Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
207
datasets available to search
ShareScore release 0.9.0
Dataset results
207 results for “spatial response”
Open Database of Spatial Room Impulse Responses at Detmold University of Music
<p>This repository contains an open source database of Spatial Room Impulse Responses (SRIR) captured at three different performance spaces of the Detmold University of Music. It includes the following rooms: </p> <ul> <li>Detmold Konzerthaus (medium sized concert hall, ~600 seats).</li> <li>Brahmssaal (small music chamber room, ~100 seats).</li> <li>Detmold Sommertheater (theater, ~300 seats).</li> </ul> <p>The collection contains approximately 600 multichannel RIRs corresponding to several source and receiver configurations. For each room we include measurement positions on stage and at the audience area captured with both an artificial head and an open microphone array compatible with the Spatial Decomposition Method (SDM).</p> <p>The Detmold Konzerthaus holds a large scale Wave Field Synthesis system and a Room Acoustic Enhancement System. SRIRs of an ensemble of focused sources on stage and with conditions of increased artificial reverberation are also included.</p> <p>If you use this dataset for your research, please cite our work:</p> <p>Amengual Gari, S. V.; Sahin, B.; Eddy, D; Kob, M.: <strong>"Open Database of Spatial Room Impulse Responses at Detmold University of Music"</strong>, <em>149th Convention of the Audio Engineering Society, </em>2020.</p> <p> </p> <p>The database is organized in 3 sets:</p> <p><strong>- Set A: </strong></p> <p>Source: Single Source measurements.</p> <p>Receiver: Open Array and Dummy Head.</p> <p>Rooms: BS, DST, KH</p> <p>Special configurations: Artificial reverberation, music stand on stage</p> <p><strong>- Set B: </strong></p> <p>Source: Loudspeaker and WFS orchestra</p> <p>Receiver: Open Array.</p> <p>Rooms: KH</p> <p><strong>- Set C:</strong></p> <p>Source: Loudspeaker orchestra</p> <p>Receiver: Dummy Head and Omni8 array</p> <p>Rooms: KH</p> <p> </p> <p>Further details on the measurement procedure and acoustical analysis of the RIRs can be found in the following publications:</p> <p><strong>Set A</strong></p> <p>Amengual Gari, S. V., Investigations on the Influence of Acoustics on Live Music Performance using Virtual Acoustic Methods, Ph.D. thesis, 2017.</p> <p>Amengual Garí, S. V.; Kob, M: "Investigating the impact of a music stand on stage using spatial impulse responses". 142nd Convention of the Audio Engineering Society, Berlin, May 2017.</p> <p><strong>Set B</strong></p> <p>Amengual Garí, S. V.; Pätynen, J.; Lokki, T.: "Physical and perceptual comparison of real and focused sound sources in a concert hall". Journal of the Audio Engineering Society, vol. 64 (12), pp. 1014-1025, December 2016.</p> <p><strong>Set C</strong></p> <p>Sahin, B., ““Investigation of the Detmold Concert Hall auditorium acoustics by comparing preference ratings and objective measurements.”, M.Sc. Thesis, 2017.</p> <p>Sahin, B., Amengual, S. V., and Kob, M., “Investigating listeners’ preferences in Detmold Concert Hall by comparing sensory evaluation and objective measurements,” Proc. 43th DAGA, Kiel, 2017.<br> </p>
Dataset of Spatial Room Impulse Responses in a Variable Acoustics Room for Six Degrees-of-Freedom Rendering and Analysis
<p>Room acoustics measurements are used in many areas of audio research, from physical acoustics modelling and speech enhancement to virtual reality applications. This paper documents the technical specifications and choices made in the measurement of a dataset of spatial room impulse responses (SRIRs) in a variable acoustics room. Two spherical microphone arrays are used: the mh Acoustics Eigenmike em32 and the Zylia ZM-1, capable of up to fourth- and third-order Ambisonic capture, respectively. The dataset consists of three source and seven receiver positions, repeated with five configurations of the room's acoustics with varying levels of reverberation. Possible applications of the dataset include six degrees-of-freedom (6DoF) analysis and rendering, SRIR interpolation methods, and spatial dereverberation techniques. </p> <p>Accompanying paper on details of the dataset measurement: https://arxiv.org/abs/2111.11882</p> <p>Changelog:</p> <p>V 1.0 - Initial version.<br> V 1.1 - SOFA files updated to latest Matlab API (1.1.3), 'SingleRoomDRIR' convention, with SourcePosition and ListenerPosition z data corrected. Changed ListenerPosition and SourcePosition x data so that it follows the convention of origin in bottom left corner (rather than the previous bottom right). Fixed the swapped x and y labels in 6dof_source_and_receiver_positions.pdf.</p>
Dataset for: Application of Machine Learning for the Spatial Analysis of Binaural Room Impulse Responses
