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[Abbreviated] The amount of integral field spectrograph (IFS) data has grown considerable over the last few decades. The demand for tools to analyze such data is therefore bigger now than ever. We present TDOSE; a flexible Python tool for Three Dimensional Optimal Spectral Extraction from IFS data cubes. TDOSE works on any three-dimensional data cube and bases the spectral extractions on morphological reference image models. In each wavelength layer of the IFS data cube, TDOSE simultaneously optimizes all sources in the morphological model to minimize the difference between the scaled model components and the IFS data. The flux optimization produces individual data cubes containing the scaled three-dimensional source models. This allows for efficient de-blending of flux in both the spatial and spectral dimensions of the IFS data cubes, and extraction of the corresponding one-dimensional spectra. We present an example of how the three-dimensional source models generated by TDOSE can be used to improve two-dimensional maps of physical parameters. By extracting TDOSE spectra of $\sim$150 [OII] emitters from the MUSE-Wide survey we show that the median increase in line flux is $\sim$5% when using multi-component models as opposed to single-component models. However, the increase in recovered line emission in individual cases can be as much as 50%. Comparing the TDOSE model-based extractions of the MUSE-Wide [OII] emitters with aperture spectra, the TDOSE spectra provides a median flux (S/N) increase of 9% (14%). Hence, TDOSE spectra optimizes the S/N while still being able to recover the total emitted flux. TDOSE version 3.0 presented in this paper is available at https://github.com/kasperschmidt/TDOSE., Comment: Accepted by A&A, 24 pages and 11 figures, code available at https://github.com/kasperschmidt/TDOSE

We present the MUSE-Wide survey, a blind, 3D spectroscopic survey in the CANDELS/GOODS-S and CANDELS/COSMOS regions. Each MUSE-Wide pointing has a depth of 1 hour and hence targets more extreme and more luminous objects over 10 times the area of the MUSE-Deep fields (Bacon et al. 2017). The legacy value of MUSE-Wide lies in providing "spectroscopy of everything" without photometric pre-selection. We describe the data reduction, post-processing and PSF characterization of the first 44 CANDELS/GOODS-S MUSE-Wide pointings released with this publication. Using a 3D matched filtering approach we detected 1,602 emission line sources, including 479 Lyman-$\alpha$ (Lya) emitting galaxies with redshifts $2.9 \lesssim z \lesssim 6.3$. We cross-match the emission line sources to existing photometric catalogs, finding almost complete agreement in redshifts and stellar masses for our low redshift (z < 1.5) emitters. At high redshift, we only find ~55% matches to photometric catalogs. We encounter a higher outlier rate and a systematic offset of $\Delta$z$\simeq$0.2 when comparing our MUSE redshifts with photometric redshifts. Cross-matching the emission line sources with X-ray catalogs from the Chandra Deep Field South, we find 127 matches, including 10 objects with no prior spectroscopic identification. Stacking X-ray images centered on our Lya emitters yielded no signal; the Lya population is not dominated by even low luminosity AGN. A total of 9,205 photometrically selected objects from the CANDELS survey lie in the MUSE-Wide footprint, which we provide optimally extracted 1D spectra of. We are able to determine the spectroscopic redshift of 98% of 772 photometrically selected galaxies brighter than 24th F775W magnitude. All the data in the first data release - datacubes, catalogs, extracted spectra, maps - are available on the website https://musewide.aip.de. [abridged], Comment: 25 pages 15+1 figures. Accepted, A&A. Comments welcome

