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HRV-ACC: a dataset with R-R intervals and accelerometer data for the diagnosis of psychotic disorders using a Polar H10 wearable sensor
<p><strong>ABSTRACT</strong></p> <p>The issue of diagnosing psychotic diseases, including schizophrenia and bipolar disorder, in particular, the objectification of symptom severity assessment, is still a problem requiring the attention of researchers. Two measures that can be helpful in patient diagnosis are heart rate variability calculated based on electrocardiographic signal and accelerometer mobility data. The following dataset contains data from 30 psychiatric ward patients having schizophrenia or bipolar disorder and 30 healthy persons. The duration of the measurements for individuals was usually between 1.5 and 2 hours. R-R intervals necessary for heart rate variability calculation were collected simultaneously with accelerometer data using a wearable Polar H10 device. The Positive and Negative Syndrome Scale (PANSS) test was performed for each patient participating in the experiment, and its results were attached to the dataset. Furthermore, the code for loading and preprocessing data, as well as for statistical analysis, was included on the corresponding GitHub repository.</p> <p><strong>BACKGROUND</strong></p> <p>Heart rate variability (HRV), calculated based on electrocardiographic (ECG) recordings of R-R intervals stemming from the heart's electrical activity, may be used as a biomarker of mental illnesses, including schizophrenia and bipolar disorder (BD) [Benjamin et al]. The variations of R-R interval values correspond to the heart's autonomic regulation changes [Berntson et al, Stogios et al]. Moreover, the HRV measure reflects the activity of the sympathetic and parasympathetic parts of the autonomous nervous system (ANS) [Task Force of the European Society of Cardiology the North American Society of Pacing Electrophysiology, Matusik et al]. Patients with psychotic mental disorders show a tendency for a change in the centrally regulated ANS balance in the direction of less dynamic changes in the ANS activity in response to different environmental conditions [Stogios et al]. Larger sympathetic activity relative to the parasympathetic one leads to lower HRV, while, on the other hand, higher parasympathetic activity translates to higher HRV. This loss of dynamic response may be an indicator of mental health. Additional benefits may come from measuring the daily activity of patients using accelerometry. This may be used to register periods of physical activity and inactivity or withdrawal for further correlation with HRV values recorded at the same time.</p> <p><strong>EXPERIMENTS</strong></p> <p>In our experiment, the participants were 30 psychiatric ward patients with schizophrenia or BD and 30 healthy people. All measurements were performed using a Polar H10 wearable device. The sensor collects ECG recordings and accelerometer data and, additionally, prepares a detection of R wave peaks. Participants of the experiment had to wear the sensor for a given time. Basically, it was between 1.5 and 2 hours, but the shortest recording was 70 minutes. During this time, evaluated persons could perform any activity a few minutes after starting the measurement. Participants were encouraged to undertake physical activity and, more specifically, to take a walk. Due to patients being in the medical ward, they received instruction to take a walk in the corridors at the beginning of the experiment. They were to repeat the walk 30 minutes and 1 hour after the first walk. The subsequent walks were to be slightly longer (about 3, 5 and 7 minutes, respectively). We did not remind or supervise the command during the experiment, both in the treatment and the control group. Seven persons from the control group did not receive this order and their measurements correspond to freely selected activities with rest periods but at least three of them performed physical activities during this time. Nevertheless, at the start of the experiment, all participants were requested to rest in a sitting position for 5 minutes. Moreover, for each patient, the disease severity was assessed using the PANSS test and its scores are attached to the dataset.</p> <p>The data from sensors were collected using Polar Sensor Logger application [Happonen]. Such extracted measurements were then preprocessed and analyzed using the code prepared by the authors of the experiment. It is publicly available on the GitHub repository [Książek et al].