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Hand-selective visual regions represent how to grasp 3D tools for use: brain decoding during real actions
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Fish tag data remotely detected using whole stream antennas or hand held tag readers in the Kuparuk, Itkilik, and Sagavanirktok drainages near Toolik Field Station, Alaska, from 2010 to 2017
From 2009 to 2017, the FISHSCAPE Project (grant numbers 1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream); The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Ailish and Atigun Rivers and the Galbraith Lakes); and The Itkillik (primarily the I-Minus outlet stream, a tributary that that feeds into the Itkilik River). Target species were primarily Arctic grayling and Lake trout, although Arctic char, Burbot, Dolly varden, round whitefish, and slimey sculpin were also captured. This file contains the detectioned fish tags using whole stream or hand-held antennas in the three watersheds. We had no field season in 2014 and thus did not deploy antennaes. Fish were tagged with Passive Integrated Transponder (PIT) tags which can be read with a whole stream antenna to track the migration of the fish, predominately Arctic grayling, throughout the systems. Fish tags detected with a handheld readers are designated in Site ID as "XXX_capture". For "capture" fish time is arbitraily set at '7:00:00'' of the day of capture and tagging because actual time was not recorded. The individual fish data (date, tag number, length, weight, species) associated with the tag can be found in the 2009-2017_FISHSCAPE_fish_tagging file.
Dataset of "Moving hands feel stimuli before stationary hands"
<p>In the flash lag effect (FLE), a moving object is seen to be ahead of a brief flash that is presented at the same spatial location; a haptic analogue of the FLE has also been observed. Some accounts of the FLE relate the effect to temporal delays in the processing of the stationary stimulus as compared to that of the moving stimulus [3–5]. We tested for movement-related processing effects in haptics. People judged the temporal order of two vibrotactile stimuli at the two hands: One hand was stationary, the other hand was executing a fast, medium, or slow hand movement. Stimuli at the moving hand had to be presented around 36 ms later, to be perceived to be simultaneous with stimuli at the stationary hand. In a control condition, where both hands were stationary, perceived simultaneity corresponded to physical simultaneity. We conclude that the processing of haptic stimuli at moving hands is accelerated as compared to stationary ones–in line with assumptions derived from the FLE.</p> <p>The dataset contains individual points of subjective simultaneity and just noticeable differences for each movement condition (stationary, fast , medium, slow) and individual response frequencies as a function of stimulus onset asynchrony (SOA) and movement condition.</p>
UC2017 Static and Dynamic Hand Gestures
<p>We introduce the UC2017 static and dynamic gesture dataset. Most researchers use vision-based systems such as the Microsoft Kinect to acquire and classify hand gesture data. Despite that, we believe that we can achieve more reliable results and allow the use of more complex gestures with wearable systems. There are not many datasets with wearable systems due to the plethora of data gloves in the market and their relative high cost. For these reasons, we opted by creating a new dataset to present and evaluate our gesture recognition framework. The objectives of the dataset are: (1) provide a superset of hand gestures for HRI, (2) have user variability, (3) to be representative of the actual gestures performed in a real-world interaction.</p> <p>We divide the dataset in two types of gestures: SG and DG. SG are described by a single timestep of data, therefore representing a single hand pose and orientation. DGs are variable-length timeseries of poses and orientations with particular meanings. Some of the gestures of the dataset are correlated with a certain meaning in the context of HRI, while others are arbitrary, to enrich the dataset and add complexity to the classification problem.</p> <p>The library is composed of 24 SG classes and 10 DG. The dataset includes SG data from eight subjects with a total of 100 repetitions for each of the 24 classes (2400 samples in total). The DG samples were obtained from six subjects and has cumulatively 131 repetitions of each class (1310 samples in total). All of the subjects are right-handed and performed the gestures with their left hand.</p> <p>We used a data glove (CyberGlove II) and a magnetic tracker (Polhemus Liberty) to capture the hand shape, position and orientation over time. The glove provides digital signals that are proportional to the bending angle of each one of the 22 sensors which are elastically attached to a subset of the hand's joints. In this way we have an approximation of the hand's shape. The tracker's sensor is rigidly attached to the glove on the wrist and measures its position and orientation in respect to a ground-fixed frame. The orientation is the rotation between the fixed frame and the frame of the sensor, given a quaternion (WXYZ). We fuse the sensor data together online since the sensors have slightly different acquisition rates -- 100Hz for the glove and 120Hz for the tracker. The tracker data are under-sampled by gathering only the closest tracker frame in time.</p> <p>The files are in the h5df format. The dimensions are (sample, time, variables).</p>
