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Dataset and program scripts for the reproducibility of the hierarchical data structure file. Related to the manuscript entitled: Hierarchical Representation of Measurement Data, Metrological Uncertainty and Metadata for Calibrated Battery Tests
<p>We present an interoperable hierarchical data representation for battery tests, leading to improved scalability of data transmission and enhanced data accessibility and comprehensibility for both human interpretation and machine processing. The hierarchical data format includes the raw trace electrical measurement data, the metrological calibration and uncertainty data, the metadata such as experimental settings, instruments and software versions, as well as post-processed data such as electrochemical model fit parameters. This data representation allows repetition of the battery test under the exact same conditions such that identical results are achieved within defined error bounds. This is in line with the general F.A.I.R. data approach and provides repeatability and traceability in the battery value chain. As an application of the hierarchical data representation, we show the classification of cells as pass/fail being performed with quantitative confidence levels. We demonstrate the complete workflow of establishing the hierarchical data structure for electrochemical impedance spectroscopy (EIS), starting from metrological traceability of the calibration and uncertainty analysis towards the storage of the structured data as a single integrated file that preserves the hierarchical data format.</p>
Datasets to "Compressible test-field method and its application to shear dynamos"
<pre>This directory contains an index.html file with links to the run directories and idl plotting routines with secondary data for the other figures for the paper "Compressible test-field method and its application to shear dynamos" by M. J. Kapyla, M. Rheinhardt, & A. Brandenburg (Astrophys. J., in press, arXiv:2106.01107). If anything turns out to be incomplete, please email maarit.kapyla@aalto.fi or brandenb@nordita.org. </pre>
Datasets for testing the robustness of LiDAR vegetation metrics to varying point densities
<p><span>The calculation of vegetation metrics from LiDAR point clouds might be affected by the available point density of a dataset. Testing how the same LiDAR vegetation metrics differ with different point densities can therefore inform about their robustness for upscaling metrics to other areas or other LiDAR point clouds. The datasets made available here were generated to test the robustness of LiDAR vegetation metrics to varying point densities and spatial resolutions (i.e., plots of 1 × 1 m, 2 × 2 m, 5 × 5 m and 10 × 10 m size). A total of 25 LiDAR vegetation metrics representing different aspects of vegetation height, vegetation cover and structural complexity were tested (see metric definition in Kissling et al. 2023, </span><span><a href="https://doi.org/10.1016/j.dib.2022.108798"><span>https://doi.org/10.1016/j.dib.2022.108798</span></a></span><span>). The metric calculation was similar to the metric calculation in the Laserchicken software (Meijer et al. 2020, </span><span><a href="https://doi.org/10.1016/j.softx.2020.100626"><span>https://doi.org/10.1016/j.softx.2020.100626</span></a></span><span>) and the Laserfarm workflow (Kissling et al. 2022, https://doi.org/10.1016/j.ecoinf.2022.101836). The Dutch AHN4 dataset from the years 2020–2022 with a point density of 20–30 points/m<sup>2</sup> was used. Initially, 100 plots (i.e., squared polygons around centre points) were randomly placed across the Netherlands in Dutch Natura 2000 sites that predominantly contain woodland habitats (using shapefiles from the European Environmental Agency). For each centre point, square polygons of the desired resolutions (i.e., 1 × 1 m, 2 × 2 m, 5 × 5 m or 10 × 10 m plot size) were generated. The square polygons were subsequently used to clip the LiDAR point clouds from the Dutch AHN4 point cloud dataset. Since not all locations of the 100 randomly placed plots contained points, the actual sample sizes were slightly smaller than 100, i.e., 94 plots for the 1 × 1 m, 2 × 2 m and 5 × 5 m resolution and 95 plots for the 10 × 10 m resolution. Metrics were calculated with the original point density of the Dutch AHN4 dataset (20–30 points/m2) and with six systematically down-sampled point clouds for the same plots (i.e., keeping 5%, 10%, 20%, 40%, 60% and 80% of the points in the original point clouds). For each clipped point cloud of a plot at a given resolution, the points were first sorted according to their GPS acquisition time (from earliest to latest). Points were then systematically discarded and only 5%, 10%, 20%, 40%, 60% and 80% of the points in the original point clouds were kept. The kept points were used for calculating the 25 LiDAR vegetation metrics. </span></p>
Dataset for "Methodology for fast testing of carbon-based nanostructured 3D electrodes in vanadium redox flow battery"
