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18 results for “Reference Quality”
Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction
<p>Updated draft genome assembly (FASTA) and annotation (GFF) for the <em>P. teres </em>f.<em> maculata </em>isolate FGOB10Ptm-1. </p>
Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction
<p>Updated draft genome assembly (FASTA) and annotation (GFF) for the <em>P. teres </em>f.<em> maculata </em>isolate P-A14. </p>
High quality white matter reference tracts
<p><strong>Overview</strong></p> <p>This dataset contains segmentations of 72 white matter tracts obtained from 105 subjects included in the Human Connectome Project (HCP) young adult dataset (https://www.humanconnectome.org/study/hcp-young-adult). The folder names correspond to the ID of the HCP subjects. This dataset only contains the tracts. It does not contain the original DWI data. This has to be downloaded from the HCP website (it is free, but you have to register to get access).</p> <p>The data is part of the following publication: <a href="https://doi.org/10.1016/j.neuroimage.2018.07.070">Wasserthal et al., TractSeg - Fast and accurate white matter bundle segmentation. NeuroImage (2018)</a>. If you use the data please cite the paper.</p> <p> </p> <p><strong>Details for generating corresponding whole brain tractograms</strong></p> <p>The tracts were extracted semi-automatically from whole-brain tractograms. For a detailed description of the tract segmentation process please refer to the paper. The following MRtrix (http://www.mrtrix.org/) commands were used to obtain the whole-brain tractograms:</p> <p>5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked<br> dwi2response msmt_5tt Diffusion.nii.gz 5TT.mif RF_WM.txt RF_GM.txt RF_CSF.txt -voxels RF_voxels.mif -fslgrad Diffusion.bvecs Diffusion.bvals<br> dwi2fod msmt_csd Diffusion.nii.gz RF_WM.txt WM_FODs.mif RF_GM.txt GM.mif RF_CSF.txt CSF.mif -mask nodif_brain_mask.nii.gz -fslgrad Diffusion.bvecs Diffusion.bvals<br> tckgen -algorithm iFOD2 WM_FODs.mif output.tck -act 5TT.mif -backtrack -crop_at_gmwmi -seed_image nodif_brain_mask.nii.gz -maxlength 250 -minlength 40 -number 10M -cutoff 0.06 -maxnum 0</p> <p>For "CA", "IFO_left", "IFO_right", "UF_left", "UF_right" we used tracking without anatomical constraints:</p> <p>tckgen -algorithm iFOD2 WM_FODs.mif output.tck -seed_image nodif_brain_mask.nii.gz -maxlength 250 -minlength 40 -number 10M -cutoff 0.06 -maxnum 0</p> <p>Due to their enormous size, the whole brain tractograms corresponding to the segmented tracts are not included this dataset. Please contact the author of the paper if you are interested in these tractograms.</p> <p> </p> <p><strong>Included tracts</strong></p> <p>1: AF_left (Arcuate fascicle)<br> 2: AF_right<br> 3: ATR_left (Anterior Thalamic Radiation)<br> 4: ATR_right<br> 5: CA (Commissure Anterior)<br> 6: CC_1 (Rostrum)<br> 7: CC_2 (Genu)<br> 8: CC_3 (Rostral body (Premotor))<br> 9: CC_4 (Anterior midbody (Primary Motor))<br> 10: CC_5 (Posterior midbody (Primary Somatosensory))<br> 11: CC_6 (Isthmus)<br> 12: CC_7 (Splenium)<br> 13: CG_left (Cingulum left)<br> 14: CG_right <br> 15: CST_left (Corticospinal tract<br> 16: CST_right <br> 17: MLF_left (Middle longitudinal fascicle)<br> 18: MLF_right<br> 19: FPT_left (Fronto-pontine tract)<br> 20: FPT_right <br> 21: FX_left (Fornix)<br> 22: FX_right<br> 23: ICP_left (Inferior cerebellar peduncle)<br> 24: ICP_right <br> 25: IFO_left (Inferior occipito-frontal fascicle) <br> 26: IFO_right<br> 27: ILF_left (Inferior longitudinal fascicle) <br> 28: ILF_right <br> 29: MCP (Middle cerebellar peduncle)<br> 30: OR_left (Optic radiation) <br> 31: OR_right<br> 32: POPT_left (Parieto‐occipital pontine)<br> 33: POPT_right <br> 34: SCP_left (Superior cerebellar peduncle)<br> 35: SCP_right <br> 36: SLF_I_left (Superior longitudinal fascicle I)<br> 37: SLF_I_right <br> 38: SLF_II_left (Superior longitudinal fascicle II)<br> 39: SLF_II_right<br> 40: SLF_III_left (Superior longitudinal fascicle III)<br> 41: SLF_III_right <br> 42: STR_left (Superior Thalamic Radiation)<br> 43: STR_right <br> 44: UF_left (Uncinate fascicle) <br> 45: UF_right <br> 46: CC (Corpus Callosum - all)<br> 47: T_PREF_left (Thalamo-prefrontal)<br> 48: T_PREF_right <br> 49: T_PREM_left (Thalamo-premotor)<br> 50: T_PREM_right <br> 51: T_PREC_left (Thalamo-precentral)<br> 52: T_PREC_right <br> 53: T_POSTC_left (Thalamo-postcentral)<br> 54: T_POSTC_right <br> 55: T_PAR_left (Thalamo-parietal)<br> 56: T_PAR_right <br> 57: T_OCC_left (Thalamo-occipital)<br> 58: T_OCC_right <br> 59: ST_FO_left (Striato-fronto-orbital)<br> 60: ST_FO_right <br> 61: ST_PREF_left (Striato-prefrontal)<br> 62: ST_PREF_right <br> 63: ST_PREM_left (Striato-premotor)<br> 64: ST_PREM_right <br> 65: ST_PREC_left (Striato-precentral)<br> 66: ST_PREC_right <br> 67: ST_POSTC_left (Striato-postcentral)<br> 68: ST_POSTC_right<br> 69: ST_PAR_left (Striato-parietal)<br> 70: ST_PAR_right <br> 71: ST_OCC_left (Striato-occipital)<br> 72: ST_OCC_right<br> </p> <p><strong>Cross-validation data splits</strong></p> <p>The following data splits were used for cross-validation in the TractSeg paper:</p> <pre><code class="language-python">fold1 = ['992774', '991267', '987983', '984472', '983773', '979984', '978578', '965771', '965367', '959574', '958976', '957974', '951457', '932554', '930449', '922854', '917255', '912447', '910241', '907656', '904044'] fold2 = ['901442', '901139', '901038', '899885', '898176', '896879', '896778', '894673', '889579', '887373', '877269', '877168', '872764', '872158', '871964', '871762', '865363', '861456', '859671', '857263', '856766'] fold3 = ['849971', '845458', '837964', '837560', '833249', '833148', '826454', '826353', '816653', '814649', '802844', '792766', '792564', '789373', '786569', '784565', '782561', '779370', '771354', '770352', '765056'] fold4 = ['761957', '759869', '756055', '753251', '751348', '749361', '748662', '748258', '742549', '734045', '732243', '729557', '729254', '715647', '715041', '709551', '705341', '704238', '702133', '695768', '690152'] fold5 = ['687163', '685058', '683256', '680957', '679568', '677968', '673455', '672756', '665254', '654754', '645551', '644044', '638049', '627549', '623844', '622236', '620434', '613538', '601127', '599671', '599469']</code></pre> <p>Hyperparameters were optimized using fold 1-3 for training and fold 4 for validation.</p> <p>The final 5-fold cross-validation (results reported in the TractSeg paper) was done by always training on 3 folds, selecting the best epoch by evaluating on the fourth fold and then reporting the final results (of the model from the best epoch) on the fifth fold.</p> <p>The pretrained TractSeg model which will automatically be used when you download TractSeg was trained on fold1+fold2+fold3.</p> <p>Please use the same data splits to make your work comparable.</p> <p> </p> <p><strong>Data format</strong></p> <p>From version 1.2.0 of this dataset onwards it uses the newest trackvis (trk) standard (using nibabel.streamlines API). Streamlines are saved in native voxel space and when loaded are transformed to coordinate space using the affine stored in the trk file header. In the previous versions of the dataset the older nibabel.trackvis API was used (streamlines are saved in real coordinate space and no affine is applied when loading them).</p>
CVD2014 - A database for evaluating no-reference video quality assessment algorithms
<p>The CVD video database is developed to provide an useful tool for researchers in the validation and developing processes of no-reference (NR) objective video quality assessment (VQA) algorithms. It consists of 234 videos from five different scenes captured by 78 different cameras (mobile phones, compact camera, video camera, SLR). The subjective experiments are conducted following the Single-Stimulus (SS) procedure to collect ratings of video quality.</p> <p><strong>Setup</strong></p> <p>We implement our experiments according to the Single Stimulus methodology using VQone MATLAB toolboxon high quality monitors (Eizo ColorEdge CG241W) with 1920x1200 pixel resolution in a dark room (ambient light < 20 lux). Video stimuli were displayed at their original size of VGA (640 x 480) or HD (1280 x 720). The subjects viewing distance (80 cm) was controlled by a string hanging from a ceiling and they were instructed to keep their head steady next to it. The monitors were calibrated to according to sRGB (target values were: 6500 K, 80 lux, and gamma 2.2) using EyeOne Pro calibrator (X-rite co.). The laboratory setup is showed in the figure below.