DeepCytometer pipeline parameter files, Klf14 mouse white adipose tissue histology and hand-traced training contours
<p>Latest description of this data set: <a href="https://github.com/MRC-Harwell/cytometer/blob/main/DATA.md">Data.md at cytometer project</a></p> <pre># Publications related to the data The data associated to the DeepCytometer project (https://github.com/MRC-Harwell/cytometer) is available from Zenodo (doi: 10.5281/zenodo.5137433 and 10.5281/zenodo.5149005). The histology and mouse measures were generated as part of the Small et al. 2018 study: > Small et al. "Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition". Nature Genetics, 50:572–580, 2018. The hand traced data set, colour maps, and automatic segmentations were generated for the Casero et al. 2021 paper: > Casero et al. "Phenotyping of Klf14 mouse white adipose tissue enabled by whole slide segmentation with deep neural networks". bioRxiv, 2021. doi: [10.1101/2021.06.03.444997](https://www.biorxiv.org/content/10.1101/2021.06.03.444997v1.full). # Data protocols ## Histology and laboratory measures To develop and evaluate our methods we used Klf14tm1(KOMP)Vlcg C57BL/6NTac (B6NTac) mice tissue samples and additional data generated as part of the Small et al. 2018 study(Small et al. 2018). It should be noted that the single exon Klf14 gene is imprinted and only expressed from the maternally inherited allele(Parker-Katiraee et al. 2007). This was taken into account by (Small et al. 2018) by crossing a Het parent with a WT parent, so that each offspring inherited a WT allele from the WT parent, and the Klf14 gene knockout or a WT allele from the other parent (from the father, PAT, or the mother, MAT). We also take Klf14 imprinting into account by using as controls the PAT mice and comparing them to the MAT WT and MAT Het (or functional KO, FKO) mice. We used a total of 76 Klf14-B6NTac mice (nfemale=nmale=38), of which 20 mice from the Control and FKO groups were used for training and testing the DeepCytometer pipeline, as well as the hand traced population experiment (summary in Table MICE). The histopathology screen involved fixing, processing and embedding in wax, sectioning and staining with Hematoxylin and Eosin (H&E) both inguinal subcutaneous and gonadal adipose depots. For paraffin-embedded sections, all samples were fixed in 10% neutral buffered formalin (Surgipath) for at least 48 hours at RT and processed using an Excelsior™ AS Tissue Processor (Thermo Scientific). Samples were embedded in molten paraffin wax and 8 μm sections were cut through the respective depots using a Finesse™ ME+ microtome (Thermo Scientific). Sampling was conducted at 2sxns per slide, 3 slides per depot block onto simultaneous charged slides, stained with haematoxylin Gill 3 and eosin (Thermo scientific) and scanned using an NDP NanoZoomer Digital pathology scanner (RS C10730 Series; Hamamatsu). Body weight (BW) and depot weight (DW) were measured with Satorius BAL7000 scales. ## White adipose tissue segmentation For cell area quantification, we applied DeepCytometer v8 to 75 inguinal subcutaneous and 72 gonadal whole histology slides with DeepCytometer (with the Corrected method), including the 20 slides sampled for the hand-traced data set, corresponding to 73 females and 74 males, to produce 2,560,067 subcutaneous and 2,467,686 gonadal cells (on average, 34,134 and 34,273 cells per slide, respectively). Full segmentation of all whole slides was performed with script [klf14_b6ntac_exp_0106_full_slide_pipeline_v8.py](https://github.com/MRC-Harwell/cytometer/blob/39358ed1d79df07d1d522b98728c7efd745513f7/scripts/klf14_b6ntac_exp_0106_full_slide_pipeline_v8.py). In this case, the segmentation contours were grouped by tiles in the output AIDA annotation `.json` file (one contour per cell, one file per slide). Non-white adipocyte contours were filtered out, and white adipocyte contours were aggregated into an AIDA annotation `.json` file with a single tile with script [klf14_b6ntac_exp_0106_annotations_postprocessing_v8.py](https://github.com/MRC-Harwell/cytometer/blob/39358ed1d79df07d1d522b98728c7efd745513f7/scripts/klf14_b6ntac_exp_0106_annotations_postprocessing_v8.py) (one contour per cell, one file per slide). # List of directories and files ## Casero et al. (2021) "DeepCytometer pipeline parameter files, Klf14 mouse white adipose