<p>Here, we describe a technique for integrating carbon-based rod-like nanomaterials into a vanadium redox flow battery and a methodology for fast nanomaterial performance testing. The technique is based on creating a fixed nanomaterial bed sandwiched between two graphite felt electrodes, forming a 3D flow-through electrode in the battery. Performing various positive and negative control experiments, we show the beneficial effect of a nanostructured bed on the primary battery characteristics obtained from short-term electrochemical experiments. We then characterize carbon nanotubes exhibiting promising electrochemical behavior in vanadium electrolytes, as observed in our previous study. The load curves obtained from charge-discharge steps at various current densities and electrolyte flow rates revealed considerable differences in the performance of the tested materials, with few-walled carbon nanotubes reaching unsurpassable characteristics. Although developed for vanadium redox flow batteries, the method enables testing tube-like and rod-like (nano-)materials as electrodes for other flow battery systems. </p>
Dataset for the comparison of two Computational Thinking (CT) test for upper primary school (grades 3-4) : the Beginners' CT test (BCTt) and the competent CT test (cCTt)
<p>This dataset contains quantitative student data acquired during the administration of two validated Computational Thinking (CT) assessments for upper primary school (grades 3 and 4): the Beginners' CT test (BCTt) [1] and the comptent CT test (cCTt) [2]</p> <p>To compare the psychometric properties of both instruments a comparative analysis was conducted with data acquired in schools in Portugal from the same school districts. More specifically, we analyse the results of: </p> <p>- the BCTt test administered in March 2020 to 374 students in grades 3-4,</p> <p>- the cCTt test administered in April 2021 to 201 different students in grades 3-4.</p> <p>These students had no prior experience in Computational Thinking, as this was not part of the national curriculum at the times of administration. </p> <p> </p> <p>The detailed psychometric comparison is published in Frontiers in Psychology - Educational Psychology [3] and provides indications regarding the use of both instruments for grades 3-4. </p> <p> </p> <p>A README is included and provides additional information regarding :</p> <p>- the requirements for re-use. </p> <p>- the specific content of the 2 csv files</p> <p> </p> <p>The BCTt is available upon request to maria.zapata@urjc.es and the cCTt items are available in [2] with an editable version being available upon request to laila.elhamamsy@epfl.ch. </p> <p>In case of other inquiries, please contact: laila.elhamamsy@epfl.ch, maria.zapata@urjc.es or pedro.marcelino@treetree2.org</p> <p> </p> <p><strong>References</strong></p> <p>[1] M. Zapata-Cáceres, E. Martín-Barroso and M. Román-González, "Computational Thinking Test for Beginners: Design and Content Validation," <em>2020 IEEE Global Engineering Education Conference (EDUCON)</em>, 2020, pp. 1905-1914, doi: 10.1109/EDUCON45650.2020.9125368.</p> <p>[2] El-Hamamsy, L., Zapata-Cáceres, M., Barroso, E. M., Mondada, F., Zufferey, J. D., & Bruno, B. (2022). The Competent Computational Thinking Test: Development and Validation of an Unplugged Computational Thinking Test for Upper Primary School. <em>Journal of Educational Computing Research</em>, <em>60</em>(7), 1818–1866. <a href="https://doi.org/10.1177/07356331221081753">https://doi.org/10.1177/07356331221081753</a></p> <p>[3] <a href="http://www.frontiersin.org/Community/WhosWhoActivity.aspx?sname=LailaEl-Hamamsy&UID=781667">Laila El-Hamamsy</a>* , <a href="http://www.frontiersin.org/Community/WhosWhoActivity.aspx?sname=Mar%C3%ADaZapata-C%C3%A1ceres&UID=2073859">María Zapata-Cáceres</a>, Pedro Marcelino, Jessica Dehler Zufferey, <a href="http://www.frontiersin.org/Community/WhosWhoActivity.aspx?sname=BarbaraBruno&UID=893934">Barbara Bruno</a>, <a href="http://www.frontiersin.org/Community/WhosWhoActivity.aspx?sname=EstefaniaMart%C3%ADn&UID=2086979">Estefanía Martín-Barroso</a> and <a href="http://www.frontiersin.org/Community/WhosWhoActivity.aspx?sname=MarcosRom%C3%A1n-Gonz%C3%A1lez&UID=760761">Marcos Román-González</a> (2022). <a href="http://www.frontiersin.org/Journal/Abstract.aspx?d=0&name=Educational_Psychology&ART_DOI=10.3389/fpsyg.2022.1082659">Comparing the psychometric properties of two primary school Computational Thinking (CT) assessments for grades 3 and 4: the Beginners' CT test (BCTt) and the competent CT test (cCTt)</a>. <em>Front. Psychol.</em> doi:10.3389/fpsyg.2022.1082659</p>
A high resolution 7-Tesla resting-state fMRI test-retest dataset with cognitive and physiological measures
Open the record for dataset details and reuse information.
A dataset recorded during development of an affective brain-computer music interface: testing session
Open the record for dataset details and reuse information.