</p> <p><strong>Subjects</strong></p> <p>Subjects (n = 30, 30, 28, 33, 30, 32 and 27 for Tests 1 - 7 respectively) were naïve in a sense that they did not study or work with image quality or related fields. They were recruited through student mailing lists consisting mainly humanities and behavioral science students. Subjects’ vision was controlled for the near visual acuity, near contrast vision (near F.A.C.T.) and color vision (Farnsworth D15) before the participation. They received movie tickets as a reward.</p> <p><strong>Procedure</strong></p> <p>Subjects evaluated one video sample at a time and all video samples of one scene were presented in a row. The order of video samples and scenes was randomized. Subjects had the option to view video samples again as many times as they wanted.</p> <p><strong>Data</strong></p> <p>The results are processed and reported in the form of Mean Opinion Score (MOS) for the tested video samples. In addition, we provide the whole raw data from the subjective experiments instead of just pre-calculated mean opinion scores from each video sample. This allows further analyses to be made by those who wish to use this database and gives them better opportunity to utilize the data to its full potential.</p> <p>Realignment study (test 7) contains the data from the additional study in which the mappings from the test and scene specific quality scales (test 1-6) to the global quality scale were formed. The global scale is valuable when studying and developing VQA algorithms. With the global scale, all of the samples (234 video samples in the case of the CVD2014) are in the same scale, and the performance analysis for algorithms can be conducted with a high number of samples.</p> <p><strong>If you use this database in your research, we kindly ask that you follow The Copyright notice below and cite the following paper:</strong></p> <p> </p> <p>M. Nuutinen, T. Virtanen, M. Vaahteranoksa, T. Vuori, P. Oittinen and J. Häkkinen, "CVD2014—A Database for Evaluating No-Reference Video Quality Assessment Algorithms," in <em>IEEE Transactions on Image Processing</em>, vol. 25, no. 7, pp. 3073-3086, July 2016. doi: 10.1109/TIP.2016.2562513</p> <p> </p> <p> </p> <p>-----------COPYRIGHT NOTICE STARTS WITH THIS LINE------------</p> <p>Copyright (c) 2014 The University of Helsinki<br> All rights reserved.</p> <p>Permission is hereby granted, without written agreement and without license or royalty fees, to use, copy, modify, and distribute this database (the videos, the images, the results and the source files) and its documentation for any purpose, provided that the copyright notice in its entirely appear in all copies of this database, and the original source of this database,Visual Cognition research group (www.helsinki.fi/psychology/groups/visualcognition/index.htm) and the Institute of Behavioral Science (www.helsinki.fi/ibs/index.html) at the University of Helsinki (www.helsinki.fi/university/), is acknowledged in any publication that reports research using this database. Individual videos and images may not be used outside the scope of this database (e.g. in marketing purposes) without prior permission.</p> <p>The database and our paper are to be cited in the bibliography as: M. Nuutinen, T. Virtanen, M. Vaahteranoksa, T. Vuori, P. Oittinen and J. Häkkinen, "CVD2014—A Database for Evaluating No-Reference Video Quality Assessment Algorithms," in <em>IEEE Transactions on Image Processing</em>, vol. 25, no. 7, pp. 3073-3086, July 2016.<br> doi: 10.1109/TIP.2016.2562513</p> <p>-----------------------------------------------------------------------------</p> <p>LIMITATION OF LIABILITY</p> <p>UNIVERSITY OF HELSINKI SHALL IN NO CASE BE LIABLE IN CONTRACT, TORT OR OTHERWISE FOR ANY LOSS OF REVENUE, PROFIT, BUSINESS OR GOODWILL OR ANY DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE COST, DAMAGES OR EXPENSE OF ANY KIND HOWEVER CAUSED OR HOWEVER ARISING UNDER OR IN CONNECTION WITH THE USE OF THIS DATABASE.</p> <p>THE UNIVERSITY OF HELSINKI SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE DATABASE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF HELSINKI HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.</p> <p>THIS AGREEMENT SHALL BE CONSTRUED AND INTERPRETED IN ACCORDANCE WITH THE LAWS OF FINLAND, EXCLUDING ITS RULES FOR CHOICE OF LAW.</p> <p>-----------COPYRIGHT NOTICE ENDS WITH THIS LINE------------</p>
AirHeritage Datalake: Multi-site, Multi-season, Multi Unit dataset including Fixed and Mobile Citizen science data from networked Air Quality Low-Cost Multi-Sensors devices and reference stations