tissue histology and hand-traced training contours" (doi: 10.5281/zenodo.5137433) ### `deepcytometer_pipeline_v8.zip` (60.6 MB) Weights, colourmaps, etc. necessary to run the pipeline (v8, with mode colour correction). This is the version of the pipeline described in the paper. There are 10 weight files per convolutional neural network (CNN), corresponding to 10-fold cross-validation * `klf14_b6ntac_exp_0086_cnn_dmap_model_fold_[0..9].h5`: Keras weights for the **EDT CNN** (Histology to Euclidean Distance Transform regression) * `klf14_b6ntac_exp_0089_cnn_segmentation_correction_overlapping_scaled_contours_model_fold_[0..9].h5`: Keras weights for the **Correction CNN** (Segmentation Correction regression) * `klf14_b6ntac_exp_0091_cnn_contour_after_dmap_model_fold_[0..9].h5`: Keras weights for the **Contour CNN** (EDT to Contour detection) * `klf14_b6ntac_exp_0095_cnn_tissue_classifier_fcn_model_fold_[0..9].h5`: Keras weights for the **Tissue CNN** (Pixel-wise tissue classifier) * `klf14_b6ntac_exp_0094_generate_extra_training_images.pickle`: training dataset description * **'file_list'**: list of SVG files with hand-traced contours for network training. Each SVG file has a corresponding TIFF file with the histology used for segmentation * **'idx_test'**: 10 lists with file indices for testing in 10-fold cross-validation * **'idx_train'**: 10 lists with file indices for training in 10-fold cross-validation * **'fold_seed'**: seed number used for the random number generator to assign file indices to folds * `klf14_b6ntac_exp_0098_filename_area2quantile.npz`: quantile colour maps calculated in `klf14_b6ntac_exp_0098_full_slide_size_analysis_v7.py` using the whole Klf14 data set with v7 of the pipeline, and used in earlier experiments, including some where v8 of the pipeline was used for segmentation. * `klf14_b6ntac_exp_0106_filename_area2quantile_v8.npz`: quantile colour maps calculated in `klf14_b6ntac_exp_0106_full_slide_pipeline_v8.py` using the whole Klf14 data set with v8 of the pipeline, and used in later experiments. * `klf14_training_colour_histogram.npz`: statistics from Klf14 histology images to be used in colour correction * **'xbins_edge'**, **'xbins'**: edges and centres of the bins used for histogram calculations * **'hist_r_q1'**, **'hist_r_q2'**, **'hist_r_q3'** * **'hist_g_q1'**, **'hist_g_q2'**, **'hist_g_q3'** * **'hist_b_q1'**, **'hist_b_q2'**, **'hist_b_q3'**: density quartiles (Q1, Q2, Q3) for RGB channels for each bin the histogram * **'mode_r'**, **'mode_g'**, **'mode_b'**: modes for RGB channels (this corresponds to the most typical background colour in the histology images) * **'mean_l'**, **'mean_a'**, **'mean_b'**: mean intensity for L*a*b channels of the image * **'std_l'**, **'std_a'**, **'std_b'**: intensity standard deviations for L*a*b channels of the image * `klf14_exp_0112_training_colour_histogram.npz`: other statistics from Klf14 histology images to be used in colour correction * **'p'**: vector of quantile values used in ECDF calculations * **'val_r_klf14'**, **'val_g_klf14'**, **'val_b_klf14'**: all intensity values for the RGB channels of Klf14 training images that contain at least a white adipocyte * **'f_ecdf_to_val_r_klf14'**, **'f_ecdf_to_val_g_klf14'**, **'f_ecdf_to_val_b_klf14'**: linear interpolation function that maps ECDF quantiles to intensity values in the Klf14 training data set. These functions can be used together with intensity->quantile interpolation functions calculated for a new histology image to perform histogram matching colour correction * **'mean_klf14'**, **'std_klf14'**: mean and standard deviation of the **'val_r_klf14'**, **'val_g_klf14'**, **'val_b_klf14'** vectors There are also weight files for the pipeline trained with all the data, instead of the 10-fold cross-validation partition. These were not used for the paper, but could be useful for future experiments * `klf14_b6ntac_exp_0101_cnn_dmap_model.h5`: Keras weights for the **EDT CNN** (Histology to Euclidean Distance Transform regression) * `klf14_b6ntac_exp_0104_cnn_segmentation_correction_overlapping_scaled_contours_model.h5`: Keras weights for the **Correction CNN** (Segmentation Correction regression) * `klf14_b6ntac_exp_0102_cnn_contour_after_dmap_model.h5`: Keras weights for the **Contour CNN** (EDT to Contour detection) * `klf14_b6ntac_exp_0103_cnn_tissue_classifier_fcn_model.h5`: Keras weights for the **Tissue CNN** (Pixel-wise tissue classifier) ### `histology.7z` (29.1 GB) 165 H&E histology whole slides from Hamamatsu scanner (`.ndpi`). ### `klf14.7z` (2.3 GB) Mice metadata, training/testing data sets for the pipeline, intermediate files created during training, and neural network weights for multiple experiments. * `klf14_b6ntac_meta_info.csv`: Klf14 mice metadata * **Animal Identifier**, **id:** unique ID for each mouse * **ko_parent:** heterozygous parent of origin for the KO allele (father, PAT or mother, MAT) * **sex:** female or male * **genotype:** wild type (KLF14-KO:WT) or heterozygous (KLF14-KO:Het) * **BW:** body weight (g) * **SC:** subcutaneous depot weight (g) * **gWAT:** gonadal depot weight (g) * **Liver:** livel weight (g) * **cull_age:** age at time of culling (days) * **BW_alive:** body weight measured before culling * **BW_alive_date:** age at time of BW_alive measure * **mother:** unique ID for mouse's mother * **mother_genotype:** mouse's mother genotype * `klf14_b6ntac_training`: Directory with hand-traced segmentations of training histology windows. 