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11 results for “Labeled points”
LigPCDS: Labeled Dataset of X-ray Protein Ligand Images in 3D Point Cloud and Validated Deep Learning Models
<p>The difference electron density from X-ray protein crystallography was used to create the first dataset of labeled ligand images in 3D point clouds, named <strong>LigPCDS</strong>. The dataset contain 244,226 entries of free organic ligands containing 3D representations labeled with two major labeling approaches: SP-based and AtomSymbol-based.</p> <p> </p> <p>The data from free organic molecules (non-covalent ligands) was retrieved from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) in december 2019 with resolutions ranging from 1.5 to 2.2 Å. The ligand images (blobs) were interpolated from their calculated difference electron density map in a 3D grid-like bounding box, around their atomic positions, and stored in point clouds. These ligand grid representations were further processed to retrive the final ligands representation in 3D point clouds using a mask of the shape of the ligand. A grid spacing of 0.5 Å gave the best results. The density value of the grid points was used as feature. The labeling approach used the structure of the ligands to propose vocabularies of chemical classes based on the chemical atoms themselves and their cyclic substructures. These structure annotations were applied pointwise to the ligand 3D representations using an atomic sphere model. Four proposed vocabularies were validated by successfully training good performance deep learning models for the semantic segmentation of a stratified dataset from LigPCDS, using 78902 entries.</p> <p>The four validated deep learning models are: (i) the LigandRegion, composed by generic atoms of any type; (ii) the AtomCycle, composed by generic atoms outside cycles and generic cycles; (iii) the AtomC347CA56, composed by generic atoms outside cycles, not aromatic cycles of size 3 to 7 and aromatic cycles of size 5 and 6; and (iv) the AtomSymbolGroups, composed by the atoms symbols with groupings. The mean accuracy of these models in their cross-validation was between 49.7% <span lang="EN-GB">[-19.4,20.</span><span lang="EN-GB">2]</span> and 77.4% <span lang="EN-GB">[-11.7,12.1]</span> in terms of Intersection over Union (mIoU) metric and between 62.4% <span lang="EN-GB">[-18.8,19.</span><span lang="EN-GB">7]</span> and 87.0% <span lang="EN-GB">[-8.4,8.8]</span> in F1-score (mF1), confidence interval between squared brackets. The models i, ii and iii and the used labeled representations in 3D point cloud are contained in the SP-based record; and model iv and its used labeled representations are contained in the AtomSymbol-based record.</p> <p>The dataset and validated models may be used to tackle problems regarding known and unknown ligand building to drug discovery and fragment screening pipelines. </p> <p>The code used to create and validated the LigPCDS is available at the following repository: https://github.com/danielatrivella/np3_ligand</p> <p>This repository also contains the NP³ Blob Label application for ligand building using the validated deep learning models from LigPCDS.</p>
NPM3D dataset with instance labels used in paper "Toward Accurate Instance Segmentation in Large-scale LiDAR Point Clouds"
<p>NPM3D (https://npm3d.fr/paris-carla-3d) consists of mobile laser scanning (MLS) point clouds collected in four different regions in the French cities of Paris and Lille, where each point has been annotated with two labels: one that assigns it to one out of 10 semantic categories and another one that assigns it to an object instance. When inspecting the data, we found 9 cases where multiple tree instances had not been separated correctly (i.e., they had the same ground truth instance label). These cases were manually corrected using the CloudCompare software (https://www.cloudcompare.org), and 35 individual tree instances were obtained. Our variant of the dataset with 10 semantic categories and enhanced instance labels is publicly available.</p>
Labeled points for four land cover classes referring to the year 2019
<p>This dataset provides hand-labeled points for four different land cover classes in coastal areas (sand, seawater, grass, trees).</p> <p>It was created based on photointerpretation of high-resolution imagery in Google Earth Pro and QGIS, referring to the year 2019.</p> <p>This dataset was used for the random forest classification of satellite imagery in the following manuscript: </p> <p>"<em>Satellite image processing for the coarse-scale investigation of sandy coastal areas</em>".</p> <p>If you use any part of this dataset, please cite as follows:</p>