<p>This datalake comprises several datasets from <strong>37 networked low cost air quality multisensors</strong> (<strong>30</strong> <strong>mobile</strong> ENEA MONICA(tm) + <strong>7</strong> <strong>fixed</strong>) along with <strong>3</strong> (fixed) + <strong>1</strong> (mobile) <strong>reference stations</strong> operated by Campania Regional Envronmental Protection Agency. The datalake is organized in 3 main directories respectively related to fixed nodes, mobile nodes and nearby reference stations including a mobile laboratory used for colocation campaigns; each subdirectory include its own metadata description file.</p> <p>Data, curated by Energy and Data Science Laboratory of ENEA, include multi-weeks colocation periods when low cost devices have been colocated with reference stations as well as operational periods during which sensors are deployed for fixed or mobile monitoring campaigns. Data have been recorded during 2021 and 2022 in a<strong> pervasive, multi-site, multi-seasonal deployment</strong> in Portici, a densely populated small area city (4km2, 55k + inhabitants) located 7km south of Naples, Italy.</p> <p>The datalake consists in actual sensors and reference intrumentations timeseries along with metadata description files with deployment dates and location data. The dataset files include high sampling frequency raw sensor data of quality-controlled sensor network along with co-located reference stations data sets. Sensor data include electrochemical sensors data (intended target pollutants: NO2, O3, CO), Optical sensor data (PM2.5, PM10, PM1) readings along with meteorological parameters. .</p> <p>Further description of sensors and reference instruments are reported in the accompanying paper (see citation request).</p> <p>The dataset can be used for </p> <ul> <li> <strong>advanced (remote/universal/in field) data driven calibration strategies</strong> test or development including <strong>machine learning </strong>models</li> <li><strong>mobile opportunistic data fusion</strong> methods development</li> <li><strong>geomatics and data assimilation</strong> models studies</li> </ul> <p>as well as low cost sensor characterization performance studies. </p>
Data from multi-sensor devices and reference station to monitoring urban air quality
<p>Data from electrochemical and optical sensors.</p> <h3>Files names</h3> <ul> <li>ECT01, ECT02, ECT06, ECT07 = device name</li> <li>ISSEP = reference station <ul> <li>"c" = calibration data</li> <li>"v" = validation data</li> </ul> </li> </ul> <h3>Variable description</h3> <table> <tbody> <tr> <td><strong>Electrochemical sensor</strong></td> <td><strong>Optical sensor</strong></td> <td><strong>Probe</strong></td> <td><strong>Reference</strong></td> </tr> <tr> <td> <p>AE = auxiliary electrode (mV)</p> <p>WE = working electrode (mV)</p> <p>N = temperature correction </p> <ul> <li>ch0 = CO sensor</li> <li>ch1 = OX sensor</li> <li>ch2 = NO2 sensor</li> <li>ch3 = NO sensor</li> </ul> </td> <td> <p>PM1, PM2.5 and PM10 in µg/m³</p> </td> <td> <p>Prs_mbar = pressure (mbar)</p> <p>Temp = temperature (°C)</p> <p>RH = relative humidity (%)</p> </td> <td> <p>DV30 = wind direction @ 30m (°)</p> <p>HR = relative humidity (%)</p> <p>NO, NO2, O3, PM10 and PM2.5 (µg/m³)</p> <p>Precipita = precipitation (mm)</p> <p>TC3 = temperature @ 3m (°C)</p> <p>VV30 = wind speed @ 30m (m/s)</p> </td> </tr> </tbody> </table> <p> </p>
Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome
<p>Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a></p>
Experiment resources for "Quality of Binaural Rendering From Baffled Microphone Arrays Evaluated Without an Explicit Reference"
<div>This data set contains the following resources to reproduce the listening experiment and statistical analysis of the referenced manuscript:</div> <div> <ul> <li>The <em>binaural room impulse responses</em> (<strong>BRIR</strong>s) of all listening conditions presented in the perceptual experiment.</li> <li>The tools to create the listening test infrastructure, including <em>Pure Data</em> (<strong>Pd</strong>) patches and configuration files for the <em>SoundScape Renderer</em> (<strong>SSR</strong>) and <em>graphical user interface</em> (<strong>GUI</strong>).</li> <li>The raw response data as gathered from the experiment subjects.