131 windows sampled from 20 whole slides, plus hand-traced contours that were used for training DeepCytometer and compute population distributions. These segmentations were used for CNN training, but note that there's a cleaned-up version of these data below, and it was the cleaned-up version that was used for the paper experiments * `ndpifile_row_YYYYYY_col_XXXXXX[.tif/.xcf/.svg]`: * **ndpifile:** name of the whole slide file (e.g. `KLF14-B6NTAC 36.1c PAT 98-16 C1 - 2016-02-11 10.45.00`) * **row_YYYYYY:** Y-coordinate of the top-left corner of the sampling window, in pixels * **col_XXXXXX:** X-coordinate of the top-left corner of the sampling window, in pixels * **.tif:** TIFF file with the histology sampling window * **.xcf:** Gimp file with the histology and hand-traced contours (the contours were drawn in Gimp) * **.svg:** SVG (Scalable Vector Graphics) that contains the hand-traced contours in the XCF file * `klf14_b6ntac_training_v2`: Same as `klf14_b6ntac_training`, but the hand-traced data set was cleaned up to remove small contours of dubious cells, or cells that are fully overlapped by others * `klf14_b6ntac_training_non_overlap`: Directory with intermediate images to train the networks. These images are generated by script [`klf14_b6ntac_training_non_overlap`](https://github.com/MRC-Harwell/cytometer/blob/main/scripts/klf14_b6ntac_exp_0077_generate_non_overlap_training_images.py) * `klf14_b6ntac_training_augmented`: Directory with intermediate images used to train the networks (using augmentation to reduce overfitting). These images are generated by script [`klf14_b6ntac_exp_0078_generate_augmented_training_images.py`](https://github.com/MRC-Harwell/cytometer/blob/main/scripts/klf14_b6ntac_exp_0078_generate_augmented_training_images.py) * `klf14_b6ntac_seg`: Deprecated. Directory to store whole slide coarse segmentations in old experiments (e.g. `klf14_b6ntac_exp_0076_generate_training_images.py`). Of little interest for most users * `klf14_b6ntac_results`: Deprecated. Directory to store miscellanea output from some experiments. Of little interest for most users ## Casero et al. (2021). "Klf14 mouse white adipose tissue histology DeepZoom files and AIDA annotations for visualisation of DeepCytometer white adipocyte segmentations" (doi: 10.5281/zenodo.5149005) ### `aida_data_Klf14_v8_images.7z` (16.9 GB) Histology images converted to DeepZoom so that they can be visualised with [AIDA](https://github.com/alanaberdeen/AIDA). To use this, decompress this file and put the resulting `images` directory in your `AIDA/dist/data/` directory. ### `aida_data_Klf14_v8_annotations.7z` (18 GB) White adipocyte segmentations in AIDA annotation `.json` files (one contour per cell, one file per whole slide). Each slide has the following files: * `SLIDENAME.json`: Soft link to the annotations file that we want to associate to slide `SLIDENAME.ndpi`, e.g. `SLIDENAME` = `KLF14-B6NTAC-PAT-39.2d 454-16 B1 - 2016-03-17 12.16.06` * `SLIDENAME.lock`: Empty file used to tell the pipeline that `SLIDENAME.ndpi` has already been processed or is being currently processed * `SLIDENAME_coarse_mask.npz`: File with the coarse tissue segmentation of `SLIDENAME.ndpi` and the internal state of the pipeline (execution times, steps, etc) * `SLIDENAME_exp_0106_auto.json`: Annotations (all segmentations without filtering from the Auto algorithm, i.e. segmentation without object overlap). Contours are grouped by the tile they were processed in * `SLIDENAME_exp_0106_auto_aggregated.json`: Filtered annotations (non-white adipocytes removed) of the Auto algorithm. All contours aggregated into a single tile * `SLIDENAME_exp_0106_corrected.json`: Annotations (all segmentations without filtering from the Corrected algorithm, i.e. segmentation with object overlap). Contours are grouped by the tile they were processed in * `SLIDENAME_exp_0106_corrected_aggregated.json`: Filtered annotations (non-white adipocytes removed) of the Corrected algorithm. All contours aggregated into a single tile To use this, decompress this file and put the resulting `annotations` directory in your `AIDA/dist/data/` directory. </pre>
Surface electromyogram (sEMG) dataset recorded from forearm for 9 hand movements and three electrode array positions
