SpikeletFCN: Counting Spikelets from Infield Wheat Crop Images Using Fully Convolutional Networks

Currently, crop management through automatic monitoring is growing momentum, but presents various challenges. One key challenge is to quantify yield traits from images captured automatically. Wheat is one of the three major crops in the world with a total demand expected to exceed 850 million tons by 2050. In this paper we attempt estimation of wheat spikelets from high-definition RGB infield images using a fully convolutional model. We propose also the use of transfer learning and segmentation to improve the model. We report cross validated Mean Absolute Error (MAE) and Mean Square Error (MSE) of 53.0, 71.2 respectively on 15 real field images. We produce visualisations which show the good fit of our model to the task. We also concluded that both transfer learning and segmentation lead to a very positive impact for CNN-based models, reducing error by up to 89%, when extracting key traits such as wheat spikelet counts

Characterizing, modelling and understanding the climate variability of the deep water formation in the North-Western Mediterranean Sea

Observing, modelling and understanding the climate-scale variability of the deep water formation (DWF) in the North-Western Mediterranean Sea remains today very challenging. In this study, we first characterize the interannual variability of this phenomenon by a thorough reanalysis of observations in order to establish reference time series. These quantitative indicators include 31 observed years for the yearly maximum mixed layer depth over the period 1980–2013 and a detailed multi-indicator description of the period 2007–2013. Then a 1980–2013 hindcast simulation is performed with a fully-coupled regional climate system model including the high-resolution representation of the regional atmosphere, ocean, land-surface and rivers. The simulation reproduces quantitatively well the mean behaviour and the large interannual variability of the DWF phenomenon. The model shows convection deeper than 1000 m in 2/3 of the modelled winters, a mean DWF rate equal to 0.35 Sv with maximum values of 1.7 (resp. 1.6) Sv in 2013 (resp. 2005). Using the model results, the winter-integrated buoyancy loss over the Gulf of Lions is identified as the primary driving factor of the DWF interannual variability and explains, alone, around 50 % of its variance. It is itself explained by the occurrence of few stormy days during winter. At daily scale, the Atlantic ridge weather regime is identified as favourable to strong buoyancy losses and therefore DWF, whereas the positive phase of the North Atlantic oscillation is unfavourable. The driving role of the vertical stratification in autumn, a measure of the water column inhibition to mixing, has also been analyzed. Combining both driving factors allows to explain more than 70 % of the interannual variance of the phenomenon and in particular the occurrence of the five strongest convective years of the model (1981, 1999, 2005, 2009, 2013). The model simulates qualitatively well the trends in the deep waters (warming, saltening, increase in the dense water volume, increase in the bottom water density) despite an underestimation of the salinity and density trends. These deep trends come from a heat and salt accumulation during the 1980s and the 1990s in the surface and intermediate layers of the Gulf of Lions before being transferred stepwise towards the deep layers when very convective years occur in 1999 and later. The salinity increase in the near Atlantic Ocean surface layers seems to be the external forcing that finally leads to these deep trends. In the future, our results may allow to better understand the behaviour of the DWF phenomenon in Mediterranean Sea simulations in hindcast, forecast, reanalysis or future climate change scenario modes. The robustness of the obtained results must be however confirmed in multi-model studies

First light of the VLT planet finder SPHERE. I. Detection and characterization of the sub-stellar companion GJ 758 B

GJ758 B is a brown dwarf companion to a nearby (15.76 pc) solar-type, metal-rich (M/H = +0.2 dex) main-sequence star (G9V) that was discovered with Subaru/HiCIAO in 2009. From previous studies, it has drawn attention as being the coldest (~600K) companion ever directly imaged around a neighboring star. We present new high-contrast data obtained during the commissioning of the SPHERE instrument at the VLT. The data was obtained in Y-, J-, H-, and Ks-bands with the dual-band imaging (DBI) mode of IRDIS, providing a broad coverage of the full near-infrared (near-IR) range at higher contrast and better spectral sampling than previously reported. In this new set of high-quality data, we report the re-detection of the companion, as well as the first detection of a new candidate closer-in to the star. We use the new 8 photometric points for an extended comparison of GJ758 B with empirical objects and 4 families of atmospheric models. From comparison to empirical object, we estimate a T8 spectral type, but none of the comparison object can accurately represent the observed near-IR fluxes of GJ758 B. From comparison to atmospheric models, we attribute a Teff = 600K $\pm$ 100K, but we find that no atmospheric model can adequately fit all the fluxes of GJ758 B. The photometry of the new candidate companion is broadly consistent with L-type objects, but a second epoch with improved photometry is necessary to clarify its status. The new astrometry of GJ758 B shows a significant proper motion since the last epoch. We use this result to improve the determination of the orbital characteristics using two fitting approaches, Least-Square Monte Carlo and Markov Chain Monte Carlo. Finally, we analyze the sensitivity of our data to additional closer-in companions and reject the possibility of other massive brown dwarf companions down to 4-5 AU. [abridged]Comment: 20 pages, 15 figures. Accepted for publication in A&