CODE-test: An annotated 12-lead ECG dataset
<pre># Annotated 12 lead ECG dataset Contain 827 ECG tracings from different patients, annotated by several cardiologists, residents and medical students. It is used as test set on the paper: "Automatic diagnosis of the 12-lead ECG using a deep neural network". https://www.nature.com/articles/s41467-020-15432-4. It contain annotations about 6 different ECGs abnormalities: - 1st degree AV block (1dAVb); - right bundle branch block (RBBB); - left bundle branch block (LBBB); - sinus bradycardia (SB); - atrial fibrillation (AF); and, - sinus tachycardia (ST). Companion python scripts are available in: https://github.com/antonior92/automatic-ecg-diagnosis -------- Citation ``` Ribeiro, A.H., Ribeiro, M.H., Paixão, G.M.M. et al. Automatic diagnosis of the 12-lead ECG using a deep neural network. Nat Commun 11, 1760 (2020). https://doi.org/10.1038/s41467-020-15432-4 ``` Bibtex: ``` @article{ribeiro_automatic_2020, title = {Automatic Diagnosis of the 12-Lead {{ECG}} Using a Deep Neural Network}, author = {Ribeiro, Ant{\^o}nio H. and Ribeiro, Manoel Horta and Paix{\~a}o, Gabriela M. M. and Oliveira, Derick M. and Gomes, Paulo R. and Canazart, J{\'e}ssica A. and Ferreira, Milton P. S. and Andersson, Carl R. and Macfarlane, Peter W. and Meira Jr., Wagner and Sch{\"o}n, Thomas B. and Ribeiro, Antonio Luiz P.}, year = {2020}, volume = {11}, pages = {1760}, doi = {https://doi.org/10.1038/s41467-020-15432-4}, journal = {Nature Communications}, number = {1} } ``` ----- ## Folder content: - `ecg_tracings.hdf5`: The HDF5 file containing a single dataset named `tracings`. This dataset is a `(827, 4096, 12)` tensor. The first dimension correspond to the 827 different exams from different patients; the second dimension correspond to the 4096 signal samples; the third dimension to the 12 different leads of the ECG exams in the following order: `{DI, DII, DIII, AVR, AVL, AVF, V1, V2, V3, V4, V5, V6}`. The signals are sampled at 400 Hz. Some signals originally have a duration of 10 seconds (10 * 400 = 4000 samples) and others of 7 seconds (7 * 400 = 2800 samples). In order to make them all have the same size (4096 samples) we fill them with zeros on both sizes. For instance, for a 7 seconds ECG signal with 2800 samples we include 648 samples at the beginning and 648 samples at the end, yielding 4096 samples that are them saved in the hdf5 dataset. All signal are represented as floating point numbers at the scale 1e-4V: so it should be multiplied by 1000 in order to obtain the signals in V. In python, one can read this file using the following sequence: ```python import h5py with h5py.File(args.tracings, "r") as f: x = np.array(f['tracings']) ``` - The file `attributes.csv` contain basic patient attributes: sex (M or F) and age. It contain 827 lines (plus the header). The i-th tracing in `ecg_tracings.hdf5` correspond to the i-th line. - `annotations/`: folder containing annotations csv format. Each csv file contain 827 lines (plus the header). The i-th line correspond to the i-th tracing in `ecg_tracings.hdf5` correspond to the in all csv files. The csv files all have 6 columns `1dAVb, RBBB, LBBB, SB, AF, ST` corresponding to weather the annotator have detect the abnormality in the ECG (`=1`) or not (`=0`). 1. `cardiologist[1,2].csv` contain annotations from two different cardiologist. 2. `gold_standard.csv` gold standard annotation for this test dataset. When the cardiologist 1 and cardiologist 2 agree, the common diagnosis was considered as gold standard. In cases where there was any disagreement, a third senior specialist, aware of the annotations from the other two, decided the diagnosis. 3. `dnn.csv` prediction from the deep neural network described in the paper. THe threshold is set in such way it maximizes the F1 score. 4. `cardiology_residents.csv` annotations from two 4th year cardiology residents (each annotated half of the dataset). 5. `emergency_residents.csv` annotations from two 3rd year emergency residents (each annotated half of the dataset). 6. `medical_students.csv` annotations from two 5th year medical students (each annotated half of the dataset). </pre>
SM2RAIN test dataset with ASCAT and SMAP satellite soil moisture (plus ERA5 evapotranspiration)
<p>Are you looking for a research contest?</p> <p>Here [SM_RAIN_EVAP_1009points.nc] you can find a 5-year dataset at 1009 points in Italy, the United States, India and Australia of co-located in space and time:</p> <ol> <li>satellite soil moisture (from ASCAT, Wagner et al., 2013, doi:10.1127/0941-2948/2013/0399)</li> <li>evapotranspiration (from ERA5 reanalysis by ECMWF: https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=overview)</li> <li>ground-based rainfall.</li> </ol> <p>and a ~3-year dataset at the same points including soil moisture from SMAP (April-2015 --> December 2017) [SM_SMAP_ASCAT_ETERA5_Pobs_1009opints.nc]</p> <p>The dataset can be used for testing multiple approaches for rainfall estimation from soil moisture, as done in <a href="https://www.linkedin.com/feed/hashtag/?keywords=%23SM2RAIN">#SM2RAIN</a> algorithm (<a href="http://hydrology.irpi.cnr.it/research/sm2rain/">http://hydrology.irpi.cnr.it/research/sm2rain/</a>).</p> <p>The global dataset we have developed is available here: <a href="https://zenodo.org/record/3635932">https://zenodo.org/record/3635932</a></p> <p>The NetCDF file contains all the data, and the figures (PNG files) represent an example of the results we have obtained in the paper and of the new dataset including SMAP.</p> <p><strong>Reference</strong><br> Brocca, L., Filippucci, P., Hahn, S., Ciabatta, L., Massari, C., Camici, S., Schüller, L., Bojkov, B., Wagner, W. (2019). SM2RAIN-ASCAT (2007-2018): global daily satellite rainfall from ASCAT soil moisture. <em>Earth System Science Data</em>, 11, 1583–1601, doi:10.5194/essd-11-1583-2019. <a href="https://doi.org/10.5194/essd-11-1583-2019">https://doi.org/10.5194/essd-11-1583-2019</a>.</p> <p>For clarifications and support contact me at <a href="mailto:luca.brocca@irpi.cnr.it?subject=SM2RAIN%20test%20dataset">luca.brocca@irpi.cnr.it</a> </p>