<p>This repository contains raw surface Electromyography signals termed surface Electromyograms (<a href="https://en.wikipedia.org/wiki/Electromyography">sEMG</a>) recorded with 8 circular surface Ag/AgCl pairs of electrodes placed circumferentially around the forearm of the dominant arm in 10 able-bodied individuals (5 Females and 5 Males). The proposed method for processing sEMG data with subjects' characteristics and protocol can be found in <a href="https://doi.org/10.1016/j.bspc.2020.102292">Miljković & Isaković 2021</a>.</p> <p>For each subject, sEMG was recorded from <strong>three recording electrode array positions</strong> termed P1, P2, and P3 for 9 hand movements. We provide a compressed .7z folder with 10 sub-folders for each subject named by <strong>subject ID</strong> (ID1, ID2, ... ID10). Each sub-folder contains 27 .txt data files (for 9 movements × 3 electrode array positions), except for subject ID7 (there are 24 .txt records, since three records for wrist extension EX in P1, P2, and P3 positions got corrupted in subject ID7). Average size of 10 sub-folders is 167.50 ± 27.02 MB with maximum of 194 MB and minimum of 117 MB.</p> <p>The subjects performed following hand movements from the reference resting position –relaxation, R (explained in-detail in <a href="https://doi.org/10.1016/j.bspc.2020.102292">Miljković & Isaković 2021</a>): (1) spherical power grasp, PS, (2) three finger sphere grasp, 3F, (3) two finger prismatic grasp, PP, (4) wrist flexion, FL, (5) wrist extension, EX, (6) radial deviation, RD, (7) ulnar deviation, UD, and then forearm rotation i.e. (8) pronation, PR, and (9) supination, SU. PS, 3F, PP, FL, EX, RD, UD, PR, and SU correspond to <strong>type of hand movement</strong> in naming convention for .txt data files.</p> <p><a href="https://www.youtube.com/playlist?list=PLI3SYeiSufnBo6UDAZt9NJO9ecb-InJqb">Hand movements YoutTube playlist</a> contains explanatory videos for 9 hand movements recorded in this study, and we also provide corresponding .wmv here in the "movies hand movements.7z". Naming convention for .wmv files is <strong>type of hand movement</strong> with both full name and abbreviation for the movement (for example "radialDeviation-RD.wmv").</p> <p>Naming convention for .txt data files within 10 sub-folders is: <strong>subjects ID _ type of hand movement _ recording electrode array position</strong> (for example: "ID1_3F_P1.txt" in sub-folder ID1, "ID9_RD_P3.txt" in sub-folder ID9).</p> <p><strong>Dataset contents</strong></p> <ol> <li><a href="https://zenodo.org/record/4039550/files/EMG%20dataset.7z?download=1">EMG dataset.7z</a>, 267 .txt data files, text format</li> <li><a href="https://zenodo.org/record/4039550/files/movies%20hand%20movements.7z?download=1">movies hand movements.7z</a>, 9 .wmv files, explanatory hand movement videos (also available on <a href="https://www.youtube.com/playlist?list=PLI3SYeiSufnBo6UDAZt9NJO9ecb-InJqb">YouTube</a>)</li> <li><a href="https://zenodo.org/record/4039550/files/README.txt?download=1">README.txt</a>, metadata for data files, text format</li> </ol> <p><strong>Data files contain numerical values with decimal point* according to the following structure</strong></p> <ol> <li>column - CH1** (recorded samples from channel 1)</li> <li>column - CH2** (recorded samples from channel 2)</li> <li>column - CH3** (recorded samples from channel 3)</li> <li>column - CH4** (recorded samples from channel 4)</li> <li>column - CH5** (recorded samples from channel 5)</li> <li>column - CH6** (recorded samples from channel 6)</li> <li>column - CH7** (recorded samples from channel 7)</li> <li>column - CH8** (recorded samples from channel 8)</li> </ol> <p>* For subjects ID1 and ID2 three decimal places are provided, while for other subjects 6 decimal places in .txt data files are provided.</p> <p>** Each data file contains at least 10 repetitions of the corresponding movement. In cases where file contains >10 repetitions (overall 162 .txt data files), we used the first or the last ten for the analysis (except for two files where short and strong artifact appeared during the measurement procedure, and corresponding movement repetitions were discarded) presented in <a href="https://doi.org/10.1016/j.bspc.2020.102292">Miljković & Isaković 2021</a>.</p> <p>Sample rate was set at 1000 Hz and <a href="https://en.wikipedia.org/wiki/Analog-to-digital_converter">A/D card</a> had 16 bits resolution. Gain of the amplifier was set at 1000. For more in-detail explanations of electrode array assemble and positioning for sEMG channels CH1, CH2, ... CH8, please refer to <a href="https://doi.org/10.1016/j.bspc.2020.102292">Miljković & Isaković 2021</a>.</p> <p>If you find these signals useful for your own research or teaching class, please cite both relevant preprint and dataset as:</p> <ol> <li> <p>Miljković, N. and Isaković, M.S., 2021. Effect of the sEMG electrode (re) placement and feature set size on the hand movement recognition. <em>Biomedical signal processing and control</em>, 64:102292. <em><a href="https://doi.org/10.1016/j.bspc.2020.102292">10.1016/j.bspc.2020.102292</a></em></p> </li> <li> <p>Miljković, N. and Isaković, M.S., 2020. Surface electromyogram (sEMG) dataset recorded from forearm for 9 hand movements and three electrode array positions. [Data set]. <em>Zenodo</em> <em><a href="https://zenodo.org/record/4039550">10.5281/zenodo.4039550</a></em>.