First light of the VLT planet finder SPHERE. II. The physical properties and the architecture of the young systems PZ Tel and HD 1160 revisited

[Abridged] Context. The young systems PZ Tel and HD 1160, hosting known low-mass companions, were observed during the commissioning of the new planet finder SPHERE with several imaging and spectroscopic modes. Aims. We aim to refine the physical properties and architecture of both systems. Methods. We use SPHERE commissioning data and REM observations, as well as literature and unpublished data from VLT/SINFONI, VLT/NaCo, Gemini/NICI, and Keck/NIRC2. Results. We derive new photometry and confirm the nearly daily photometric variability of PZ Tel A. Using literature data spanning 38 yr, we show that the star also exhibits a long-term variability trend. The 0.63-3.8 mic SED of PZ Tel B allows us to revise its properties: spectral type M7+/-1, Teff=2700+/-100 K, log(g)<4.5 dex, log(L/L_Sun)=-2.51+/-0.10 dex, and mass 38-72 MJ. The 1-3.8 mic SED of HD 1160 B suggests a massive brown dwarf or a low-mass star with spectral type M5.5-7.0, Teff=3000+/-100 K, [M/H]=-0.5-0.0 dex, log(L/L_Sun)=-2.81+/-0.10 dex, and mass 39-168 MJ. We confirm the deceleration and high eccentricity (e>0.66) of PZ Tel B. For e<0.9, the inclination, longitude of the ascending node, and time of periastron passage are well constrained. The system is seen close to an edge-on geometry. We reject other brown dwarf candidates outside 0.25" for both systems, and massive giant planets (>4 MJ) outside 0.5" for the PZ Tel system. We also show that K1-K2 color can be used with YJH low-resolution spectra to identify young L-type companions, provided high photometric accuracy (<0.05 mag) is achieved. Conclusions. SPHERE opens new horizons in the study of young brown dwarfs and giant exoplanets thanks to high-contrast imaging capabilities at optical and near-infrared wavelengths, as well as high signal-to-noise spectroscopy in the near-infrared from low (R~30-50) to medium resolutions (R~350).Comment: 25 pages, 23 figures, accepted for publication in A&A on Oct. 13th, 2015; version including language editing. Typo on co-author name on astroph page corrected, manuscript unchange

Current status of the Spectrograph System for the SuMIRe/PFS

The Prime Focus Spectrograph (PFS) is a new facility instrument for Subaru Telescope which will be installed in around 2017. It is a multi-object spectrograph fed by about 2400 fibers placed at the prime focus covering a hexagonal field-of-view with 1.35 deg diagonals and capable of simultaneously obtaining data of spectra with wavelengths ranging from 0.38 um to 1.26 um. The spectrograph system is composed of four identical modules each receiving the light from 600 fibers. Each module incorporates three channels covering the wavelength ranges 0.38-0.65 mu ("Blue"), 0.63-0.97 mu ("Red"), and 0.94-1.26 mu ("NIR") respectively; with resolving power which progresses fairly smoothly from about 2000 in the blue to about 4000 in the infrared. An additional spectral mode allows reaching a spectral resolution of 5000 at 0.8mu (red). The proposed optical design is based on a Schmidt collimator facing three Schmidt cameras (one per spectral channel). This architecture is very robust, well known and documented. It allows for high image quality with only few simple elements (high throughput) at the expense of the central obscuration, which leads to larger optics. Each module has to be modular in its design to allow for integration and tests and for its safe transport up to the telescope: this is the main driver for the mechanical design. In particular, each module will be firstly fully integrated and validated at LAM (France) before it is shipped to Hawaii. All sub-assemblies will be indexed on the bench to allow for their accurate repositioning. This paper will give an overview of the spectrograph system which has successfully passed the Critical Design Review (CDR) in 2014 March and which is now in the construction phase.Comment: 9 pages, 7 figures, submitted to "Ground-based and Airborne Instrumentation for Astronomy V, Suzanne K. Ramsay, Ian S. McLean, Hideki Takami, Editors, Proc. SPIE 9147 (2014)