<p>This repository contains supplementary material for the paper titled `Application of Machine Learning for the Spatial<br> Analysis of Binaural Room Impulse Responses' Available at: <a href="http://dx.doi.org/10.3390/app8010105">dx.doi.org/10.3390/app8010105</a> . These programs and audio files are distributed in the hopes that they will prove useful under the Creative Commons Attribution 4.0, with no warranty; or the implied warranty of merchantability or fitness for a particular problem. Please give appropriate credit for use of the material provided in this repository back to the author. </p> <p>In order to use the MatLab code the Auditory Toolbox by Malcolm Slaney [1] and the Cochleagram function distributed by Bin Gao [2] are required.</p> <p>The python scrips require the following Python libraries to be installed: Numpy[3], SciPy[4] and Tensorflow [5].</p> <p>The MatLab code was tested using MatLab R2017a on a Computer running windows 7.</p> <p>The python code was tested using Python 3.2.5, using an anaconda Python environment - in windows command line.</p> <p>--</p> <p>The repository contains:</p> <p>Folders:</p> <p><br> 1.) neg90 - This folder contains the gaussian normalisation parameters stored as text files and the weights and biases for the trained neural network - these are all for the -90° rotation neural network.</p> <p>2.) pos90 - This folder contains the gaussian normalisation parameters stored as text files and the weights and biases for the trained neural network - these are all for the +90° rotation neural network.</p> <p>3.) testData - this folder contains pre-generated test data for the different binaural dummy head microphones, speaker, and signal type combinations.</p> <p>Python Scripts:</p> <p><br> 1.) AnalyseDoA.py - A python script that can be run to test the neural network using the pre-generated test data - running the script will allow the user to input the binaural dummy head, speaker, and signal type. The important variables generated by this script are DoA - the direction of arrival for each signal in the feature vector, and yDiff - the difference between the predicted DoA and the expected direction of arrival</p> <p>2.) DirectionAnalysis.py - This python file contains a set of function that are used to define the neural network, and run it. The function called DoAPrediction takes the feature vector generated by the MatLab code as its input argument, these features will then be passed to the neural network, and the output of this function is the direction of arrival predicted by the neural network for each signal. The functions: DoAAnalysis_neg90 and DoAAnalysis_pos90 are called by the DoAPrediction function, these functions create the neural network using the NN function, import the weights and biases, and passes the feature matrix (provided as input) through the neural network - the output of these functions are the predicted direction of arrival.</p> <p>MatLab files:</p> <p><br> 1.) runAnalysis.m - This MatLab script analyses the dataset provided as part of this repository. Users can change the variables head ('KEMAR' or 'KU100'), signalType ('directSound' or 'reflection'), and speaker ('EquatorD5' or 'Genelec8030'). This script will produce the gaussian normalised feature vector and expected direction of arrival for all signals with the defined head, signal type, and speaker combination. These variables are then saved in .mat files so they can be imported by the python scripts.</p> <p>2.) BinauralModelCochlea.m - This MatLab function analyses a given binaural signal and outputs the interaural cross-correlation, interaural level difference, interaural time difference, the cochlea output for the left and right channel and the centre frequencies of the gammatone filter band. The input variables are: IR - the signal to be analysed, N - the number of gammatone filters, freqLow - the lowest centre frequency of the gammatone filter bank (centre frequency of the first gammatone filter), and freqHigh - the highest centre frequency of the gammatone filter bank (the centre frequency of the Nth gammatone filter). This function requires Malcolm Slaney's Auditory Toolbox [1] and Bin Gao's Cochleagram function [2] in order to work.</p> <p>3.) generateFeatureVector.m - This MatLab function generates a feature vector from an input binaural signal x, and a version of the signal captured after the binaural dummy head has been rotated by either +90° or -90° degree (variables xPos90 and xNeg90 respectively). If the sampling frequency (Fs) isn't 44100, the signals are resampled to be at 44100. This file also contains a function 'gaussianNormalisationTestData' which gaussian normalises the data using the mean and standard deviation calculated from the data used to train the neural networks - the mean and standard deviation values are stored in the folder GMParams in the pos90 and neg90 folders.</p> <p>4.) generateTestData.m - This MatLab function analyses the included binaural dataset, it takes the input variables: head - the binaural dummy head used for the measurements either 'KEMAR' or 'KU100', speaker - the speaker used for the measurements either 'EquatorD5' or 'Genelec8030', and signalType - the type of signal being analysed either 'directSound' or 'reflection'.