</p> </li> </ol> <p><strong>ACKNOWLEDGEMENTS</strong> (from <a href="https://doi.org/10.1016/j.bspc.2020.102292">Miljković & Isaković 2021</a>): "Special appreciation the authors owe to Professor Mirjana B. Popović from the University of Belgrade for her kind support,precious guidance, and advice regarding this research which significantly improved the manuscript. Also, the authors would like to thank Dr Matija Štrbac from Tecnalia Serbia Ltd. for providing advice throughout the study.The authors thank all volunteers for their participation."</p>
More precise tracking of horizontal than vertical target motion with both the eyes and hand
<p>Those files contain individual data from a large cohort of participant (N=62). </p> <p>In the excel file (DATAmain), each sheet presents one set of variables (with individual value for each trial).</p> <p>This file contains information regarding eye and hand tracking performance (distance+lags), as well as smooth pursuit gains. </p> <p>The other files contain data that we used for the detailed analysis of saccades and lags, as well as the scripts that can be run with Perl. One script is for analysing the lag (Danion.pl) and the other one for analysing the saccades (saccades.pl). The other files (.txt and .dat) that were used for these analyses. Note that some library is needed (common_subroutines, draw_figure, and for the anova’s routines_that_use_R), meaning that you need to have R installed. </p> <pre>Regarding data acquisition we employed a program called Docometre that can be uploaded at the following address: http://139.124.68.1/buloup/index.php?selectedMenu=DOCoMETRe&lang=_fr When this program is installed, it needs to be run with BaselineTracking.dcm We also provide .BAS and .T91 files that correspond to the compiled version of each pattern Regarding visual stimuli, another program called ICE needs to be installed on a separate computer that receives information (target+cursor) from docometer, it can be uploaded at : https://trello.com/b/EtNCNrZH/icehttps://trello.com/b/EtNCNrZH/ice ICE needs to be run with Visuomotor.ice Visuomotor.icepro Visuomotor.txt and Visuomotor.icemat in the respective folder (icepro in Protocol folder, icemat and ice in Scenario Folder, and txt in Serie folder) Note that both Docometre and ICE need to be run with similar equipement as our (including Adwin Gold systems, Megatron joystick, video screen, graphic cards, and desktop eyelink providing analog signals to docometre). Adequate numbering of analogic channels needs also to be ensured. </pre>
Dataset: Reinforcing Cybersecurity Hands-on Training With Adaptive Learning
<p>This repository contains supplementary materials for the following conference paper:<br> <br> Pavel Seda, Jan Vykopal, Valdemar Švábenský, Pavel Čeleda.<em><br> Reinforcing Cybersecurity Hands-on Training With Adaptive Learning. </em><br> In Proceedings of the 51st IEEE Frontiers in Education Conference (FIE 2021).<br> <a href="https://doi.org/10.1109/FIE49875.2021.9637252">https://doi.org/10.1109/FIE49875.2021.9637252</a><br> <br> Preprint available at: <a href="https://arxiv.org/abs/2201.01574">https://arxiv.org/abs/2201.01574</a></p> <p><strong>How to cite</strong></p> <p>If you use or build upon the materials, please use the BibTeX entry below to cite the original paper (not only this web link).</p> <p>Some of the linked repositories have their separate citation entry; please use that one as well, if possible.</p> <pre><code>@inproceedings{Seda2021reinforcing, author = {Seda, Pavel and Vykopal, Jan and \v{S}v\'{a}bensk\'{y}, Valdemar and \v{C}eleda, Pavel}, title = {{Reinforcing Cybersecurity Hands-on Training With Adaptive Learning}}, booktitle = {Proceedings of the 51st IEEE Frontiers in Education Conference}, series = {FIE '21}, location = {Lincoln, NE, USA}, publisher = {IEEE}, address = {New York, NY, USA}, month = {10}, year = {2021}, pages = {1--9}, numpages = {9}, isbn = {978-1-6654-3851-3}, url = {https://doi.org/10.1109/FIE49875.2021.9637252}, doi = {10.1109/FIE49875.2021.9637252}, }</code></pre> <p> </p>
Acquired data necessary to perform the control algorithm introduced in the scientific paper: "Multilevel control of an anthropomorphic prosthetic hand for grasp and slip prevention" (Advances in Mechanical Engineering, 2016, vol. 8, pp. 1-13)
<p>Acquired data necessary to perform the control algorithm introduced in this paper.</p> <p>a) Figure 6: Calibration data for the three FSRs placed on the prosthetic hand and covered with silicon caps.<br> b) Figure 9: Data for the cost during the learning of two grasping tasks of an egg: bi-digital grasp and tri-digital grasp.<br> c) Figure 10 and Figure 11: Data for the experimental results with the plastic cup and with the highlighter shown in the paper.<br> </p> <p> </p>
