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IMIS Phenology Data Since 1998
Long-term phenological data in alpine regions are often limited to a few locations and thus, little is known about climate-change induced plant phenological shifts above the treeline. Because plant growth initiation in seasonally snow-covered regions is largely driven by snowmelt timing and local temperature, it is essential to simultaneously track phenological shifts, snowmelt, and near-ground temperatures. In this study, we make use of ultrasonic snow height sensors installed at climate stations in the Swiss Alps to reveal phenological advance of grassland ecosystems and relate them to climatic changes over 25 years (1998 – 2023). When snow is absent, these snow height sensors additionally provide information on plant growth at a uniquely fine temporal scale. Daily temperatures and snow- / plant height values, annual phenological- and melt-out dates were derived from IMIS climate station data (doi.org/10.16904/envidat.406). We observed an advance of green-up by -2.4 days/decade coinciding with strong warming of up to +0.8°C/decade. Although the timing of melt-out has not changed significantly over the study period in this focal region, phenological responses to early melt-out years varied due to differing influences of photoperiodic and thermal constraints, which were not equally important across elevations and communities. Phenological shifts of alpine grasslands are thus likely to become even more pronounced if melt-out timing advances in the future as predicted. This repository relates to the publication Zehnder et al. (2025). Snow height sensors reveal phenological advance in alpine grasslands. Global Change Biology. accepted. The model data and code that support our findings are deposited in this repository.
Soil microbial diversity and multifunctionality across European biomes
The diversity and network complexity of prokaryotic and fungal communities and their relationships with soil multifunctionality (SMF) – an integrative index for C-, N- and P-cycling functions – was investigated along a 3,000-km latitudinal transect across Europe (37° to 62°N), spanning biomes from Mediterranean drylands, temperate to boreal forests.
Anthropogenic change and soil net N mineralization
This dataset contains all data on which the following publication below is based. Paper Citation: Risch Anita C., Zimmermann, Stefan, Moser, Barbara, Schütz, Martin, Hagedorn, Frank, Firn, Jennifer, Fay, Philip A., Adler, Peter B., Biederman, Lori A., Blair, John M., Borer, Elizabeth T., Broadbent, Arthur A.D., Brown, Cynthia S., Cadotte, Marc W., Caldeira, Maria C., Davies, Kendi F., di Virgilio, Augustina, Eisenhauer, Nico, Eskelinen, Anu, Knops, Johannes M.H., MacDougall, Andrew S., McCulley, Rebecca L., Melbourne, Brett A., Moore, Joslin L., Power, Sally A., Prober, Suzanne M., Seabloom, Eric W., Siebert, Julia, Silveira, Maria L. , Speziale, Karina L., Stevens, Carly J., Tognetti, Pedro M., Virtanen, Risto, Yahdjian, Laura, Ochoa-Hueso, Raul (accepted). Global impacts of fertilization and herbivore removal on soil net nitrogen mineralization are modulated by local climate and soil properties. Global Change Biology Please cite this paper together with the citation for the datafile. We assessed how the removal of mammalian herbivores (Fence) and fertilization with growth-limiting nutrients (N, P, K, plus nine essential macro- and micronutrients; NPK) individually, and in combination (NPK+Fence), affected potential and realized soil net Nmin across 22 natural and semi-natural grasslands on five continents. Our sites spanned a comprehensive range of climatic and edaphic conditions found across the grassland biome. We focused on grasslands, because they cover 40-50% of the ice-free land surface and provide vital ecosystem functions and services. They are particularly important for forage production and C sequestration. Worldwide, grasslands store approximately 20-30% of the Earth’s terrestrial C, most of it in the soil (Schimel, 1995; White et al., 2000).