</p> <p>Text files:</p> <p><br> 1.) noLayers.txt - a text file containing the number of layers used when training the neural network - with the current version of the code the neural network contains only 1 layer.</p> <p>2.) README.txt - Read me file containing information about the repository.</p> <p>Audio files:</p> <p><br> This repository contains 1152 binaural signals half of which are direct sounds segmented from a binaural room impulse responses and the other half are reflections segmented from binaural room impulse responses (detailed in the paper this material supports) the direct sounds are recorded at angles from 0° to 357.5° in steps of 2.5° and the reflections are recorded at angles of 1° to 358.5° in steps of 2.5°. In the paper only recordings relating to signals recorded with the Equator D5 are analysed.</p> <p>The combination of audio files include:</p> <p>1.) 144 direct sound recordings captured with the KEMAR 45BC binaural dummy head microphone and the Equator D5 speaker<br> 2.) 144 reflection recordings captured with the KEMAR 45BC binaural dummy head microphone and the Equator D5 speaker<br> 3.) 144 direct sound recordings captured with the KU100 binaural dummy head microphone and the Equator D5 speaker<br> 4.) 144 reflection recordings captured with the KU100 binaural dummy head microphone and the Equator D5 speaker<br> 5.) 144 direct sound recordings captured with the KEMAR 45BC binaural dummy head microphone and the Genelec 8030 speaker<br> 6.) 144 reflection recordings captured with the KEMAR 45BC binaural dummy head microphone and the Genelec 8030 speaker<br> 7.) 144 direct sound recordings captured with the KU100 binaural dummy head microphone and the Genelec 8030 speaker<br> 8.) 144 reflection recordings captured with the KU100 binaural dummy head microphone and the Genelec 8030 speaker</p> <p>The files are stored using the following file naming convention:<br> head_Test3_speaker_signalType_000_0_Degrees.wav - where _000_0 defines the azimuth direction of arrival so for example for a direct sound measured with the KEMAR unit and the Genelec8030 at 5 degrees would be 'KEMAR_Test3_Genelec8030_directSound_005_0Degrees.wav' and for a reflection measured with the KU100 and the Equator D5 at 298.5 degrees would be 'KU100_Test3_EquatorD5_reflection_298_5Degrees.wav'</p> <p>--</p> <p>Bibliography:<br> [1] Slaney, M. (1998). Auditory Toolbox. Palo Alto, CA. [Online]. Available: https://engineering.purdue.edu/~malcolm/interval/1998-010/ [Accessed: Oct. 27, 2017]</p> <p>[2] Gao, B. (2014). Cochleagram and IS-NMF2D for Blind Source Separation. [Online] Available: http://uk.mathworks.com/matlabcentral/fileexchange/48622-cochleagram-and-is-nmf2d-for-blind-source-separation?focused=3855900&tab=function [Accessed: Oct. 27, 2017]</p> <p>[3] NumFocus. (n.d.). NumPy. [Online]. Available: http://www.numpy.org/ [Accessed: Oct. 27, 2017]</p> <p>[4] SciPy. (n.d.). SciPy. [Online]. Available: https://www.scipy.org/ [Accessed: Oct. 27, 2017]</p> <p>[5] Google. (n.d.). TensorFlow. [Online] Available: https://www.tensorflow.org/ [Accessed: Oct. 27, 2017]</p> <p>--</p> <p>All code and audio produced by: Michael Lovedee-Turner, PhD candidate in Music Technology at the Audio Lab, Department of Electronic Engineering, University of York</p> <p>Contact: mjlt500@york.ac.uk</p>
Data for: Crall et al., Spatial fidelity of workers predicts collective response to disturbance in a social insect
<p>Dataset for: Crall et al., Spatial fidelity of workers predicts collective response to disturbance in a social insect, in final revision for Nature Communications.</p> <p>Includes two files - one behavioral data from uniquely identified worker bumblebees, and the second containing metadata for the colonies from which these data were generated (including experimental treatments, locations, sizes, etc.).</p>
Modeling biogeochemical responses of tundra ecosystems to temporal and spatial variations in climate in the Kuparuk River Basin , Alaska, 1921 to 2100.
Output data set of the MBL-GEM III model run for tussock tundra in the Kuparuk River Basin, Alaska, described in detail in Le Dizès, S., B. L. Kwiatkowski, E. B. Rastetter, A. Hope, J. E. Hobbie, D. Stow, and S. Daeschner, Modeling biogeochemical responses of tundra ecosystems to temporal and spatial variations in climate in the Kuparuk River Basin (Alaska), J. Geophys. Res., 108(D2), 8165, doi:10.1029/2001JD000960, 2003. We ran the model at a 10 km x 10 km resolution for 123 cells at a yearly time step for 180 years, from 1921 to 2100. Two scenarios enabled the investigation of the effects of two opposing climate change scenarios for the 2001-2100 future period: warmer and wetter ("wet scenario" or Scenario 1) and warmer and drier ("dry scenario" or Scenario 2). These 246 files contain all simulation results for each scenario for individual cells in the Kuparuk River basin.