</li> <li>The R and Stan scripts to perform the statistical analysis and generate the resulting plots and tables.</li> </ul> </div> <div> <p> </p> <p>The archive contains the following components described below.</p> <p>Directory "dependencies/":</p> <ul> <li>Matlab, R, Stan, and Pd functions that are utilized in the code and experimental setup</li> <li>Additional dependencies of available open-source projects may be required for certain code functions. If so, the source and setup process for the necessary dependencies are documented in the file header.</li> </ul> </div> <div> <p>Directory "plots/4_Equalization/":</p> <ul> <li>Plots of all available headphone equalization filters as generated by the following Matlab scripts.</li> </ul> <p>Directory "plots/8_User_study/":</p> <ul> <li>Plots of the raw and analyzed experimental results as generated by the following Matlab and R scripts.</li> </ul> </div> <div> <p>Directory "resources/BRIR_auralization/":</p> <ul> <li>Audio files with static binaural auralizations of all listening conditions presented in the perceptual experiment as generated by the following Matlab scripts.</li> <li>The files in "Kemar_HRTF_sofa_N44_adjusted" do not include a headphone equalization.</li> <li>The files in "Kemar_HRTF_sofa_N44_adjusted+Sennheiser_HD650_lin" include the equalization for the <em>Sennheiser HD650</em> headphones employed in the listening experiment. The files are identical to the annotated <a href="http://www.ta.chalmers.se/research/audio-technology-group/audio-examples/jaes-2024a/" target="_blank" rel="noopener">listening examples</a> published for the manuscript.</li> </ul> <p>Directory "resources/BRIR_rendered/":</p> <ul> <li>BRIRs and rendering parameters of all listening conditions presented in the perceptual experiment as generated from the associated <a href="../doi/10.5281/zenodo.8206570" target="_blank" rel="noopener">data set</a> and <a href="https://github.com/HaHeho/baffled-arrays-to-binaural/releases/tag/v2024.JAES" target="_blank" rel="noopener">rendering code</a>.</li> <li>Scene configuration files for the SSR with all listening conditions presented in the perceptual experiment as generated from the following Matlab scripts.</li> </ul> <p>Directory "resources/HPCF_KEMAR/":</p> <ul> <li>Impulse responses of equalization filters for various headphones on the G.R.A.S KEMAR acoustic dummy head as measured for this experiment.</li> </ul> <p>Directory "resources/User_study/":</p> <ul> <li>Various resources for the listening experiment.</li> <li>The files in "Exp1_analysis" include intermediate and final statistical analysis results as generated from the following R scripts.</li> <li>"Exp1_config.json" contains the configuration of the study GUI with conditions presented in the listening experiment.</li> <li>"Exp1_Introduction.pdf" contains the instructions presented to the subjects at the start of the listening experiment.</li> <li>"Exp1_Part2_data_strings.xls" contains all subjects' raw perceptual response data gathered from the listening experiment.</li> <li>"Questionnaire.pdf" contains the questionnaire given to the subjects at the end of the listening experiment.</li> </ul> <p>Matlab script "x4_Gather_Headphone_Compensations.m":</p> <ul> <li>Generate plots of measured headphone compensation filters. Furthermore, the generated minimum phase filters and filters to yield a linear phase response from the headphones are extracted as separate WAV files.</li> </ul> </div> <div> <p>Matlab script "x6_Gather_SSR_Configurations.m":</p> <ul> <li>Collect several specified pre-rendered binaural room impulse response sets into an ASD file. The SSR can load this scene to present all gathered configurations in direct comparison with head tracking.</li> </ul> </div> <div> <p>Readme file "x6a_Normalize_SSR_Loudnesses.txt":</p> </div> <div> <div> <div> <ul> <li>Ideally, the rendering script would implement a measure to provide a reliable estimation of the binaural loudness of the rendered configuration. This could be used to normalize all stimuli levels. However, such a measure is currently not available or implemented.</li> <li>Therefore, tuning the stimuli loudness for the user study was performed beforehand by ear. The adjusted playback levels are set in a modified SSR configuration file for the listening experiment.