Post conjunction detection of β\beta Pictoris b with VLT/SPHERE

With an orbital distance comparable to that of Saturn in the solar system, \bpic b is the closest (semi-major axis $\simeq$\,9\,au) exoplanet that has been imaged to orbit a star. Thus it offers unique opportunities for detailed studies of its orbital, physical, and atmospheric properties, and of disk-planet interactions. With the exception of the discovery observations in 2003 with NaCo at the Very Large Telescope (VLT), all following astrometric measurements relative to \bpic have been obtained in the southwestern part of the orbit, which severely limits the determination of the planet's orbital parameters. We aimed at further constraining \bpic b orbital properties using more data, and, in particular, data taken in the northeastern part of the orbit. We used SPHERE at the VLT to precisely monitor the orbital motion of beta \bpic b since first light of the instrument in 2014. We were able to monitor the planet until November 2016, when its angular separation became too small (125 mas, i.e., 1.6\,au) and prevented further detection. We redetected \bpic b on the northeast side of the disk at a separation of 139\,mas and a PA of 30$^{\circ}$ in September 2018. The planetary orbit is now well constrained. With a semi-major axis (sma) of $a = 9.0 \pm 0.5$ au (1 $\sigma$), it definitely excludes previously reported possible long orbital periods, and excludes \bpic b as the origin of photometric variations that took place in 1981. We also refine the eccentricity and inclination of the planet. From an instrumental point of view, these data demonstrate that it is possible to detect, if they exist, young massive Jupiters that orbit at less than 2 au from a star that is 20 pc away.Comment: accepted by A&

Global Wheat Head Detection (GWHD) dataset: a large and diverse dataset of high resolution RGB labelled images to develop and benchmark wheat head detection methods

Detection of wheat heads is an important task allowing to estimate pertinent traits including head population density and head characteristics such as sanitary state, size, maturity stage and the presence of awns. Several studies developed methods for wheat head detection from high-resolution RGB imagery. They are based on computer vision and machine learning and are generally calibrated and validated on limited datasets. However, variability in observational conditions, genotypic differences, development stages, head orientation represents a challenge in computer vision. Further, possible blurring due to motion or wind and overlap between heads for dense populations make this task even more complex. Through a joint international collaborative effort, we have built a large, diverse and well-labelled dataset, the Global Wheat Head detection (GWHD) dataset. It contains 4,700 high-resolution RGB images and 190,000 labelled wheat heads collected from several countries around the world at different growth stages with a wide range of genotypes. Guidelines for image acquisition, associating minimum metadata to respect FAIR principles and consistent head labelling methods are proposed when developing new head detection datasets. The GWHD is publicly available at http://www.global-wheat.com/ and aimed at developing and benchmarking methods for wheat head detection.Comment: 16 pages, 7 figures, Dataset pape

SUBARU prime focus spectrograph: integration, testing and performance for the first spectrograph

The Prime Focus Spectrograph (PFS) of the Subaru Measurement of Images and Redshifts (SuMIRe) project for Subaru telescope consists in four identical spectrographs fed by 600 fibers each. Each spectrograph is composed by an optical entrance unit that creates a collimated beam and distributes the light to three channels, two visibles and one near infrared. This paper presents the on-going effort for the tests & integration process for the first spectrograph channel: we have developed a detailed Assembly Integration and Test (AIT) plan, as well as the methods, detailed processes and I&T tools. We describe the tools we designed to assemble the parts and to test the performance of the spectrograph. We also report on the thermal acceptance tests we performed on the first visible camera unit. We also report on and discuss the technical difficulties that did appear during this integration phase. Finally, we detail the important logistic process that is require to transport the components from other country to Marseille

SPHERE: the exoplanet imager for the Very Large Telescope

Observations of circumstellar environments to look for the direct signal of exoplanets and the scattered light from disks has significant instrumental implications. In the past 15 years, major developments in adaptive optics, coronagraphy, optical manufacturing, wavefront sensing and data processing, together with a consistent global system analysis have enabled a new generation of high-contrast imagers and spectrographs on large ground-based telescopes with much better performance. One of the most productive is the Spectro-Polarimetic High contrast imager for Exoplanets REsearch (SPHERE) designed and built for the ESO Very Large Telescope (VLT) in Chile. SPHERE includes an extreme adaptive optics system, a highly stable common path interface, several types of coronagraphs and three science instruments. Two of them, the Integral Field Spectrograph (IFS) and the Infra-Red Dual-band Imager and Spectrograph (IRDIS), are designed to efficiently cover the near-infrared (NIR) range in a single observation for efficient young planet search. The third one, ZIMPOL, is designed for visible (VIR) polarimetric observation to look for the reflected light of exoplanets and the light scattered by debris disks. This suite of three science instruments enables to study circumstellar environments at unprecedented angular resolution both in the visible and the near-infrared. In this work, we present the complete instrument and its on-sky performance after 4 years of operations at the VLT.Comment: Final version accepted for publication in A&