Identifying the drivers and responses of abrupt changes across spatial and temporal scales in ecology: a review
Recently, the theoretical basis for understanding abrupt changes in ecosystems relative to regime shifts has emerged (Ratajczak et al. 2018). Abrupt changes are defined as, “substantial changes in the mean or variability of a system that occur in a short period of time relative to typical rates of change” (Ratajczak et al. 2018). Despite a driver-response framework to guide the environmental conditions under which abrupt changes are likely to occur coupled with many examples of unexpected changes from long-term ecological research, our theoretical basis of understanding of abrupt changes doesn’t include long-term scales, variability in drivers and responses, changes in the magnitude or direction of drivers, or the interactions among multiple drivers across spatiotemporal scales (sensu Ratajczak et al. 2018). Further, a critical review of the literature is lacking and essential to further understanding how common abrupt changes are detected and reported, as well as patterns and scales of drivers and responses of abrupt change in ecosystems. To address this knowledge gap, we searched the existing ecological literature for evidence and commonalities of abrupt change across ecosystems to identify commonalities and differences of abrupt change drivers and responses across terrestrial, freshwater, and marine ecosystems. We specifically asked the following questions: (1) How common are abrupt changes reported in the ecological literature? (2) How do driver and response temporal and spatial scales of abrupt changes compare and vary across terrestrial, freshwater, and marine ecosystem types? (3) Is there relative congruence between the temporal and spatial scale of drivers and responses? (3) What are common types of drivers and responses to abrupt changes, and how do they vary across ecosystem types? (4) What terms are most associated with drivers and responses of abrupt changes among ecosystem types?
Spatially corrected dataset for natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The spatially corrected data of Arabidopsis thaliana accessions, which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic.</p> <p>The spatial correction was done using the asreml package. The data was subsequently used for the Genome-Wide Association Study. </p>
Preference and familiarity mediate spatial responses of a large herbivore to experimental manipulation of resource availability: datasets
<p>Publicly available dataset for:</p> <p>N. Ranc, P.R. Moorcroft, K.W. Hansen, F. Ossi, T. Sforna, E. Ferraro, A. Brugnoli & F. Cagnacci. 2020. Preference and familiarity mediate spatial responses of a large herbivore to experimental manipulation of resource availability. Scientific Reports. https://doi.org/10.1038/s41598-020-68046-7</p>
Data from: A species' response to spatial climatic variation does not predict its response to climate change
<p>The dominant paradigm for assessing ecological responses to climate change assumes that future states of individuals and populations can be predicted by current, species-wide performance variation across spatial climatic gradients. However, if the fates of ecological systems are better predicted by past responses to <em>in situ</em> climatic variation through time, this current analytical paradigm may be severely misleading. Empirically testing whether spatial or temporal climate responses better predict how species respond to climate change has been elusive, largely due to restrictive data requirements. Here we leverage a newly collected network of ponderosa pine tree-ring time series to test whether statistically inferred responses to spatial versus temporal climatic variation better predict how trees have responded to recent climate change. When compared to observed tree growth responses to climate change since 1980, predictions derived from spatial climatic variation were wrong in both magnitude and direction. This was not the case for predictions derived from climatic variation through time, which were able to replicate observed responses well. Future climate scenarios through the end of the 21st century exacerbated these disparities. These results suggest that the currently dominant paradigm of forecasting the ecological impacts of climate change based on spatial climatic variation may be severely misleading over decadal to centennial timescales.</p>
Stability of rocky intertidal communities in response to species removal varies across spatial scales
<p>Improving our understanding of stability across spatial scales is crucial in the current scenario of biodiversity loss. Still, most empirical studies of stability target small scales. Here we experimentally removed the local space-dominant species (macroalgae, barnacles, or mussels) at eight sites spanning more than 1000 km of coastline in north- and south-central Chile, and quantified the relationship between area (the number of aggregated sites) and stability in aggregate community variables (total cover) and taxonomic composition. Resistance, recovery, and invariability increased nonlinearly with area in both functional and compositional domains. Yet, the functioning of larger areas achieved a better, albeit still incomplete, recovery than composition. Compared with controls, smaller disturbed areas tended to overcompensate in terms of total cover. These effects were related to enhanced available space for recruitment (resulting from the removal of the dominant species), and to increasing beta diversity and decaying community-level spatial synchrony (resulting from increasing area). This study provides experimental evidence for the pivotal role of spatial scale in the ability of ecosystems to resist and recover from chronic disturbances. This knowledge can inform further ecosystem restoration and conservation policies.</p>