CLDF dataset with data and supplements for Barlow "Loss of colexification of 'hand' and 'five' in Austronesian languages"
CLDF dataset with data and supplements for Barlow "Loss of colexification of 'hand' and 'five' in Austronesian languages"
Quantitative Content Analysis Data for Hand Labeling Road Surface Conditions in New York State Department of Transportation Camera Images
<p><strong>Foundational Codebook and Data: </strong></p> <p>Traffic camera images from the New York State Department of Transportation (511ny.org) are used to create a hand-labeled dataset of images classified into to one of six road surface conditions: 1) severe snow, 2) snow, 3) wet, 4) dry, 5) poor visibility, or 6) obstructed. Six labelers (authors Sutter, Wirz, Przybylo, Cains, Radford, and Evans) went through a series of four labeling trials where reliability across all six labelers were assessed using the Krippendorff’s alpha (KA) metric (Krippendorff, 2007). The online tool by Dr. Freelon (Freelon, 2013; Freelon, 2010) was used to calculate reliability metrics after each trial, and the group achieved inter-coder reliability with KA of 0.888 on the 4th trial. This process is known as quantitative content analysis, and three pieces of data used in this process are shared, including: 1) a PDF of the codebook which serves as a set of rules for labeling images, 2) images from each of the four labeling trials, including the use of New York State Mesonet weather observation data (Brotzge et al., 2020), and 3) an Excel spreadsheet including the calculated inter-coder reliability (ICR) metrics and other summaries used to asses reliability after each trial. The data are included in NYSDOT_quantitative_content_analysis.zip.</p> <p>The broader purpose of this work is that the six human labelers, after achieving inter-coder reliability, can then label large sets of images independently, each contributing to the creation of larger labeled dataset used for training supervised machine learning models to predict road surface conditions from camera images. The xCITE lab (xCITE, 2023) is used to store camera images from 511ny.org, and the lab provides computing resources for training machine learning models.</p> <p><strong>Obstructed Class Variation: </strong></p> <p>There are many applications for labeling roadside camera images, and as a variation of the foundational codebook, an addendum codebook provides another version of labeling the obstructed class. Specifically, this variation prioritizes labeling an image as “obstructed” only in extreme circumstances where there is a camera- or image- specific problem that prevents the assessment of any road surfaces. For labelers who want to use this version of the obstructed class (in this document) and also the other five weather-related classes (in the foundational codebook), the guidance is to use both documents in tandem, making sure to use the obstructed rules/definitions in this document while disregarding the obstructed rules/definitions in the foundational codebook. Alternatively, this codebook may be used alone in applications where the goal is to solely classify obstructed vs not obstructed. To ensure reliability and quality of this variation, quantitative content analysis was conducted on this addendum codebook, just as it was for the foundational codebook. Two labelers were tested with a sample of 30 images and achieved inter-coder reliability with Krippendorff's Alpha of 0.934 after one trial. The data, including the addendum codebook and labeling trial data (images and results) are included in ObstructedVariation_quantitative_content_analysis.zip.</p> <p>This material is based upon work supported by the U.S. National Science Foundation under Grant No. RISE-2019758.</p>
HandCT: hands-on computational dataset for X-Ray Computed Tomography
<p>HandCT is a computational dataset to train machine-learning models for X-Ray Computed Tomography (CT). It consists of a meshed hand model, of which pose and anatomical properties are computed at run-time from a script. As such, it is an accurate modeling of anatomical phantoms of only 1.35 mB, and reproducibility is ensured using random seeds. It allows the user to have full control over the imaging chain, from projection to reconstruction, and over the X-Ray interaction with the different parts of the model by a simple variable editing. This open-source solution relies on the freeware Blender for the modelling and Python for the computations. The first deals with modelling, rigging and deformations, whilst the later ensures transformations such as scaling, translation, or else forward projection. This dataset can be used to train and evaluate regularisation procedures for low-energy, dual-energy and scarce-view CT.</p>
video_rotating_blowpipe_left-hand
This is the process of making a carafe Bontemps. The step depicted is called "Annealing"(from the Mingei project).