</p> <p>Firstly, we performed a manual artifact detection to remove abnormal heartbeats due to non-sinus beats and technical issues of the device (e.g. temporary disconnections and inappropriate electrode readings). We also performed anomaly detection using Daubechies wavelet transform. Nevertheless, the dataset includes raw data, while a full code necessary to reproduce our anomaly detection approach is available in the repository. Optionally, it is also possible to perform cubic spline data interpolation. After that step, rolling windows of a particular size and time intervals between them are created. Then, a statistical analysis is prepared, e.g. mean HRV calculation using the RMSSD (Root Mean Square of Successive Differences) approach, measuring a relationship between mean HRV and PANSS scores, mobility coefficient calculation based on accelerometer data and verification of dependencies between HRV and mobility scores.</p> <p><strong>DATA DESCRIPTION</strong></p> <p>The structure of the dataset is as follows. One folder, called <em>HRV_anonymized_data</em> contains values of R-R intervals together with timestamps for each experiment participant. The data was properly anonymized, i.e. the day of the measurement was removed to prevent person identification. Files concerned with patients have the name <em>treatment_X.csv</em>, where <em>X</em> is the number of the person, while files related to the healthy controls are named <em>control_Y.csv</em>, where <em>Y</em> is the identification number of the person. Furthermore, for visualization purposes, an image of the raw RR intervals for each participant is presented. Its name is <em>raw_RR_{control,treatment}_N.png</em>, where <em>N</em> is the number of the person from the control/treatment group. The collected data are raw, i.e. before the anomaly removal. The code enabling reproducing the anomaly detection stage and removing suspicious heartbeats is publicly available in the repository [Książek et al]. The structure of consecutive files collecting R-R intervals is following:</p> <table> <tbody> <tr> <td><strong>Phone timestamp</strong></td> <td><strong>RR-interval [ms]</strong></td> </tr> <tr> <td>12:43:26.538000</td> <td>651</td> </tr> <tr> <td>12:43:27.189000</td> <td>632</td> </tr> <tr> <td>12:43:27.821000</td> <td>618</td> </tr> <tr> <td>12:43:28.439000</td> <td>621</td> </tr> <tr> <td>12:43:29.060000</td> <td>661</td> </tr> <tr> <td>...</td> <td>...</td> </tr> </tbody> </table> <p>The first column contains the timestamp for which the distance between two consecutive R peaks was registered. The corresponding R-R interval is presented in the second column of the file and is expressed in milliseconds. <br> The second folder, called <em>accelerometer_anonymized_data</em> contains values of accelerometer data collected at the same time as R-R intervals. The naming convention is similar to that of the R-R interval data: <em>treatment_X.csv </em>and <em>control_X.csv</em> represent the data coming from the persons from the treatment and control group, respectively, while <em>X </em>is the identification number of the selected participant. The numbers are exactly the same as for R-R intervals. The structure of the files with accelerometer recordings is as follows:</p> <table> <tbody> <tr> <td><strong>Phone timestamp</strong></td> <td><strong>X [mg]</strong></td> <td><strong>Y [mg]</strong></td> <td><strong>Z [mg]</strong></td> </tr> <tr> <td>13:00:17.196000</td> <td>-961</td> <td>-23</td> <td>182</td> </tr> <tr> <td>13:00:17.205000</td> <td>-965</td> <td>-21</td> <td>181</td> </tr> <tr> <td>13:00:17.215000</td> <td>-966</td> <td>-22</td> <td>187</td> </tr> <tr> <td>13:00:17.225000</td> <td>-967</td> <td>-26</td> <td>193</td> </tr> <tr> <td>13:00:17.235000</td> <td>-965</td> <td>-27</td> <td>191</td> </tr> <tr> <td>...</td> <td>...</td> <td>...</td> <td>...</td> </tr> </tbody> </table> <p>The first column contains a timestamp, while the next three columns correspond to the currently registered acceleration in three axes: X, Y and Z, in milli-g unit.</p> <p>We also attached a file with the PANSS test scores (<em>PANSS.csv</em>) for all patients participating in the measurement. The structure of this file is as follows:</p> <table> <tbody> <tr> <td><strong>no_of_person</strong></td> <td><strong>PANSS_P</strong></td> <td><strong>PANSS_N</strong></td> <td><strong>PANSS_G</strong></td> <td><strong>PANSS_total</strong></td> </tr> <tr> <td>1</td> <td>8</td> <td>13</td> <td>22</td> <td>43</td> </tr> <tr> <td>2</td> <td>11</td> <td>7</td> <td>18</td> <td>36</td> </tr> <tr> <td>3</td> <td>14</td> <td>30</td> <td>44</td> <td>88</td> </tr> <tr> <td>4</td> <td>18</td> <td>13</td> <td>27</td> <td>58</td> </tr> <tr> <td>...