A dataset of measured spatial room impulse responses in different rooms including visualization
<p>An open-source dataset of captured spatial room impulse responses (SRIRs) is presented. The<br> data was collected in different enclosed spaces at the Technische Universität Ilmenau using an open self-build<br> microphone array design following the spatial decomposition method (SDM) guidelines. The included rooms<br> were selected based on their distinctive acoustical properties resulting from their general build and furnishing as<br> required by their utility. Three different classes of spaces can be distinguished, including seminar rooms, offices,<br> and classrooms. For each considered space different source-receiver positions were recorded, including 360°<br> images for each condition. The dataset can be utilized for various augmented or virtual reality applications, using<br> either a loudspeaker or headphone-based reproduction alongside the appropriate head-related transfer function sets.<br> In future, we plan to add more rooms and more source-receiver positions.</p> <p>Please cite our corresponding paper:</p> <p>Klein, F., Surdu, T., Aretz, A., Birth, K., Edelmann, N., Seitelman, F., Ziener, C., Werner, S., and Sporer, T., “A dataset of measured spatial room impulse responses in different rooms including visualization,” in 152nd AES Convention, 2022, https://www.aes.org/e%E2%80%90lib/browse.cfm?elib=21728</p> <p> </p>
Supplementary material 1 from: Dainese M, Poldini L (2012) Does residence time affect responses of alien species richness to environmental and spatial processes? NeoBiota 14: 47-66. https://doi.org/10.3897/neobiota.14.3273
Supplementary material 1 from: Dainese M, Poldini L (2012) Does residence time affect responses of alien species richness to environmental and spatial processes? NeoBiota 14: 47-66. https://doi.org/10.3897/neobiota.14.3273
Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy
<p>Data associated with Chen, Nieman, Spurrell et al "Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy" Nature Immunology, 2024. </p> <p>(1) Multiplex RNA scope. Processed cell-level data from 3 datasets, separated into manually selected "Stem Immunity" regions and "Tumor" regions, in separate files. </p> <p>(2) GeoMx. Unprocessed GeoMex data, with standard fields provided by Nanostring software. </p> <p>(3) MERFISH. Transcript-level information, including CellPose and Baysor segmentation. </p> <p>(4) Co-registered multispectral RNA and protein images. Processed cell-level data from 46 patients. Patient-level meta data information is available in supplementary table 1, tab B_Patient_Metadata. Fluorophore channel information is Figure 1a. </p> <p>Paper: <a title="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2" href="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2">https://www.nature.com/articles/s41590-024-01792-2</a></p>
Multi-Purpose Room Impulse Response Dataset Measured on a 3D Spatial Grid
<h1>Introduction</h1> <p>The sound field inside a room depends on many factors, such as the room shape, the absorption characteristics of the materials that comprise the bounding surfaces, the furniture present in the room, and the source position and its acoustic characteristics. An increasing number of publicly available room impulse response (RIR) databases that aim to provide detailed descriptions of interior sound fields can be found in the literature. These databases can be utilized in research as well as in the development and verification of signal processing algorithms that use this information on the acoustic environment. The availability of many RIR databases covering diverse scenarios is beneficial to the community.</p> <p>We provide a database of RIRs, namely the <strong>M</strong>ulti-<strong>P</strong>urpose <strong>RIR</strong> (<strong>MP-RIR</strong>) dataset, which contains 68736 RIRs measured on a dense 3D grid inside a complex-shaped room. We used a measurement robot with a rotating arm that operates as a linear guide and is capable of moving a vertical, linear array of eight omni-directional microphones. Four different sources have been used and were placed at eight different positions inside the room. A detailed desciption of the measurement campaign and the dataset is presented in the paper (https://aes2.org/publications/elibrary-page/?id=22515). </p> <h1>Contents of the MP-RIR dataset</h1> <p>In the following, the contents and the structure of the provided dataset are described:</p> <ul> <li>Sk_Mrir.npy:<br>Matrix, which contains the RIRs for all measured grid points for the loudspeaker Sk, k = 1, 2, ..., 8.<br>The matrix has the shape [N_xy, N_z, N] = [1074 x 8 x 100096], where N_xy is the number of 2D grid positions to which the robot is moving the vertical microphone array of N_z microphones. The length of each RIR is described by N.</li> <li>Mxyz.npy:<br>Matrix, which contains the microphone coordinates of the measured RIRs and corresponds to the matrices Sk_Mrir.<br>The matrix has the shape [N_xy, N_z, N_d] = [1074 x 8 x 3]. The indexing for the first two dimensions is the same as for the matrices Sk_Mrir, so that the microphone coordinates can be immediately retrieved for the provided RIRs. The third dimension with the length N_d gives access to the x-, y- and z-coordinate values in meters.</li> <li>Setup.npz<br>Dictionary, which contains parameters related to the measurement setup, with the following keys:<br> <ul> <li>angles_speaker<br>Dictionary of azimuth angles in degrees of the loudspeakers, with the keys S1, S2, ..., S8.