Test dataset for copick
<p>A test dataset for <a href="https://github.com/uermel/copick">copick</a>.</p> <p>In order to use the filesystem-based models, adjust the overlay root path in <code>filesystem_overlay_only.json</code> or <code>filesystem.json</code> after extraction.</p>
Dataset on the experimental investigation of the seismic response of moment-resisting steel frames using shaking table tests
<h2>Description:</h2> <p>This dataset contains data from experimental shake table tests conducted on a two-storey steel-frame structure, involving linear sweep, white noise, impulse, and seismic excitations (see 'Load_Protocols_v1.0.0.pdf'). The experiments were carried out using the uniaxial shaking table at the <a href="https://www.lbb.rwth-aachen.de/cms/lbb/der-lehrstuhl/~bjlfvq/geraetezentzrum/?lidx=1">RWTHDynLab</a> of the <a href="https://www.lbb.rwth-aachen.de/go/id/eaxh/">Chair of Structural Analysis and Dynamics (LBB) - RWTH Aachen University</a>, in cooperation with the <a href="https://www.stb.rwth-aachen.de/cms/~iozv/STB/">Institute of Structural Steel (STB) - RWTH Aachen</a> and the <a href="https://www.cwe.rwth-aachen.de/home-2/">Center for Wind and Earthquake Engineering (CWE) – RWTH Aachen</a>.</p> <p>The experimental campaign was developed to gain a better understanding of the interaction between the main structure and non-structural components, to investigate the reliability and accuracy of analytical methods to predict response floor spectra and non-structural component acceleration described in various guidelines and seismic codes. Regarding applications of Structural Health Monitoring the necessity for additional sensors on non-structural components was studied. Three single-degree-of-freedom oscillators (SDOFs) were connected to the upper floor representing non-structural components. The test structure was subjected to a total of twelve earthquake excitations with different spectral properties. The main objectives of the test campaign were:</p> <ul> <li>Identification of the modal properties of the test structure.</li> <li>Measurement of the floor response in terms of acceleration and displacement.</li> <li>Determination of the real floor response spectra based on the measurements of the acceleration sensors installed on the first and second floors.</li> <li>Comparison of the expected peak accelerations from the floor response spectra with the peak accelerations measured by the accelerometers attached to the three SDOFs.</li> </ul> <h3>Test structure:</h3> <p>The test structure consisted of a two-storey steel structure which was stabilised in the direction of excitation by moment resisting frames (MRFs). In the transverse direction the global stability was ensured by concentrically braced frames (braces QRo 50x5). The structure was designed in accordance with provisions of prEN-1998-1 for energy dissipation and ductile seismic behaviour. As ductile members were considered the frame beams so that the columns and connections remain undamaged. An illustration of the test structure is depicted in 'Test_Structure_Sketch_v1.0.0.pdf'. The dimensions of the test structure are: 2.40 m in length, 2.40 m in width and 3.78 m in total height (1st storey: 2.02 m; 2nd storey: 1.76 m). Four large steel I-sections, each with a dead weight of 1700 kg, were attached to the main structure as masses and secured by U-Profiles. A tank with a dead load of approx. 100 kg and a volume of 400 litres was mounted onto the first floor. The tank remained empty during this test series. HEA200 profiles (S355-J2) were selected as column profiles, whereas IPE160 profiles (S235-JR) as frame beams. All main and secondary beams were realised by HEA140 profiles (S235-JR). Four L60x6 bars were arranged in a rhombus shape in the floor plane to ensure a diaphragm action. In the area of the MRF connections, the columns were reinforced with an additional double web plate (t = 10 mm) and with three ribs (t = 10 mm) at the level of the beam top flange, the beam bottom flange and the haunch flange. The beam-to-column connections were classified as full strength and semi-rigid in terms of capacity and stiffness. The critical welds connecting the frame transom to the top plate (t = 15 mm) were designed as full penetration groove welds in accordance with the specifications of Annex E of prEN1998-1 for seismically standardised connections. Twelve M16-10.9 bolts were used to ensure the force transfer between the beam and column. All connections of the secondary beams to the main beams were realised as end plate connections to prevent premature failure due to combined loading by normal and shear forces. The arrangement of the secondary beams and the corresponding force transmission was conceptualized in such a way that the frame beams could be replaced after a series of tests without having to remove the masses and the tank. The columns were hinged to the shaking table (see 'Column_Base_Anchorage_v1.0.0.pdf'). Slots in the anchor plates allow the rotation of the support base around the strong axis of the columns. The anchoring to the shaking table was realised using four M24-8.8 threaded rods. To simulate non-structural components, three SDOFs were attached to the centre of the secondary beams that run across the frame transom on the second floor (see 'Test_Structure_v1.0.0.pdf'). The SDOFs consisted of a flat steel and a mass. Depending on the thickness of the flat steel and the position of the mass, the three SDOFs were calibrated so that the natural frequency of the first SDOF matches the natural frequency of the second modal shape of the test structure in the frame direction, and the natural frequency of the third SDOF corresponds the first natural frequency of the structure. The natural frequency of the second SDOF was set so that it lies between those of the other SDOFs, creating a staggered range of dynamic responses.