</li> </ul> </div> <div> <p>Matlab script "x6_Gather_SSR_Configurations.m":</p> <ul> <li>Perform convolution of (rendered) binaural room impulse responses with a source audio signal. This is done for a specified selection of static head orientations and a continuous rotation over all horizontal head orientations.</li> <li>The resulting auralizations are published as <a href="http://www.ta.chalmers.se/research/audio-technology-group/audio-examples/jaes-2024a/">supplementary materials</a> to the manuscript.</li> </ul> <p>Shell script "x7_Start_Study_GUI.sh":</p> <ul> <li>Initialize all required components to perform the perceptual user study, including: <ul> <li>SSR to perform the real-time rendering of the BRIRs with head tracking</li> <li>SSR to extract head-tracking data (in case a Polhemus tracker is used)</li> <li>Pd to extract head-tracking data (in case a Supperware tracker is used)</li> <li>Pd to perform real-time convolution to apply headphone compensation</li> <li>Pd to receive OSC messages from the study GUI</li> <li>Pd to trigger audio file playback from received OSC messages</li> <li>Pd to translate OSC messages into FUDI messages for the SSR</li> <li>The GUI to be used by the participants and implement the study procedure</li> </ul> </li> <li>Some static configuration variables can be adjusted, whereas other parameters are chosen during script execution.</li> </ul> <p>Matlab script "x8_Gather_Study_Data.m":</p> <ul> <li>Transform the raw result data from the questionnaire (*.xls) and the study GUI (*.json) into a compact format (*.xls) that can be loaded to plot the raw data and imported by software for the subsequent statistical analysis.</li> <li>Note that this contains the responses from all subjects, whereas responses from the investigators must be excluded from the statistical analysis (which is implemented in the analysis scripts).</li> </ul> <p>Matlab script "x8a_Plot_Study_Data.m":</p> <ul> <li>Generate a set of violin plots to visualize the initial distribution of the raw perceptual data. The data is split by specified attributes and plotted separately for visual inspection.</li> <li>The data may also be transformed into ranks for a first distribution inspection. Note that implementing the ranking method, notably how ties are resolved, may differ from the technique employed in the statistical analysis.</li> <li>Note that this contains the responses from all subjects, whereas responses from the investigators must be excluded from the statistical analysis (which is implemented in the analysis scripts).</li> </ul> <p>R script "x8b_Analyze_Exp1_Data.R":</p> <ul> <li>Perform the statistical analysis by transforming the observed subject ratings into a predicted distribution of ranks using a hierarchical generalized linear regression model.</li> <li>Executing the statistical model may take some time due to the Bayesian framework employing Markov-chain Monte Carlo simulations.</li> <li>Data is exported at various intermediate steps to be loaded and visualized by the following R script.</li> </ul> <p>R markdown script "x8c_Plot_Exp1_Results.Rmd":</p> <ul> <li>Generate various plots and data tables of the observed data and the predicted results to visualize the distribution and influence of different analysis parameters.</li> <li>Some of the resulting plots were used in the manuscript.</li> <li>"x8c_Plot_Exp1_Results.html" conveniently summarizes all plots and data tables generated by "knitting" the R markdown script.</li> </ul> </div> </div> </div>
CID2013: A Database for Evaluating No-Reference Image Quality Assessment Algorithms
<p>The CID2013 Camera Image Database consists of real images taken by consumer cameras and mobile phones. It is developed to provide useful tool to allow researchers target more commercially relevant distortions when developing processes of objective image quality assessment algorithms.</p> <p>The CID2013 database consists of 480 evaluated images captured by 79 imaging devices (mobile phones, DSC, DSLR) in six Image Sets. Note that the actual number of images in the database is 474. In Image Set II, Device 6 is evaluated twice as we wanted to test inter-observer reliablity. The scores are later combined into a single MOS value as the two evaluations correlated strongly.