Historical Vegetation Height Model NFI
The main datasets available are 4 nationwide **Digital Surface Models (DSMs)** and corresponding **Vegetation Height Models (VHMs)** with a spatial resolution of 1 m. The Vegetation Height Models are calculated by subtraction of a Digital Terrain Model (swissAlti3d version 2017, swisstopo) from the generated DSMs. DSMs were derived by image matching of **scanned historical images** (panchromatic 8-bit) acquired with a RC10 frame camera, in the context of the swisswide image acquisition campaigns of swisstopo. Nationwide products could be generated for the **four epochs** 1979-1985 / 1985-1991 / 1990-1998 / 1998-2006. Additional information about successful image matching vs. interpolation of pixels and about the year of image acquisition are available in the corresponding files (**matched_area_xxxx_xxxx_binay.tif** and **meta_acquisition_year_xxxx_xxxx.json**, respectively). To separate vegetation from non-vegetation areas a mask derived from a combination of information of the Topographic landscape model - TLM (swisstopo) and a NDVI layer was used and is supplied as **"TLM_mask.tif"** Due to the occurrence of unrealistic vegetation height values caused by the failure of the image matching process (mainly overexposed images and clouds or very steep rocky terrain), pixel values > 60 m were set to NoData and < 0 m to 0. All datasets are available in the Reference System **LV95 (EPSG: 2056) LN02 (EPSG: 5728)** and share the common **extent definition** (xmin ymin xmax ymax): 2480000 1070000 2840000 1300000
Data and Code on Extreme Inflow and Lowflow Analysis for Alpine Reservoirs
Summary * Dataset of daily inflow to Luzzone reservoir in Ticino, Switzerland * R scripts used to generate return levels for low reservoir inflow, low precipitation, high inflow, and extreme high precipitation based on various methods from extreme value analysis Data The dataset included here is the "natural" reservoir inflow for the Luzzone reservoir. Additional analyses were conducted on daily total precipitation of 6 meteorological stations (abbreviations: TIOLI, TIOLV, COM, VRN, VLS, ZEV). These precipitation data are freely available for teaching and research from the MeteoSwiss IDAweb portal (https://www.meteoswiss.admin.ch/services-and-publications/service/weather-and-climate-products/data-portal-for-teaching-and-research.html). Codes R scripts used to determine return levels of the data set are included for both extreme high events and low events. The scripts include the following methods for calculating return levels: * GEV (Generalized Extreme Value) * GPD and GPDd (Generalized Pareto Distribution including declustered version) * eGPD (extended Generalized Pareto Distribution) * MEV (Metastatistical Extreme Value)
Cloud Optimized Raster Encoding (CORE) format
Acknowledgements: The CORE format was proudly inspired by the Cloud Optimized GeoTIFF ([COG](https://www.cogeo.org/)) format, by considering how to leverage the ability of clients issuing HTTP GET range requests for a time-series of remote sensing and aerial imagery (instead of just one image). License: The Cloud Optimized Raster Encoding (CORE) specifications are released to the public domain under a Creative Commons 1.0 CC0 "No Rights Reserved" international license. You can reuse the information contained herein in any way you want, for any purposes and without restrictions. ----------------------- Summary: The Cloud Optimized Raster Encoding (CORE) format is being developed for the efficient storage and management of gridded data by applying video encoding algorithms. It is mainly designed for the exchange and preservation of large time series data in environmental data repositories, while in the same time enabling more efficient workflows on the cloud. It can be applied to any large number of similar (in pixel size and image dimensions) raster data layers. CORE is not designed to replace COG but to work together with COG for a collection of many layers (e.g. by offering a fast preview of layers when switching between layers of a time series). WARNING: Currently only applicable to RGB/Byte imagery. The final CORE specifications may probably be very different from what is written herein or CORE may not ever become productive due to a myriad of reasons (see also 'Major issues to be solved'). With this early public