</p> <h3>Test setup:</h3> <p>The shaking table specifications are:</p> <ul> <li>Table size: 3.0x3.0 m</li> <li>Max. specimen mass: 10 t</li> <li>Max. overturning moment: 30 m t</li> <li>Max. actuator stroke: +/- 250 mm</li> <li>Max. table velocity: +/- 1 m/s at rated load</li> <li>Max. table acceleration: +/- 1g at rated load</li> <li>Test frequency: 0 to 50 Hz</li> </ul> <p>The instrumentation scheme of the test setup consisted of accelerometers and displacement tranducers, measuring the excitation provided by the shaking table and the response of the structure. Regarding the global response of the test structure, the recordings of the accelerometers and displacement tranducers indicated in the uploaded file 'Instrumentation_Scheme_v1.0.0.pdf' are provided. </p> <p>The properties of the accelerometers are:</p> <ul> <li>Type: M3701-series</li> <li>Manufacturer: PCB Piezotronics, Inc.</li> <li>Measurement range: +/- 3g</li> <li>Frequency range: 0-500 Hz</li> <li>Sensitivity: 900 mV/g</li> <li>Resolution: 2.2e-5g</li> <li>Noise: 1 µg/Hz<sup>-0.5</sup></li> </ul> <p>The properties of the displacement tranducers are:</p> <ul> <li>Type: LZW-M-500</li> <li>Manufacturer: WayCon Positionsmesstechnik GmbH</li> <li>Measurement range: +/- 250 mm</li> <li>Linearity: +/- 0.05%</li> <li>Repeatability: 0.01 mm</li> <li>Displacement force: ≤15 N</li> <li>Displacement speed: ≤5 m/s</li> </ul> <h2>Files:</h2> <ul> <li>Column_Base_Anchorage_v1.0.0.pdf <ul> <li>Photo of the column-base anchorage.</li> </ul> </li> <li>Data_v1.0.0.zip <ul> <li>Contains all data files according to the load protocols.</li> <li>The experimental data is provided as .csv files for each load protocol. </li> </ul> </li> <li>Instrumentation_Scheme_v1.0.0.pdf <ul> <li>.pdf file illustrating the sensor placements on the test structure.</li> </ul> </li> <li>Load_Protocols_v1.0.0.pdf <ul> <li>.pdf file listing all load protocols applied to the structure.</li> </ul> </li> <li>References_v1.0.0.bib <ul> <li>Contains a bibtex reference with the associated publications.</li> </ul> </li> <li>Shake_Table.jpg <ul> <li>Photo of the shaking table without any specimen.</li> </ul> </li> <li>Test_Structure_v1.0.0.pdf <ul> <li>Photo of the shaking table including the test structure.</li> </ul> </li> <li>Test_Structure_Sketch_v1.0.0.pdf <ul> <li>.pdf file illustrating the test structure.</li> </ul> </li> <li>Time_Histories_v1.0.0.pdf <ul> <li>.pdf file including plots of the measurement data.</li> </ul> </li> </ul> <h2>File format of the datasets:</h2> <p>The data is stored in .csv files, where each file contains the following columns (see also 'Instrumentation_Scheme_v1.0.0.pdf'):</p> <ul> <li>Time (s): Time in seconds since the start of the test (time step equals 0.0025 s).</li> <li>Acc_0 (m/s2): Acceleration signal measured in m/s<sup>2</sup> on the shaking table in the direction of excitation (Axis A-A).</li> <li>Acc_1 (m/s2): Acceleration response of the structure measured in m/s<sup>2</sup> on the first floor in the direction of excitation (Axis A-A).</li> <li>Acc_2 (m/s2): Acceleration response of the structure measured in m/s<sup>2</sup> on the second floor in the direction of excitation (Axis A-A).</li> <li>Acc_L (m/s2): Acceleration response of SDOF I measured in m/s<sup>2</sup> in the direction of excitation.</li> <li>Acc_F (m/s2): Acceleration response of SDOF II measured in m/s<sup>2</sup> in the direction of excitation.</li> <li>Acc_H (m/s2): Acceleration response of SDOF III measured in m/s<sup>2</sup> in the direction of excitation.</li> <li>Acc_G (m/s2): Acceleration response of the structure measured in m/s<sup>2</sup> on the second floor in the direction of excitation (Axis B-B).</li> <li>Acc_J (m/s2): Acceleration response of the structure measured in m/s<sup>2</sup> on the second floor in the transverse direction of excitation (Axis B-B).</li> <li>Dis_0 (mm): Displacement signal measured mm on the shaking table in the direction of excitation (Axis A-A).</li> <li>Dis_1 (mm): Displacement response of the structure measured in mm on the first floor in the direction of excitation (Axis A-A).</li> <li>Dis_2 (mm): Displacement response of the structure measured in mm on the second floor in the direction of excitation (Axis A-A).</li> </ul> <p>These data files can easily be uploaded using the pandas library in Python. For example by:</p> <pre><code>import pandas as pd df = pd.read_csv('1_IM_4mm.csv') time = df["Time (s)"] acc_0 = df["Acc_0 (m/s2)"] dis_0 = df["Dis_0 (mm)"]</code></pre> <h2>Contact:</h2> <p>Please send your enquiries regarding the shaking table to <a href="dynamics@lbb.rwth-aachen.de">dynamics@lbb.rwth-aachen.de</a>. Further information can be found on our <a href="https://www.lbb.rwth-aachen.de/cms/lbb/der-lehrstuhl/~bjlfvq/geraetezentzrum/?lidx=1">website</a>.</p> <h2>Usage/License:</h2> <ul> <li>The data is licensed under CC BY-SA 4.0.</li> <li>If you have used our data and are publishing your work, we ask you to please reference both <ul> <li>this database by its DOI, and</li> <li>any publication that is associated with the experiments. See the "References_v1.0.0.bib" for the associated publication references.</li> </ul> </li> </ul> <h2>Fundings:</h2> <ul> <li>Deutsche Forschungsgemeinschaft - <em>Grant number: INST 222/1161-1 FUGG</em>. Einaxialer Schwingtisch für dynamische Modell- und Bauteilversuche.</li> <li>Bundesministerium für Bildung und Forschung - <em>Grant number: 03G0892A</em>. ROBUST – Nutzerorientiertes Erdbebenfrühwarnsystem mit intelligenten Sensorsystemen und digitalen Bauwerksmodellen – Entwicklung Installation und Anwendung von sensorbasierten Monitoringsystemen mit BIM-Integration zur Echtzeit-Schadenerkennung in kritischen Infrastrukturen.</li> </ul>