</li> <li>coord_speaker_center<br>Dictionary, which contains the x-, y- and z-coordinates of the loudspeaker positions at the center of the base of each loudspeaker. The coordinate arrays can be accessed with the keys S1, S2, ..., S8.</li> <li>coord_polygon<br>Array of shape [4,2], which contains the x- and y-coordinates in meters of the room corners C_q, q=0,1,2,3.<br>The first dimension of the array relates to the room corners and the second dimension relates to the coordinates. </li> <li>fs<br>Sampling rate in Hz.</li> <li>T_guard<br>Guard time in samples. The guard time provides additional samples at the beginning of the RIR to increase the quality of the RIR.</li> <li>T_system<br>Delay of the measurement system in samples.</li> </ul> </li> </ul> <h1>Further Information</h1> <p>The delay of the RIRs is composed of the guard time T_guard, the system delay T_system and the acoustic delay T_ac. The guard time and system delay can be retrieved from the file Setup.npz described above.</p> <p>A gain alignment procedure was applied to align the output SPL between the loudspeakers, as described in the paper. Additionally, all RIRs were scaled by the same value, the maximum absolute peak of all measured RIRs. As a result, the maximum absolute value in each individual RIR is less or equal to 1.</p>
Spatial Room Impulse Response Dataset: A Robot's Journey Through Coupled Rooms of a Reverberant University Building
<p>This is a dataset of Spatial Room Impulse Responses obtained by a robot equipped with a microphone array.</p> <p>The measurements were conducted in a reverberant university building, the <em>Helmholtz</em> building at<em> Technische Universität Ilmenau</em> (coordinates: N50.6815788133375°, E10.939294371903342°). All the floors in the building are covered with bare stone tiles, the walls are not acoustically treated. Only the hallway has a suspended acoustic ceiling. The file "Pictures Overview.jpg" shows some impressions of the building. Note that the floorplan only shows parts of the building that were connected to the measurement area by open doors.</p> <p>The area covered by the robot is in a hallway on the top floor (2nd floor starting with ground floor) with two stairwells at both ends. To specifically study the behavior of coupled rooms and occluded sources, the sound sources were placed in adjacent sections of the building and on multiple floors. See the file "Measurement Overview.jpg" for an overview of the source positions and the receiver areas covered. Areas 2 and 3 were captured with a higher spatial resolution than area 1 to analyze the transition between the hallway and the staircases. The receiver positions form a uniform grid, the pitch between positions is shown in the following table. Due to time and technical constraints, only a maximum of 3 sources were used per run, so there are not all combinations of sources and receiver areas. Refer to the following table to see which source was active for which area and which zip file contains the according data:</p> <table> <tbody> <tr> <th>Filename</th> <th>Sources</th> <th>Receiver Area</th> <th>Receiver Positions [ct]</th> <th>Pitch [cm]</th> </tr> </tbody> <tbody> <tr> <td>Helmholtzbau_OG2_HM_HS.zip</td> <td>HM, HS</td> <td>Area 1</td> <td>143</td> <td>50</td> </tr> <tr> <td>Helmholtzbau_OG2_SML_SSL_SSU.zip</td> <td>SML, SSL, SSU</td> <td>Area 1</td> <td>154</td> <td>50</td> </tr> <tr> <td>Helmholtzbau_OG2_SMU_SML_HM.zip</td> <td>SMU, SML, HM</td> <td>Area 2</td> <td>88</td> <td>25</td> </tr> <tr> <td>Helmholtzbau_OG2_SSU_SSL_HS.zip</td> <td>SSU, SSL, HS</td> <td>Area 3</td> <td>92</td> <td>25</td> </tr> </tbody> </table> <p>As an example "Plot Reverberation Time.jpg" shows the reverberation times for all measured positions of Area 1 and 2 with speaker HM.</p>
A High-Resolution Spatial Room Impulse Response Database
<p><strong>A High-Resolution Spatial Room Impulse Response Database:</strong></p> <p>A Database of various SRIRs measured in three rooms, for two receiver and 3 source positions each. The positions are shown in the floor plans. </p> <p><strong>Naming Convention:</strong></p> <p><strong>Receivers</strong>: SMA (DRIRs): spherical microphone array impulse responses on a 2702 sampling point Lebedev grid.</p> <p> KU100 (BRIRs): Neumann KU100 dummy head impulse responses on a 360 sampling point horizontal grid</p> <p> Omni_ir: Omnidirectional impulse responses measured with an Earthworks M30 microphone </p> <p><strong>Receiver positions:</strong> P1, P2 as indicated in the floor plans</p> <p><strong>Source positions:</strong> LSL: left speaker, LSR: right speaker, LSC: center speaker as indicated in the floor plans </p> <p><strong>Rooms: </strong>Audiolab, Classroom, Audimax</p> <p>_______________________________________________________________________________________</p> <p><strong>Contact:</strong><br> Tim Lübeck, Johannes M. Arend, and Christoph Pörschmann<br> TH Köln - University of Applied Sciences<br> Institute of Communications Engineering<br> Department of Acoustics and Audio Signal Processing<br> Betzdorfer Str. 2, D-50679 Cologne, Germany</p> <p><a href="https://www.th-koeln.de/personen/tim.luebeck/">https://www.th-koeln.de/personen/tim.luebeck/</a></p> <p><a href="https://www.th-koeln.de/personen/johannes.arend/">https://www.th-koeln.de/personen/johannes.arend/</a></p> <p><a href="http://www.th-koeln.de/personen/christoph.poerschmann/">https://www.th-koeln.de/personen/christoph.poerschmann/</a><br> <br> </p>
Data from: Restoring marine ecosystems: spatial reef configuration triggers taxon-specific responses among early colonizers