MC-hands-1M: A glove-wearing hand dataset for pose estimation
<p>We introduce MC-hands-1M, a synthetic glove-wearing hand dataset for pose estimation. In the zip folder, there exist two subfolders: one containing roughly 750K images (Big set) and another with 250K images (Small set) along with the 2D camera plane and 3D world ground truth data of the corresponding poses. Each set is organized in folders named as Rendered View X, representing a specific camera in the 3D space with a fixed rotation and location. In each of those folders, there exist a json file containing corresponding data for the camera (location, rotation, intrinsics' matrix and images' relative paths) along with the aforementioned ground truth per image (pose). For each of those views, there exist other subfolders named as Scene 's Collection 's Objects' States' Combination Y. Each of those folders contains images of the different poses from the set camera view, given a different combination of background, lighting, glove- and cloth-like materials, and hand's a priori scaling state.</p><p>!!!!! IMPORTANT NOTE !!!!!</p><p>After some testing, an error in the ground truth of the small set of images was found. Please use only the big set found in the zip. For further instructions and questions, please contact us at prod@iti.gr.</p>
Data to Three-Dimensional Binocular Eye-Hand Coordination in Normal Vision and with Simulated Visual Impairment
<p>This record contains experimental and analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p> <p>Maiello, G., Kwon, M. & Bex, P.J. (2018) Three-dimensional binocular eye--hand coordination in normal vision and with simulated visual impairment. <em>Experimental Brain Research</em>. https://doi.org/10.1007/s00221-017-5160-8</p>
Leap Motion Hand Gestures for Interaction with 3D Virtual Music Instruments (LMHGIf3DVMI)
<p>The aim of the dataset is to investigate machine learning real-time gesture recognizer captured with a Leap Motion sensor to control the performance of a virtual 3D musical instrument. The dataset includes from 10-15 samples for each of the 8 gesture classes collected from 10 participants (5 female and 5 male) using the Leap Motion sensor.</p> <p> </p>
UC2018 DualMyo Hand Gesture Dataset
<p>This is set of data obtained from two consumer-market EMG sensors (Myo) with a subject performs 8 distinct hand gestures.</p> <p>There are a total of 110 repetitions of each class of gesture obtained across 5 recording sessions.</p> <p>Besides the data set, which is saved in a python pickle file, we include a python test script to load the data, generate random synthetic sequences of gestures and classify them with multiple models.</p> <p><strong>Gesture library:</strong></p> <ol> <li>Rest</li> <li>Closed fist</li> <li>Open hand</li> <li>Wave in</li> <li>Wave out</li> <li>Double-tap</li> <li>Hand down</li> <li>Hand up</li> </ol> <p><strong>Device placement:</strong></p> <ol> <li>The two Myos are placed on the forearm with the usb port pointing outwards, palm and sensor 5 facing upwards.</li> <li>The Myos are next to one another with their middle position close the the thickest section of the forearm.</li> <li>The outwards Myo is rotated slightly so that sensor 5 is aligned with the axis of the palmaris longus tendon.</li> <li>The Myo inside is rotated so that it has an angle of 22.5 degrees with the first Myo, in clockwise direction (subject perspective).</li> </ol> <p><strong>Acquisition protocol:</strong></p> <p>The subjects wear the armbands according to the instructions above. The sensors are run for a few minutes to warm-up.</p> <p>The subjects are requested to hold the positions of the gestures for a few seconds while we record 2 seconds of data. The gestures are repeated in random order in several sessions.</p>
Hand gesture dataset based on sEMG data captured from the Technaid human-robot interaction system
<p>Two files with a dataset of five different/independent hand gestures are provided. The data were generated in a sEMG system with two bracelets (eight sEMG sensors and six sEMG sensors) worn in the right forearm of a human. The Technaid human-robot interaction system was used to captured the data. The file "datasetForSegmentation.mat" was used to train a classifier whose purpose is the execution of Segmentation process. On the other hand, the file "datasetForRecognition.mat" was used to train a classifier whose purpose is the execution of gesture Recognition process.</p> <p> </p>
Herbarium specimen image of Aletris pauciflora (Klotzsch) Hand.-Mazz., part of the collection of Botanic Garden and Botanical Museum Berlin
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Herbarium specimen image of Rhododendron roxieanum var. cucullatum (Hand.-Mazz.) D.F.Chamb., part of the collection of Royal Botanic Garden Edinburgh
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
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.