</td> <td>...</td> <td>...</td> <td>...</td> <td>..</td> </tr> </tbody> </table> <p><br> The first column contains the identification number of the patient, while the three following columns refer to the PANSS scores related to positive, negative and general symptoms, respectively.</p> <p><strong>USAGE NOTES</strong></p> <p>All the files necessary to run the HRV and/or accelerometer data analysis are available on the GitHub repository [Książek et al]. HRV data loading, preprocessing (i.e. anomaly detection and removal), as well as the calculation of mean HRV values in terms of the RMSSD, is performed in the <em>main.py</em> file. Also, Pearson's correlation coefficients between HRV values and PANSS scores and the statistical tests (Levene's and Mann-Whitney U tests) comparing the treatment and control groups are computed. By default, a sensitivity analysis is made, i.e. running the full pipeline for different settings of the window size for which the HRV is calculated and various time intervals between consecutive windows. Preparing the heatmaps of correlation coefficients and corresponding p-values can be done by running the <em>utils_advanced_plots.py</em> file after performing the sensitivity analysis. Furthermore, a detailed analysis for the one selected set of hyperparameters may be prepared (by setting <em>sensitivity_analysis = False</em>), i.e. for 15-minute window sizes, 1-minute time intervals between consecutive windows and without data interpolation method. Also, patients taking quetiapine may be excluded from further calculations by setting <em>exclude_quetiapine = True</em> because this medicine can have a strong impact on HRV [Hattori et al].</p> <p>The accelerometer data processing may be performed using the <em>utils_accelerometer.py</em> file. In this case, accelerometer recordings are downsampled to ensure the same timestamps as for R-R intervals and, for each participant, the mobility coefficient is calculated. Then, a correlation coefficient between mean HRV values and mobility coefficient is computed. The plotting of the pure accelerometer signal may be done by running the <em>utils_loading.py </em>file.</p> <p>The comparison of age distribution between the tested groups can be made by the histogram plotted with the use of the <em>utils_basic_plots.py</em> file.</p>
CSV equivalent of LOFAR ACC files
<p>These are conversions of LOFAR ACC files by Griffin Foster from <a href="https://zenodo.org/record/840405/files/20120513_052251_acc_512x192x192.dat">https://zenodo.org/record/840405</a> to demonstrate the use of the ACC to CSV converter developed at DIAS</p>
Sample ACC Data Set for LOFAR Station IE613 LBA whole sky observation
<p>This is a large sample of data from Station IE613 suitable for use with <a href="https://github.com/creaneroDIAS/beamModelTester">beamModelTester</a> and <a href="https://github.com/2baOrNot2ba/iLiSA">iLiSA</a>. To use with these systems, transfer it to a directory of the form :</p> <p><em>{STN_ID}_YYYYMMDD_HHMMSS_rcu{RCU_MODE}<em>dur{DURATION}</em>{SOURCE}_acc</em><br> e.g. IE613_20180406_091321_rcu3_dur85635_CasA_acc</p>
Gaussian16 data for "Dynamic electronic structure fluctuations in the de novo peptide ACC-dimer revealed by first-principles theory and machine learning"
<p>This is the Gaussian 16 input and corresponding output, which was used as input into the machine learning presented in the paper titled "Dynamic electronic structure fluctuations in the de novo peptide ACC-dimer revealed by first-principles theory and machine learning". This upload is required before submission of the paper.<br><br>The 1001 and 100 snapshots from different extractions are preserved in separated directories. Each snapshot directory <code>*_snapshot</code> has the initial GROMACS snapshot <code>test_*.pdb</code> , the geometry after truncating the solvation shell in various formats, the Gaussian16 input, qsub input and the output directory <code>*.1</code> with a JobID number assigned by qsub. The output directory has the standard output from Gaussian in a <code>.log</code> file and <code>grep</code>ed output from the <code>.fchk</code> file in <code>*.out</code> .</p>
Análisis de correspondencia canónicas (ACC), ordenación de los dos primeros ejes.