Health Record Hiccups - 5526 real-world time series with change points labelled by crowd-sourced visual inspection
<p>5526 real-world time series with labels for the location of all abrupt changes in level, variability, trend, presence/absence of data points, and irregular outliers. The time series were produced from a range of electronic health record data extracts from a large UK hospital group. Values in each data field were aggregated by day/week/month, and numeric summary values calculated for each timepoint from the (often non-numeric) data by applying simple functions (e.g. number of values present, percentage of missing values, number of distinct values, median value). Labels were produced by visual inspection of time series plots from ~2000 volunteers, via the Health Record Hiccups project on the Zooniverse platform (https://www.zooniverse.org/projects/phuongquan/health-record-hiccups). Volunteers drew a vertical line on the image wherever they saw a change point (green line if they were certain, yellow line if they were unsure). Consensus labels per image were calculated using density based clustering with noise (R v3.6.3, dbscan v1.1-5), and converted back to a date.</p>
UVA laser scanning labelled las data over tropical moist forest classified as leaf or wood points
<p>UAV Laser Scanning data collected over neotropical forest (Paracou French Guiana). Four flights conducted over one ha plot in 2021 and 2022.</p> <p>Leaf wood labels were transferred from contemporaneous (2021) TLS acquisition, for which segmentation was done using LeWoS and onscreen post correction.</p> <p>Predicted values using SOUL model (see ref below) for a single UAV-LS acquisition are provided as separate file.</p> <p> </p>
Dataset: An Open Dataset and Collection Tool for BMS Point Labels
<p>This dataset consists of a set of CSV files each representing a "dump" of point labels from a set of buildings. Most of the files only contain a single column (point labels); several of them also contain other dimensions such as engineering units, Haystack tags and other BACnet object properties.</p>
NPM3D dataset with instance label. Dataset used in paper "A Review of Panoptic Segmentation for Mobile Mapping Point Clouds"
<p>NPM3D is a public benchmark for point cloud semantic segmentation, with 10 classes including: ground, building, pole (road sign and traffic light), bollard, trash can, barrier, pedestrian, car, natural (vegetation) and unclassified. Results are evaluated only w.r.t. 9 classes, disregarding the "unclassified" label. The data has been captured with a mapping-grade mobile laser scanning system in different cities in France. There are 4 regions designated for training, all captured in Paris and Lille; and 3 regions for testing, captured in Dijon and Ajaccio. The standard 10-class version described above has actually been derived from a more fine-grained version of the dataset by keeping only the most frequent labels. The original annotations feature 50 different semantic classes (most of which are very rare), and also individual object instance labels for the training regions. For panoptic segmentation, a new version has been generated that still uses the 10 semantic category labels listed above, but also includes instance labels. The classes ground, building and barrier are considered "stuff" and are not separated into instances. As no instance labels are available for the 3 test regions, our version for panoptic (or pure instance) segmentation only contains 4 different regions from Paris and Lille. Instead of a fixed training/test split all experiments therefore use 4-fold cross-validation.</p>
Graph-based Leaf–Wood Separation Method for Individual Trees Using Terrestrial Lidar Point Clouds: Labeled validation data
<p>Set of 10 manually labeled point clouds used in the performance assessment of "Graph-based Leaf–Wood Separation Method for Individual Trees Using Terrestrial Lidar Point Clouds". This dataset is a collection of single trees scanned from different regions covering tropical, temperate, and boreal species—with heights ranging from 5.4 to 43.7 m, using the Riegl VZ-400 and Leica ScanStation C10 terrestrial laser scanner. These data have been preprocessed. For the original data, see https://doi.org/10.5061/dryad.10hq7;<br> https://doi.org/10.5061/dryad.np5hqbzp6;<br> https://doi.org/10.1594/PANGAEA.942856.</p>
Safety and Efficacy of Apixaban Versus Warfarin in Peritoneal Dialysis Patients With Non Valvular Atrial Fibrillation: a Prospective, Randomised, Open-label, Blinded End-point Trial (APIDP2)
ClinicalTrials.gov study NCT06045858. IPD Sharing: YES. Countries: 0. Publications: 1.