sharing of the format we explicitly support the Open Science agenda, which implies "shifting from the standard practices of publishing research results in scientific publications towards sharing and using all available knowledge at an earlier stage in the research process" (quote from: European Commission, Directorate General for Research and Innovation, 2016. Open innovation, open science, open to the world). CORE Specifications: 1) a MP4 or WebM video digital multimedia container format (or any future video container playable as HTML video in major browsers) 2) a free to use or open video compression codec such as H.264, VP9, or AV1 (or any future video codec that is open sourced or free to use for end users) Note: H.264 is currently recommended because of the wide usage with support in all major browsers, fast encoding due to acceleration in hardware (which is currently not the case for AV1 or VP9) and the fact that MPEG LA has allowed the free use for streaming video that is free to the end users. However, please note that H.264 is restricted by patents and its use in proprietary or commercial software requires the payment of royalties to [MPEG LA](https://www.mpegla.com/programs/avc-h-264/). However, when AV1 matures and accelerated hardware encoding becomes available, AV1 is expected to offer 30% to 50% smaller file size in comparison with H.264, while retaining the [same quality](https://trac.ffmpeg.org/wiki/Encode/AV1). 3) the encoding frame rate should be of one frame per second (fps) with each layer segmented in internal tiles, similar to COG, ordered by the main use case when accessing the data: either layer contiguous or tile contiguous; Note: The internal tile arrangement should support an easy navigation inside the CORE video format, depending on the use case. 4) a CORE file is optimised for streaming with the moov atom at the beginning of the file (e.g. with -movflags faststart) and optional additional optimisations depending on the codec used (e.g. -tune fastdecode -tune zerolatency for H.264) 5) metadata tags inside the moov atom for describing and using geographic image data (that are preferably compatible with the [OGC GeoTIFF standard](https://www.ogc.org/standards/geotiff) or any future standard accepted by the geospatial community) as well as list of original file names corresponding to each CORE layer 6) it needs to encode similar source rasters (such as time series of rasters with the same extent and resolution, or different tiles of the same product; each input raster should be having the same image and pixel size) 7) it provides a mechanism for addressing and requesting overviews (lower resolution data) for a fast display in web browser depending on the map scale (currently external overviews) Major issues to be solved: - Internal overviews (similar to COG), by chaining lower resolution videos in the same MP4 container for fast access to overviews first); Currently, overviews are kept as separate files, as external overviews. - Metadata encoding (how to best encode spatial extent, layer names, and so on, for each of the layer inside the series, which may have a different geographical extent, etc...; Known issues: adding too many tags with FFmpeg which are not part of the standard MP4 moov atom; metadata tags have a limited string length. - Applicability beyond RGB/Byte datasets; defining a standard way of converting cell values from Int16/UInt16/UInt32/Int32/Float32/Float64/ data types into multi-band Byte values (and reconstructing them back to the original data type within acceptable thresholds) Example Notice: The provided CORE (.mp4) examples contain modified Copernicus Sentinel data [2018-2021]. For generating the CORE examples provided, 50 original Sentinel 2 (S-2) TCI data images from an area located inside Switzerland were downloaded from www.copernicus.eu, and then transformed into CORE format using ffmpeg with H.264 encoding using the [x264 library](https://www.videolan.org/developers/x264.html). DISCLAIMER: Basic scripts are provided for the Geomatics peer review (in 2021) and kept as additional information for the dataset. Nevertheless, please note that software dependencies and libraries, as well as cloud storage paths, may quickly become deprecated over time (after 2021). For compatibility, stable dependencies and libraries released around 2020 should be used.