Training and test dataset of STED images of microtubules in fixed cells
<p>Training and test dataset of microtubule used in the manuscript "Denoising diffusion models for high-resolution microscopy image restoration".</p>
Dataset for "Machine learning predictions on an extensive geotechnical dataset of laboratory tests in Austria"
<p>This dataset comprises over 20 years of geotechnical laboratory testing data collected primarily from Vienna, Lower Austria, and Burgenland. It includes 24 features documenting critical soil properties derived from particle size distributions, Atterberg limits, Proctor tests, permeability tests, and direct shear tests. Locations for a subset of samples are provided, enabling spatial analysis.</p> <p>The dataset is a valuable resource for geotechnical research and education, allowing users to explore correlations among soil parameters and develop predictive models. Examples of such correlations include liquidity index with undrained shear strength, particle size distribution with friction angle, and liquid limit and plasticity index with residual friction angle.</p> <p>Python-based exploratory data analysis and machine learning applications have demonstrated the dataset's potential for predictive modeling, achieving moderate accuracy for parameters such as cohesion and friction angle. Its temporal and spatial breadth, combined with repeated testing, enhances its reliability and applicability for benchmarking and validating analytical and computational geotechnical methods.</p> <p>This dataset is intended for researchers, educators, and practitioners in geotechnical engineering. Potential use cases include refining empirical correlations, training machine learning models, and advancing soil mechanics understanding. Users should note that preprocessing steps, such as imputation for missing values and outlier detection, may be necessary for specific applications.</p> <p><strong>Key Features</strong>:</p> <ul> <li><strong>Temporal Coverage</strong>: Over 20 years of data.</li> <li><strong>Geographical Coverage</strong>: Vienna, Lower Austria, and Burgenland.</li> <li><strong>Tests Included</strong>: <ul> <li>Particle Size Distribution</li> <li>Atterberg Limits</li> <li>Proctor Tests</li> <li>Permeability Tests</li> <li>Direct Shear Tests</li> </ul> </li> <li><strong>Number of Variables</strong>: 24</li> <li><strong>Potential Applications</strong>: Correlation analysis, predictive modeling, and geotechnical design.</li> </ul> <p><strong>Technical Details</strong>:</p> <ul> <li>Missing values have been addressed using K-Nearest Neighbors (KNN) imputation, and anomalies identified using Local Outlier Factor (LOF) methods in previous studies.</li> <li>Data normalization and standardization steps are recommended for specific analyses.</li> </ul> <p><strong>Acknowledgments</strong>:<br>The dataset was compiled with support from the European Union's MSCA Staff Exchanges project 101182689 Geotechnical Resilience through Intelligent Design (GRID).</p>
Dataset for the validation of a Computational Thinking test for upper primary school (grades 3-4)
<p>This dataset contains quantitative student data acquired during the administration of a new computational thinking assessment for upper primary school (grades 3 and 4). Over 1500 students (approximately half in grade 3 and half in grade 4) participated in the data collection which took place in January 2021 in the Canon Vaud in Switzerland. The data was used to validate the psychometric properties of the instrument in the referenced article. </p> <p> </p> <p>If you use any of the resources provided in this repository, please cite the following</p> <p>• The Zenodo repository, DOI: 10.5281/zenodo.5865573</p> <p>• The corresponding journal article</p> <p>• Licence : CC-BY-NC</p> <p> </p> <p>In case of inquiries, please contact laila.elhamamsy@epfl.ch</p>
RvSpectML/EchelleCCFs.jl Test dataset
<p>Dataset used in continuous integration test for <a href="https://github.com/RvSpectML/EchelleCCFs.jl">RvSpectML/EchelleCCFs.jl</a>. </p> <p>Source: Gilbertson, Ford & Dumuseque (2020) Research Notes of the AAS, Volume 4, Issue 4, id.59 <a href="https://ui.adsabs.harvard.edu/link_gateway/2020RNAAS...4...59G/doi:10.3847/2515-5172/ab8d44">10.3847/2515-5172/ab8d44</a> with full data set at <a href="https://doi.org/10.5281/zenodo.3753254">https://doi.org/10.5281/zenodo.3753254</a>. <br> </p>
Minimal dataset to test multiplexed DNA imaging (Hi-M) software pipelines
<p>This is a dataset of nuclei (DAPI), and 3 multiplexed DNA imaging cycles to test and validate processing software packages, such as pyHiM (https://github.com/marcnol/pyHiM). This dataset was acquired in a nc14 Drosophila embryo.</p> <p>File contents:</p> <p>scan_001_RT27_001_ROI_converted_decon_ch00.tif barcode 27, fiducial <br> scan_001_RT27_001_ROI_converted_decon_ch01.tif barcode 27<br> scan_001_RT29_001_ROI_converted_decon_ch00.tif barcode 29, fiducial <br> scan_001_RT29_001_ROI_converted_decon_ch01.tif barcode 29 <br> scan_001_RT37_001_ROI_converted_decon_ch00.tif barcode 37, fiducial <br> scan_001_RT37_001_ROI_converted_decon_ch01.tif barcode 37 <br> scan_006_DAPI_001_ROI_converted_decon_ch00.tif DAPI <br> scan_006_DAPI_001_ROI_converted_decon_ch01.tif DAPI, fiducial <br> scan_006_DAPI_001_ROI_converted_decon_ch02.tif RNA</p> <p> </p> <p>To test this dataset please refer to <a href="https://github.com/marcnol/pyHiM">pyHiM documentation page</a>.</p>
Test datasets for Hi-C scaffolding