<p>1. The longstanding debate in conservation biology on the importance of single large or several small (SLOSS) habitats for preserving biodiversity remains highly relevant, given the ongoing degradation and loss of natural habitats worldwide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have important implications if restoration efforts can be optimized by manipulating the spatial configuration of restored habitats. Yet, the relevance of SLOSS for habitat restoration remains largely unexplored.</p> <p>2. Here, we report the effects of spatial reef configuration on early colonization of marine organisms after restoring boulder reef habitats. Reefs were restored in single large (SL) and several small (SS) designs in the western Baltic Sea, where century-long boulder extraction has severely degraded large reef areas and likely exacerbated regional declines in commercially important gadoids (<i>Gadidae spp.</i>). We sampled the field sites using remote underwater video systems in a before-after control-impact (BACI) design and obtained probabilistic inferences on restoration and SLOSS effects from Bayesian hierarchical models.</p> <p>3. Probabilities of a positive restoration effect were high (>95%) for gadoids, labrids and demersal gobies, moderate (60-75%) for species richness and sand gobies, and low (<5%) for flatfish abundance. Notably, gadoid abundance increased 60-fold and 129-fold on average at SL and SS, respectively. The species composition at restored reefs deviated from control sites, mainly driven by large-bodied piscivores.</p> <p>4. Spatial reef configuration had the strongest effect on small-bodied mesopredators, including gobies, which were more abundant and driving a distinct species assemblage at SS. In addition to providing suitable conditions for reef species, results suggest that SS can also benefit soft-bottom taxa, possibly through a dispersed predator-mediated effect relative to SL. </p> <p><i>5. Synthesis and applications.</i> This study demonstrates that boulder reef restoration can strongly promote the abundance of exploited gadoids and is therefore a promising management tool to support top-down controls by predatory fishes in degraded marine systems. The higher abundance of mesopredators at SS reefs suggests that SLOSS could have long-term implications for trophic structure and resilience of restored habitats, and should therefore become an important facet within restoration strategies. </p>
Codes in R for spatial statistics analysis, ecological response models and spatial distribution models
<p>In the last decade, a plethora of algorithms have been developed for spatial ecology studies. In our case, we use some of these codes for underwater research work in applied ecology analysis of threatened endemic fishes and their natural habitat. For this, we developed codes in Rstudio® script environment to run spatial and statistical analyses for ecological response and spatial distribution models (e.g., Hijmans & Elith, 2017; Den Burg <em>et al.</em>, 2020). The employed R packages are as follows: caret (Kuhn et al., 2020), corrplot (Wei & Simko, 2017), devtools (Wickham, 2015), dismo (Hijmans & Elith, 2017), gbm (Freund & Schapire, 1997; Friedman, 2002), ggplot2 (Wickham et al., 2019), lattice (Sarkar, 2008), lattice (Musa & Mansor, 2021), maptools (Hijmans & Elith, 2017), modelmetrics (Hvitfeldt & Silge, 2021), pander (Wickham, 2015), plyr (Wickham & Wickham, 2015), pROC (Robin et al., 2011), raster (Hijmans & Elith, 2017), RColorBrewer (Neuwirth, 2014), Rcpp (Eddelbeuttel & Balamura, 2018), rgdal (Verzani, 2011), sdm (Naimi & Araujo, 2016), sf (e.g., Zainuddin, 2023), sp (Pebesma, 2020) and usethis (Gladstone, 2022).</p> <p>It is important to follow all the codes in order to obtain results from the ecological response and spatial distribution models. In particular, for the ecological scenario, we selected the Generalized Linear Model (GLM) and for the geographic scenario we selected DOMAIN, also known as Gower's metric (Carpenter <em>et al.</em>, 1993). We selected this regression method and this distance similarity metric because of its adequacy and robustness for studies with endemic or threatened species (<em>e.g.</em>, Naoki <em>et al.</em>, 2006). Next, we explain the statistical parameterization for the codes immersed in the GLM and DOMAIN running:</p> <p>In the first instance, we generated the background points and extracted the values of the variables (<a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code2_Extract_values_DWp_SC.R?versionId=c1ea0c61-53fe-4f95-ab88-0c1cb28399cb">Code2_Extract_values_DWp_SC.R</a>). Barbet-Massin <em>et al. </em>(2012) recommend the use of 10,000 background points when using regression methods (<em>e.g.</em>, Generalized Linear Model) or distance-based models (<em>e.g.</em>, DOMAIN). However, we considered important some factors such as the extent of the area and the type of study species for the correct selection of the number of points (Pers. Obs.). Then, we extracted the values of predictor variables (<em>e.g.</em>, bioclimatic, topographic, demographic, habitat) in function of presence and background points (<em>e.g.</em>, Hijmans and Elith, 2017).</p> <p>Subsequently, we subdivide both the presence and background point groups into 75% training data and 25% test data, each group, following the method of Soberón & Nakamura (2009) and Hijmans & Elith (2017). For a training control, the 10-fold (cross-validation) method is selected, where the response variable presence is assigned as a factor. In case that some other variable would be important for the study species, it should also be assigned as a factor (Kim, 2009).