheet is 72 m lower and the area of ice sheet grounded on bed below sea level is increased by 10%. The Bedmap2 compilation highlights several areas beneath the ice sheet where the bed elevation is substantially lower than the deepest bed indicated by Bedmap1. These products, along with grids of data coverage and uncertainty, provide new opportunities for detailed modelling of the past and future evolution of the Antarctic ice sheets