<p>We provided two datasets for testing Hi-C scaffolding tools. For the CHM13 test dataset, we randomly chunked the first 10Mb of chr1, chr2 and chr3 of the T2T-CHM13v1.1 human genome assembly (Nurk et al. 2022) into 57 contigs. The Hi-C data downloaded from the telomere-to-telomere consortium GitHub repository (https://github.com/marbl/CHM13) were mapped to the reference genome and the reads mapped to these regions were extracted to generate Hi-C alignment files. For the LYZE01 test dataset, the Saccharomyces cerevisiae strain W303 genome assembly (Matheson et al. 2017) was split at positions with gaps (‘N’) to get the original contigs. An independent Hi-C data library was downloaded from the NCBI repository (GEO Accession GSM2417297) and downsampled to approximately 20X. The downsampled Hi-C data were mapped to the contigs to generate Hi-C alignment files.</p> <p>We provided five files for each test dataset: the contig file in FASTA format, the FASTA index file generated with SAMtools faidx command, and the Hi-C alignment file in BAM format sorted by coordinate, in BAM format sorted by query names (with the identifier 'qn' in the file name), and in BED format.</p>
Test-Retest qt-dMRI datasets for "Non-Parametric GraphNet-Regularized Representation of dMRI in Space and Time"
<p>We release these four diffusion MRI data sets as part of our recent journal publication; Fick, Rutger H.J., et al. "Non-Parametric GraphNet-Regularized Representation of dMRI in Space and Time." <em>Medical Image Analysis</em> (2017). More detailed information about the use of these data sets can also be found in the publication.</p> <p>We acquired test-retest diffusion MRI spin echo sequences from two C57Bl6 wild-type mice on an 11.7 Tesla Bruker scanner. The test and retest acquisition were taken 48 hours from each other. The data consists of 80x160x5 voxels of size 110x110x500<span class="math-tex">\(\mu\)</span>m. Each data set consists of 515 Diffusion-Weighted Images (DWIs) spread over 35 acquisition shells. The shells are spread over 7 gradient strength shells with a maximum gradient strength of 491 mT/m, 5 pulse separation shells between [10.8 - 20.0]ms, and a pulse length of 5ms. We manually created a brain mask and corrected the data from eddy currents and motion artifacts using FSL's eddy. We then drew a region of interest in the middle slice in the corpus callosum, where the tissue is reasonably coherent.</p> <p>- The diffusion MRI data are contained in the files with 'dwis' in the name.<br> <br> - The corpus callosum masks are contained in the files with 'mask' in the name.</p> <p>- The acquisition parameters are contained in the .txt files.</p>
Survey of participant experience in workshop for testing IGP software setup: supplemental dataset for SimAUD 2018
<p>This is a supplemental dataset for a SimAUD 2018 paper. For the context of the dataset, plots, and description text given here, please refer to the paper:</p> <blockquote> <p><strong>Heinrich, M.K., Zahadat, P., Harding, J., et al. Using interactive evolution to design behaviors for non-deterministic self-organized construction. In <em>Proc. of SimAUD</em> (2018). <em>In print</em>.</strong></p> </blockquote> <p>These survey results <em><strong>(see attached file dataset_survey-responses)</strong></em>, are regarding the experience of participants in a workshop testing the <em>Integrated Growth Projection</em> software setup, including an implementation of the <em>Vascular Morphogenesis Controller</em>, and the Interactive Evolution software <em>Biomorpher</em>.</p> <p>The full-time one-week workshop was held as part of the normal coursework of the Master's degree program <em>CITAstudio: Computation in Architecture</em>, in the Institute of Architecture and Technology, at [KADK] The Royal Danish Academy, School of Architecture, Copenhagen, Denmark. It was part of the first semester of the 2017-2018 school year. Workshop participants were current Master's students in the <em>CITAstudio </em>program. The workshop teaching was led by Mary Katherine Heinrich and Phil Ayres, with guest teaching by Payam Zahadat and John Harding, overall program teaching supervision by Paul Nicholas, and teaching assistance by Sebastian Gatz.</p> <p><strong>Survey method:</strong></p> <p>The workshop participants gave survey responses anonymously.</p> <p>Survey responses were collected via Google Forms (https://www.google.com/forms/about/). At the start of the survey, participants gave permissions for use and publication, and verified that they participated in the workshop and had not previously taken the survey. The platform discourages duplicate responses by requiring an email sign-in (which is not visible to the surveyor).</p> <p>Although workshop participants gave permission for survey results to be published before taking the survey, the participants were unaware of the specific intended context and purpose of publishing, prior to taking the survey. Authors of the related paper who were workshop participants had no contact with the process of survey preparation, analysis of its results, or writing of related paper sections. </p> <p>There were 26 workshop participants. Participants were architects or architectural designers. </p> <p>Participants were asked about 1) their prior experience, 2) their understanding of topics before and after the workshop, 3) the helpfulness of specific software aspects for their understanding and their project work, and 4) their likelihood to use specific software aspects in the future.</p> <p>In addition to looking at the full surveyed group, we compare experience sub-groups. Participants select relevant tasks that they have previously completed, from a provided list. They are placed in the <em>Less Experience</em> sub-group if they select one or no tasks, and in the <em>More Experience</em> sub-group if they select two or more. </p> <p><strong>Survey results:</strong></p> <p>Close to two-thirds of workshop participants submitted survey responses (16 of 26, or 61.5%), with at least two respondents per group. One respondent indicated workshop absence; their responses were removed. One respondent indicated that they did not understand two questions, so those two responses were removed. All responses were submitted within 18 days of workshop end.