</p> <p>After that, we ran the code for the GBM method (Gradient Boost Machine; <a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code3_GBM_Relative_contribution.R?versionId=1656bbae-66aa-409e-bb91-d8007dee8f95">Code3_GBM_Relative_contribution.R</a> and <a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code4_Relative_contribution.R?versionId=0e1d9352-e6b2-43da-984b-d6853a914258">Code4_Relative_contribution.R</a>), where we obtained the relative contribution of the variables used in the model. We parameterized the code with a Gaussian distribution and cross iteration of 5,000 repetitions (<em>e.g.</em>, Friedman, 2002; kim, 2009; Hijmans and Elith, 2017). In addition, we considered selecting a validation interval of 4 random training points (Personal test). The obtained plots were the partial dependence blocks, in function of each predictor variable.</p> <p>Subsequently, the correlation of the variables is run by Pearson's method (<a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code5_Pearson_Correlation.R?versionId=275f8dd4-b056-44d2-bfe5-f6264bc3298b">Code5_Pearson_Correlation.R</a>) to evaluate multicollinearity between variables (Guisan & Hofer, 2003). It is recommended to consider a bivariate correlation ± 0.70 to discard highly correlated variables (<em>e.g.</em>, Awan <em>et al.</em>, 2021).</p> <p>Once the above codes were run, we uploaded the same subgroups (<em>i.e.</em>, presence and background groups with 75% training and 25% testing) (<a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code6_Presence&backgrounds.R?versionId=d797b528-782f-4a19-bd61-cfb197f38513">Code6_Presence&backgrounds.R</a>) for the GLM method code (<a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code7_GLM_model.R?versionId=e4aca276-d601-49ec-a62c-a9223b05a7ed">Code7_GLM_model.R</a>). Here, we first ran the GLM models per variable to obtain the <em>p</em>-significance value of each variable (alpha ≤ 0.05); we selected the value one (<em>i.e.</em>, presence) as the likelihood factor. The generated models are of polynomial degree to obtain linear and quadratic response (<em>e.g.</em>, Fielding and Bell, 1997; Allouche <em>et al.</em>, 2006). From these results, we ran ecological response curve models, where the resulting plots included the probability of occurrence and values for continuous variables or categories for discrete variables. The points of the presence and background training group are also included.</p> <p>On the other hand, a global GLM was also run, from which the generalized model is evaluated by means of a 2 x 2 contingency matrix, including both observed and predicted records. A representation of this is shown in Table 1 (adapted from Allouche et al., 2006). In this process we select an arbitrary boundary of 0.5 to obtain better modeling performance and avoid high percentage of bias in type I (omission) or II (commission) errors (e.g., Carpenter et al., 1993; Fielding and Bell, 1997; Allouche et al., 2006; Kim, 2009; Hijmans and Elith, 2017).</p> <p>Table 1. Example of 2 x 2 contingency matrix for calculating performance metrics for GLM models. A represents true presence records (true positives), B represents false presence records (false positives - error of commission), C represents true background points (true negatives) and D represents false backgrounds (false negatives - errors of omission).</p> <table align="center"> <tbody> <tr> <td> <p> </p> </td> <td> <p>Validation set</p> </td> </tr> <tr> <td> <p>Model</p> </td> <td> <p>True</p> </td> <td> <p>False</p> </td> </tr> <tr> <td> <p>Presence</p> </td> <td> <p>A</p> </td> <td> <p>B</p> </td> </tr> <tr> <td> <p>Background</p> </td> <td> <p>C</p> </td> <td> <p>D</p> </td> </tr> </tbody> </table> <p>We then calculated the Overall and True Skill Statistics (TSS) metrics. The first is used to assess the proportion of correctly predicted cases, while the second metric assesses the prevalence of correctly predicted cases (Olden and Jackson, 2002). This metric also gives equal importance to the prevalence of presence prediction as to the random performance correction (Fielding and Bell, 1997; Allouche <em>et al.</em>, 2006).</p> <p>The last code (<em>i.e.</em>, <a href="https://zenodo.org/api/files/fdd5446b-dee9-4b52-ad4f-cf556443d3dd/Code8_DOMAIN_SuitHab_model.R?versionId=d951a8f2-d3a4-4804-b862-1b2762061876">Code8_DOMAIN_SuitHab_model.R</a>) is for species distribution modelling using the DOMAIN algorithm (Carpenter <em>et al.</em>, 1993). Here, we loaded the variable stack and the presence and background group subdivided into 75% training and 25% test, each. We only included the presence training subset and the predictor variables stack in the calculation of the DOMAIN metric, as well as in the evaluation and validation of the model.</p> <p>Regarding the model evaluation and estimation, we selected the following estimators:</p> <p>1) partial ROC, which evaluates the approach between the curves of positive (<em>i.e.</em>, correctly predicted presence) and negative (i.e., correctly predicted absence) cases. As farther apart these curves are, the model has a better prediction performance for the correct spatial distribution of the species (Manzanilla-Quiñones, 2020).</p> <p>2) ROC/AUC curve for model validation, where an optimal performance threshold is estimated to have an expected confidence of 75% to 99% probability (De Long <em>et al.</em>, 1988).</p>
Data from: The duration of high spring light for understory plants: contrasting responses to spatial and temporal temperature variation
Open the record for dataset details and reuse information.
Differential responses to weather and land-cover conditions explain spatial variation in winter abundance trends in a migratory bird of conservation concern
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.