Drifting and blowing snow distribution around structures for Alpine PV applications
This dataset groups numerical simulation outputs and validation measurement data produced in the context of the following [publication]: _not published yet_ The snow transport model [snowBedFoam] was used to analyse snow deposition around a specific type of Alpine PV structures named HELIOPLANT®. The results of a sensitivity analysis of multiple key parameters that govern the spatial organisation of these structures are provided here. Measurements of snow distribution taken from the test-site of the [Gondosolar] project, are provided too. To reproduce the results of the aforementioned publication, follow the instructions on this [repository]. [publication]: https:// [snowBedFoam]: https://www.doi.org/10.16904/envidat.223 [Gondosolar]: https://www.gondosolar.ch [repository]: https://github.com/frischwood/snowbed-helio.git
Flow and tracer data for overland flow and topsoil interflow during rainfall simulation experiments in the Studibach catchment - Alptal - Switzerland
Description: This dataset comprises the time series of overland flow (OF) and topsoil interflow (TIF) discharge, and tracer concentrations during artificial rainfall simulation experiments at two large (>80 m2) trenched runoff plots in the Studibach catchment in the Alptal, a typical pre-Alpine headwater catchment in Switzerland. One plot is located in a natural clearing in an open mixed forest and the other in a grassland. Together, they represent the dominant land cover types in the region. We applied streamwater to the surface of the plots using sprinklers and added tracers after OF and TIF had reached steady state. Deuterium enriched water was applied to the surface of the plots via the sprinklers, while Uranine and NaCl were applied as a line tracer at multiple distances from the trench. NaBr was injected into the topsoil at ~20 cm depth. Samples of overland flow and topsoil interflow were collected for several hours after tracer application, while the sprinklers continued to apply water to the surface. The runoff was collected into self-made "Upwelling Bernoulli Tubes" and the water level inside these tubes was measured using pressure sensors (DCX-22-CTD, Keller Druck, Switzerland) at a 1-min resolution during the day and 5-min resolution during the night. Uranine concentrations and electrical conductivity (EC) were recorded at a 1-minute interval. Samples for deuterium and Bromide were analysed in the lab. The celerity of overland flow and topsoil interflow was determined during another experiment by temporarily adding more water to the surface of the plots at different distances from the trench after steady state conditions had been reached. The overland flow and topsoil interflow discharge were again measured using the Upwelling Bernoulli Tubes and pressure transducers.
The influence of snow microstructure on the compressive mechanical properties of weak snowpack layers
This repository hosts the experimental data accompanying our publication "The influence of snow microstructure on the compressive mechanical properties of weak snowpack layers" feautured in Acta Materialia. - Experimental Data and microstructural descriptors: Full dataset used for the main analysis of the paper. Contains the measured mechanical properties, µCT parameters, further analysis, etc. The column "ID" (e.g. 363) links this data with the 3D µCT dataset (e.g. e0000363). - 3D Data of the segmented µCT scans: Full dataset containing the raw segmented µCT scans in the MetaIO format. They can be opened using the SimpleITK package (`pip install SimpleITK`). Note: the Files can be idenfied by their scan number in the filename, (e.g, e0000363) `import SimpleITK as sitk ` `img = sitk.ReadImage("e0000363_crop_seg.mhd") ` `array = sitk.GetArrayFromImage(img) ` shape: [z, y, x] `array_xyz = np.transpose(array, (2, 1, 0))` (Optional) for array axes in [x, y, z] `spacing = img.GetSpacing() ` voxel size (x,y,z)
Environmental DNA Marine France Calanques 2022
Description: Fish environmental DNA data set collected in 2022 in the Calanques National Park The eDNA samples were collected in 2022 in two locations (Moyades, M−FPA and “Impérial du large”, I-LPA), during the winter (January- February), the summer (June to August)and fall (mid-September to November) seasons, with the sampling dates depending on the weather conditions. For the M−FPA, samples were collected between Moyades island and Riou island, while for the I-LPA, they were collected on the south side of the “Impérial du large” island. To account for the existing bathymetry, in the M−FPA the samples were taken at two sampling sites with depths of 20 and 40 m, while in the I-LPA they were taken at two sites with depths of 20 and 80 m. At each site, in-situ filtration of seawater was performed using a double-head submersible pump (Subspace, Geneva, Switzerland; nominal flow of ca. 1 L/min) strapped to an underwater scooter with 2 VigiDNA 0.20 µm filtration capsules (SPYGEN, le Bourget du Lac, France), along with disposable sterile tubing. The samples were collected along two horizontal transects (up to 400 m in length) during each closed-circuit rebreather dive, enabling the filtration of a water volume of 15 L/filter per depth, as close as possible to the substrate. Two filter replicates were collected by two divers at each sampling site, except in two cases where bad weather conditions or logistical issues meant that only one replicate was sampled. After the filtration, the remaining seawater was emptied from the capsule back on the boat and replaced by a 80 mL CL1 conservation buffer (SPYGEN, le Bourget du Lac, France). To prevent any contamination, a strict protocol was followed during the entire process, requiring disposable gloves and single-use filtration equipment. Finally, the samples were stored at room temperature. We followed a strict contamination control protocol in both field and laboratory stages. Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris). Data content: * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)