Galaxies are surrounded by large reservoirs of gas, mostly hydrogen, fed by inflows from the intergalactic medium and by outflows due to galactic winds. Absorption-line measurements along the sightlines to bright and rare background quasars indicate that this circumgalactic medium pervades far beyond the extent of starlight in galaxies, but very little is known about the spatial distribution of this gas. A new window into circumgalactic environments was recently opened with the discovery of ubiquitous extended Lyman-alpha emission from hydrogen around high-redshift galaxies, facilitated by the extraordinary sensitivity of the MUSE instrument at the ESO Very Large Telescope. Due to the faintness of this emission, such measurements were previously limited to especially favourable systems or to massive statistical averaging. Here we demonstrate that low surface brightness Lyman-alpha emission surrounding faint galaxies at redshifts between 3 and 6 adds up to a projected sky coverage of nearly 100%. The corresponding rate of incidence (the mean number of Lyman-alpha emitters penetrated by any arbitrary line of sight) is well above unity and similar to the incidence rate of high column density absorbers frequently detected in the spectra of distant quasars. This similarity suggests that most circumgalactic atomic hydrogen at these redshifts has now been detected also in emission., Comment: published in Nature, online on 01 Oct 2018, in print on 11 Oct 2018. This is the Authors' version, for the published version see https://www.nature.com/articles/s41586-018-0564-6 ; free viewing access via https://rdcu.be/8eCx

We present a clustering analysis of a sample of 238 Ly{$\alpha$}-emitters at redshift 3

We present a first instalment of the MUSE-Wide survey, covering an area of 22.2 arcmin$^2$ (corresponding to $\sim$20% of the final survey) in the CANDELS/Deep area of the Chandra Deep Field South. We use the MUSE integral field spectrograph at the ESO VLT to conduct a full-area spectroscopic mapping at a depth of 1h exposure time per 1 arcmin$^2$ pointing. We searched for compact emission line objects using our newly developed LSDCat software based on a 3-D matched filtering approach, followed by interactive classification and redshift measurement of the sources. Our catalogue contains 831 distinct emission line galaxies with redshifts ranging from 0.04 to 6. Roughly one third (237) of the emission line sources are Lyman $\alpha$ emitting galaxies with $3 < z < 6$, only four of which had previously measured spectroscopic redshifts. At lower redshifts 351 galaxies are detected primarily by their [OII] emission line ($0.3 \lesssim z \lesssim 1.5$), 189 by their [OIII] line ($0.21 \lesssim z \lesssim 0.85$), and 46 by their H$\alpha$ line ($0.04 \lesssim z \lesssim 0.42$). Comparing our spectroscopic redshifts to photometric redshift estimates from the literature, we find excellent agreement for $z<1.5$ with a median $\Delta z$ of only $\sim 4 \times 10^{-4}$ and an outlier rate of 6%, however a significant systematic offset of $\Delta z = 0.26$ and an outlier rate of 23% for Ly$\alpha$ emitters at $z>3$. Together with the catalogue we also release 1D PSF-weighted extracted spectra and small 3D datacubes centred on each of the 831 sources., Comment: 24 pages, 14 figures, accepted for publication in A&A, data products are available for download from http://muse-vlt.eu/science/muse-wide-survey/ and later via the CDS

We describe the execution and data reduction of the European Southern Observatory Large Programme "Quasars and their absorption lines: a legacy survey of the high-redshift universe with VLT/XSHOOTER" (hereafter `XQ-100'). XQ-100 has produced and made publicly available an homogeneous and high-quality sample of echelle spectra of 100 QSOs at redshifts z~3.5-4.5 observed with full spectral coverage from 315 to 2500 nm at a resolving power ranging from R~4000 to 7000, depending on wavelength. The median signal-to-noise ratios are 33, 25 and 43, as measured at rest-frame wavelengths 1700, 3000 and 3600 Angstrom, respectively. This paper provides future users of XQ-100 data with the basic statistics of the survey, along with details of target selection, data acquisition and data reduction. The paper accompanies the public release of all data products, including 100 reduced spectra. XQ-100 is the largest spectroscopic survey to date of high-redshift QSOs with simultaneous rest-frame UV/optical coverage, and as such enables a wide range of extragalactic research, from cosmology and galaxy evolution to AGN astrophysics., Comment: In press at A&A. Table A.2 updated to match the summary table in the ESO archive