<p>Publicado en:</p> <p>Hernández Escobar, L., Granados-Martínez, C. & Fuentes-Reinés, J. (2022). Descomposición acuática de la hojarasca foliar en tres especies de mangle en la desembocura del río Ranchería (Brazo Riíto) y su relación con los macroinvertebrados en el municipio de Riohacha, departamento de La Guajira. <em>Ciencia e Ingeniería</em>, 9 (1):e6709388. https://www.doi.org/10.5281/zenodo.6709388</p>
ACC-Lists for GLASSgo >=1.5.1
<p>Accession lists are compatible with GLASSgo version >= 1.5.1 (Publikation: https://www.frontiersin.org/articles/10.3389/fgene.2018.00124/full). </p>
RB1832 acc-4(ok2371)III | 2011-09-15T12:17:58+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=kWaZtVtXvHg</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-15T12:17:58+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food L_2011_09_15__12_17_58___1___4</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.48743</li> <li><b>number of segmented skeletons</b> : 26637</li> </ul>
RB1832 acc-4(ok2371)III | 2011-08-11T11:58:57+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=eexg8mUvf0g</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-08-11T11:58:57+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)II on food R_2011_08_11__11_58_57___1___7</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.56571</li> <li><b>number of segmented skeletons</b> : 26486</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-13T15:57:42+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=En7Df95BLhw</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-13T15:57:42+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food L_2011_09_13__15_57_42___1___11</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.48743</li> <li><b>number of segmented skeletons</b> : 26928</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-13T12:43:09+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=ZDlUO1AYvMM</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-13T12:43:09+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_09_13__12_43_09___8___5</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 5.06577</li> <li><b>number of segmented skeletons</b> : 26678</li> </ul>
RB1832 acc-4(ok2371)III | 2011-08-11T11:25:22+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=IT70N_qim9c</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-08-11T11:25:22+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food L_2011_08_11__11_25_22___8___5</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.89022</li> <li><b>number of segmented skeletons</b> : 26917</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-15T14:11:28+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=xNKSsUOlxRI</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-15T14:11:28+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_09_15__14_11_28__7</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 3.93211</li> <li><b>number of segmented skeletons</b> : 26939</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-13T11:42:56+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=M6rJXzEo42A</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-13T11:42:56+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_09_13__11_42_56__2</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 3.93211</li> <li><b>number of segmented skeletons</b> : 26727</li> </ul>
RB1832 acc-4(ok2371)III | 2011-08-11T10:23:19+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=uvOH-oukH4I</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-08-11T10:23:19+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_08_11__10_23_19__2</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 3.99113</li> <li><b>number of segmented skeletons</b> : 26358</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-15T13:18:00+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=-xHp4YPET4M</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-15T13:18:00+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_09_15__13_18___4___7</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.68379</li> <li><b>number of segmented skeletons</b> : 26987</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-13T11:20:00+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=N7EFYMmlvW8</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-13T11:20:00+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food L_2011_09_13__11_20___4___1</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.68379</li> <li><b>number of segmented skeletons</b> : 26631</li> </ul>
RB1832 acc-4(ok2371)III | 2011-08-11T09:59:00+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=0f66exYYojw</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-08-11T09:59:00+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_08_11__09_59___4___1</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.76371</li> <li><b>number of segmented skeletons</b> : 26620</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-13T11:59:48+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=KkOSbbrQooc</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-13T11:59:48+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food R_2011_09_13__11_59_48___6___3</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.57571</li> <li><b>number of segmented skeletons</b> : 26998</li> </ul>
RB1832 acc-4(ok2371)III | 2011-08-11T10:39:30+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=w4pM0DFk4pI</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-08-11T10:39:30+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food L_2011_08_11__10_39_30___6___3</li> <li><b>total time (s)</b> : 899.033</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.57167</li> <li><b>number of segmented skeletons</b> : 26742</li> </ul>
RB1832 acc-4(ok2371)III | 2011-09-15T12:39:15+01:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=YKtTqbCWKXk</li> <li><b>strain</b> : RB1832</li> <li><b>timestamp</b> : 2011-09-15T12:39:15+01:00</li> <li><b>gene</b> : acc-4</li> <li><b>chromosome</b> : III</li> <li><b>allele</b> : ok2371</li> <li><b>strain_description</b> : acc-4(ok2371)III</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : T27E9.9 (ok2371)III on food l_2011_09_15__12_39_15___2___5</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 4.48768</li> <li><b>number of segmented skeletons</b> : 26885</li> </ul>
ScienceDex guides
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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.