</p> <p>If you use this database in your research, we kindly ask that you follow the copyright notice bellow and cite the following paper:</p> <p>Virtanen, T., Nuutinen, M., Vaahteranoksa, M., Oittinen, P. and Häkkinen, J. “CID2013: a database for evaluating no-reference image quality assessment algorithms”, IEEE Transactions on Image Processing, vol. 24, no. 1, pp. 390-402, Jan. 2015. <a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6975172">[pdf]</a></p> <p><strong>Method</strong></p> <p>The images are evaluated by 188 observers using Dynamic Reference (DR-ACR) method (explained below). A separate scale realignment ACR data consisting evaluations from 34 observers is also included that allows to combine the data from the six image sets</p> <p>In other respects the DR-ACR method resembles very much a basic Absolute Category Rating (ACR) method (ITU-R 500-11), except the observers saw a slideshow of all the other images in the test depicting the same scene before every evaluation (See DR_demo.mp4). By seeing the other images in the test setup as reference the observers were more aware of the total variation of quality represented within a single image set. This improved their evaluation as they didn’t need to save the far ends of the scale in case there would be even more better or worse image later on the experiment. The DR-ACR method is explained in detail in:</p> <p>Mikko Nuutinen, Toni Virtanen, Tuomas Leisti, Terhi Mustonen, Jenni Radun, Jukka Häkkinen (2014) A new method for evaluating the subjective image quality of photographs : dynamic reference Multimedia Tools and Applications 75: 4. 2367-2391 Dec.</p> <p>Database contains consumer camera images and their subjective evaluations in mean opinion score (MOS), sharpness, graininess, lightness and color saturation scales. It includes the complete raw data and background information from the naïve observers used to evaluate the images. Subjects’ vision was controlled for the near visual acuity, near contrast vision (near F.A.C.T.) and color vision (Farnsworth D15) before the participation. They received movie tickets as a reward. Outlier removal is made for mean opinion score (MOS) evaluations using ITU-R 500-11 recommendations to ease out the implementation of the database.</p> <p><strong>Material</strong></p> <p>The images in CID2013 are intended to represent typical photographs that consumers might capture with their cameras. The photographed scenes were based partly on the Photospace approach described by I3A (CPIQ Initiative Phase 1 White Paper: Fundamentals and review of considered test methods, I3A, 2007) The I3A CPIQ project has migrated under IEEE.</p> <p><strong>The test environment</strong></p> <p>The room has been covered with medium gray curtains to diffuse the ambient illumination. Fluorescent lights (5800K) were positioned behind the monitors and reflected from the back wall covered with grey curtain to create dim and uniform ambient illumination in the room. The light hitting the monitors measured below 20 lx. The subject’s viewing distance (approximately 80 cm) was controlled by a line hanging from the ceiling, and they were instructed to keep their forehead steady next to the line. Because of the display size, images were scaled to a size of 1600 x 1200 pixels using the bicubic interpolation method. Eizo ColorEdge CG241W, with 1920x1200 pixel resolution, monitors in was calibrated to sRGB having target values of: 80 cd/m2, 6500K and gamma 2.2 using EyeOne Pro calibrator (X-rite co.).</p> <p> </p> <p>-----------COPYRIGHT NOTICE STARTS WITH THIS LINE------------</p> <p>Copyright (c) 2014 The University of Helsinki<br> All rights reserved.</p> <p>Permission is hereby granted, without written agreement and without license or royalty fees, to use, copy, modify, and distribute this database (the videos, the images, the results and the source files) and its documentation for any purpose, provided that the copyright notice in its entirely appear in all copies of this database, and the original source of this database,Visual Cognition research group (www.helsinki.fi/psychology/groups/visualcognition/index.htm) and the Institute of Behavioral Science (www.helsinki.fi/ibs/index.html) at the University Helsinki (www.helsinki.fi/university/), is acknowledged in any publication that reports research using this database. Individual videos and images may not be used outside the scope of this database (e.g. in marketing purposes) without prior permission.