</p> <p>Attached file:<em><strong> Plot_1</strong></em>, caption:</p> <blockquote> <p>Plot 1: <em>Participants' scoring of their understanding of the topics "self-organization" and "Interactive Evolution" respectively, comparing scores before and after the workshop.</em></p> </blockquote> <p>Attached file:<em><strong> Plot_2</strong></em>, caption:</p> <blockquote> <p>Plot 2: <em>(Left) Participants' scoring of their likelihood to use certain aspects of the software setup again, if they were to design a non-deterministic self-organizing behavior, and (right) participants' indications of the helpfulness of those same software aspects.</em></p> </blockquote> <p>Responses regarding understanding <em><strong>(see attached file, Plot_1)</strong></em> give evidence that the <em>Integrated Growth Projection</em> software setup helped participants of both experience levels improve their understanding of related topics. Those with less prior experience improved their understanding more than others, and understanding of "Interactive Evolution" improved slightly more than understanding of "self-organization." </p> <p>Responses regarding the usefulness of certain software aspects <em><strong>(see attached file, Plot_2)</strong></em> give evidence that: 1) Interactive Evolution helped participants to understand and design a non-deterministic self-organizing behavior <em><strong>(see Plot_2, a)</strong></em>; 2) visualization of the environment and simultaneous viewing of multiple results helped them to understand and design such behaviors <em><strong>(see Plot_2, b and c)</strong></em>; and 3) the <em>Integrated Growth Projection</em>'s features of environment visualization and simultaneous results <em>inside</em> the artificial selection preview windows of the IE setup helped them to evolve behaviors to solve their chosen tasks<em> <strong>(see Plot_2, d and e)</strong></em>. </p> <p>____________________________________</p> <p>The research work involved here is part of EU project<em> flora robotica</em>.<br> <a href="http://www.florarobotica.eu/">http://www.florarobotica.eu/</a><br> Project<em> flora robotica</em> has received funding from the European Union's Horizon 2020 research and innovation program under the FET grant agreement, no. 640959.</p>
Test dataset for omero-vitessce
<h1>Test datasets for omero-vitessce</h1> <p>Dataset designed for testing the omero-vitessce <a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce" target="_blank" rel="noopener">(https://github.com/NFDI4BIOIMAGE/omero-vitessce</a>) plugin for OMERO (<a href="https://www.openmicroscopy.org/omero/" target="_blank" rel="noopener">https://www.openmicroscopy.org/omero/</a>). The omero-vitessce repository contains a cropped version of this dataset for automated testing (<a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce/tree/main/test/data/MB266" target="_blank" rel="noopener">https://github.com/NFDI4BIOIMAGE/omero-vitessce/tree/main/test/data/MB266</a>).</p> <h2>Files</h2> <ul> <li><code>MAX_MBEN_ff_Xenium_0018446_MB-266_DAPI_2024-01-23_12.47.34_Fused_405nm_corr_cropped.png</code> = PNG image with the DAPI channel.</li> <li><code><span>MAX_MBEN_ff_Xenium_0018446_MB-266_DAPI_2024-01-23_12.47.34_Fused_405nm_corr_cropped_cp_masks.png</span></code>= Cell segmentation mask pixel values correspond to cell identities, 0 = background).</li> <li><code>cells.csv</code> = </li> <li><code>embeddings.csv</code> = UMAP embeddings for drawing an interactive scatterplot.</li> <li><code>feature_matrix.csv</code> = Transcript counts in each cell.</li> <li><code>transcripts.csv</code> = Gene name and coordinates (pixel) of each transcript.</li> <li><code>VitessceConfig.json</code> = Example configuration file generated by the omero-vitessce plugin for the Vitessce, an equivalent file can be generated by using the form provided by the plugin in OMERO.web.</li> </ul> <p>See the repository README file for more details on the formats of these files:<a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#config-files"> </a><a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#config-files" target="_blank" rel="noopener">https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#config-files</a></p> <h2>Usage</h2> <ol> <li>Add the omero-web-zarr and omero-vitessce plugins to your OMERO.web installation.</li> <li>Import the images into OMERO in the same dataset.</li> <li>Attach all the .csv data files.</li> <li>Use the form in the "Vitessce" tab of the right-panel to generate a configuration file and open the Vitessce viewer.</li> </ol> <p>See the repository README file for more details on usage (<a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#usage" target="_blank" rel="noopener">https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#usage</a>) and installation (<a href="https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#installation" target="_blank" rel="noopener">https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#installation</a>)</p> <h2>Data Sources</h2> <p>Adapted from the full original data at: <a href="https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093" target="_blank" rel="noopener">https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093</a> (<a href="https://doi.org/10.6019/S-BIAD1093">10.6019/S-BIAD1093</a>).</p> <p>The original data were produced and analysed in the course of this study:</p> <p><a href="https://www.biorxiv.org/content/10.1101/2024.04.03.586404v1" target="_blank" rel="noopener">https://www.biorxiv.org/content/10.1101/2024.04.03.586404v1</a></p>
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.