</p> <p>The database and our paper are to be cited in the bibliography as:</p> <p>-----------------------------------------------------------------------------<br> Virtanen, T., Nuutinen, M., Vaahteranoksa, M., Oittinen, P. and Häkkinen, J. “CID2013: a database for evaluating no-reference image quality assessment algorithms”, IEEE Transactions on Image Processing, 2014, In press.<br> -----------------------------------------------------------------------------</p> <p>LIMITATION OF LIABILITY</p> <p>UNIVERSITY OF HELSINKI SHALL IN NO CASE BE LIABLE IN CONTRACT, TORT OR OTHERWISE FOR ANY LOSS OF REVENUE, PROFIT, BUSINESS OR GOODWILL OR ANY DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE COST, DAMAGES OR EXPENSE OF ANY KIND HOWEVER CAUSED OR HOWEVER ARISING UNDER OR IN CONNECTION WITH THE USE OF THIS DATABASE.</p> <p>THE UNIVERSITY OF HELSINKI SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE DATABASE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF HELSINKI HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.</p> <p>THIS AGREEMENT SHALL BE CONSTRUED AND INTERPRETED IN ACCORDANCE WITH THE LAWS OF FINLAND, EXCLUDING ITS RULES FOR CHOICE OF LAW.</p> <p>-----------COPYRIGHT NOTICE ENDS WITH THIS LINE------------</p> <p> </p>
Literature references for the Explainability Quality Model
<p>This is the supplementary material to the paper "How Explainable is Your System? Towards a Quality Model for Explainability", which was published at the 30th International Working Conference on Requirement Engineering: Foundation for Software Quality (REFSQ) in 2024.</p> <p>This document indicates om which papers each aspect, criterion and metric originates. It also indicates for each paper from which snowballing phase it originates.</p>
Dataset - No Reference Image Quality assessment Scores for Humanities Online Repositories
<p>The dataset contains data on No-Reference Image Quality Assessment (NR-IQA) scores for online repositories in the humanities.</p>
4G/LTE Channel Quality Reference Signal Traces Data Set
<p>Mobile networks, especially LTE networks are used more and more for high-bandwidth services like multimedia or video streams. The quality of the data connection plays a major role in the perceived quality of a service. Videos may be presented in a low quality or experience a lot of stalling events when the connection is to slow to buffer the next frames for playback. So far, no publicly available data set exists that has a larger number of LTE network traces and can be used for deeper analysis. In this data set, we provide 546 traces of 5 minutes each with a sample rate of 100 ms. Thereof 377 traces are pure LTE data. We furthermore provide an Android app to gather further traces as well as R scripts to clean, sort, and analyze the data. </p>
Complexity and Quality Dockerfile Reference Dataset
<p>A manually curated dataset comprising 60 docker files. These are taken from the ten most popular images of Docker-Hub, the Docker-library provided by Docker and various GitHub repositories. These files have been classified according to their complexity and quality.</p>
High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae
<p>Output files from the assembly of 2 reference genomes detailed in the publication Rivera et al. 2024. High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks <em>Spondylurus nitidus</em> and <em>S. culebrae. Genome Biology and Evolution</em>, evae079.</p>
Evaluation of the Quality of Life in Patients Referred for Transjugular Intrahepatic Portosystemic Shunt
ClinicalTrials.gov study NCT05204251. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
A Three-phase Study That Will Compare the ECG Data Recorded Using the Test Device With the Data Recorded by a Reference Device, Evaluate the ECG Signal Quality of the Test Device Over a 10-day Simulat
ClinicalTrials.gov study NCT07200232. IPD Sharing: NO. Countries: 1. Publications: 0.
New Approaches for Evaluating the Interchangeability of Reference Materials and Quality Controls (COMET-MPL)
ClinicalTrials.gov study NCT07173114. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
A high-quality chromosomal-level reference genome of Dendrobium nobile L. provides new insights into the biosynthesis and accumulation of picrotoxane-type sesquiterpenoid alkaloids
GEO Series GSE254169. Dendrobium nobile. 12 samples. Type: Expression profiling by high throughput sequencing.
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.