Plot-level semantically labelled terrestrial laser scanning point clouds
<p><strong>Abstract</strong></p> <p>Point clouds from Terrestrial Laser Scanning (TLS) are an increasingly popular source of data for studying plant structure and function. However, unlocking their full potential currently requires extensive manual processing to extract ecologically important information. One key task is the accurate semantic segmentation of different plant material within point clouds, particularly wood and leaves, which is required to understand plant productivity, architecture, competition, space optimisation and physiology, and is a key step in common approaches to individual tree extraction. Existing automated semantic segmentation methods are primarily developed for single ecosystem types, and whilst they show good accuracy for biomass assessment from the trunk and large branches, often perform less well within the crown. In this study, we demonstrate a new framework that uses a deep learning architecture developed from PointNet++ and pointNEXT for processing 3D point clouds to provide a reliable semantic segmentation of wood and leaf in TLS point clouds from the tree base to branch tips, applied to diverse natural European forests. Our model combines meticulously labelled data with voxel-based sampling and a novel gated reflectance integration module embedded throughout the feature extraction layers. We evaluate its performance across an extensive dataset, encompassing diverse ecosystem types and sensor characteristics. Our results show consistent outperformance against the most widely used PointNet++-based approach for leaf/wood segmentation on a high-density TLS dataset collected across diverse mixed forest plots across all major biomes in Europe. We tested our model against others’ open data from China, Eastern Cameroon, Germany and Finland, collected using both time-of-flight and phase-shift sensors, finding consistently strong performance, showcasing the transferability of our model to a wide range of ecosystems and sensors. Our newly developed evaluation metric for assessing performance in the outer parts of the canopy, such as in twigs and small branches, found our model to clearly outperform the most widely used approach.</p> <p><strong>Methods</strong></p> <p>Within each country, we scanned a subset of the 30 m x 30 m FUNDIV plots using a Riegl VZ400i TLS instrument (RIEGL Gmbh, Horn, Austria), scanning at 600MHz and with an angular resolution of 0.04 mrad. All plots were scanned following a 10m grid system with a minimum of 16 upright and 16 tilt scans (following Wilkes et al. 2017), with additional scans to minimise occlusion in dense areas, and on the plot perimeter. To ensure high-quality data with minimal noise, scanning was paused when wind conditions rose above 5 m/s (measured with an anemometer on the ground) or when gusts were visually evident. In order to create our labelled dataset, we used a semi-automated approach informed by existing approaches followed by significant manual cleaning. Vicari et al. (2019) found anisotropy, verticality and linearity to be informative features for leaf-wood separation, so we created these geometric features at spatial scales of approx. 5 cm - 0.5 m (using CloudCompare, 2023). Alongside these, we used reflectance and xyz information for each point and labelled leaf-wood by thresholding these features. We followed this with intensive manual checking and cleaning to ensure high label quality, especially in the smaller branches and twigs. Our dense scanning and labelling strategy means that this dataset is an ideal candidate for training and testing the capabilities of processing algorithms. Our dataset comprises nine 10 m x 10 m blocks of x, y, z coordinates with corresponding reflectance values and labels, all at 1 cm resolution achieved through voxel downsampling. This data was used for training and validation. For comprehensive evaluation, we incorporated additional openly available datasets, which we cropped to reduce size and cleaned to rectify erroneous labels. The original, unmodified versions of these datasets can be accessed as follows:</p> <div> <p>*Mspace Lab (2024) ‘ForestSemantic: A Dataset for Semantic Learning of Forest from Close-Range Sensing’, Geo-spatial Information Science. Zenodo. <a href="https://doi.org/10.5281/zenodo.13285640">https://doi.org/10.5281/zenodo.13285640</a>. Distributed under a Creative Commons Attribution Non Commercial No Derivatives 4.0 International licence.</p> <p>Wang, Di; Takoudjou, Stéphane Momo; Casella, Eric (2021). LeWoS: A universal leaf‐wood classification method to facilitate the 3D modelling of large tropical trees using terrestrial LiDAR [Dataset]. Dryad. <a href="https://doi.org/10.5061/dryad.np5hqbzp6">https://doi.org/10.5061/dryad.np5hqbzp6</a>. Distributed under a Creative Commons 0 1.0 Universal licence.</p> <p>Wan, Peng; Zhang, Wuming; Jin, Shuangna (2021). Plot-level wood-leaf separation for terrestrial laser scanning point clouds [Dataset]. Dryad. <a href="https://doi.org/10.5061/dryad.rfj6q5799">https://doi.org/10.5061/dryad.rfj6q5799</a>. Distributed under a Creative Commons CC0 1.0 Universal licence.</p> <p>Weiser, Hannah; Ulrich, Veit; Winiwarter, Lukas; Esmorís, Alberto M.; Höfle, Bernhard, 2024, "Manually labeled terrestrial laser scanning point clouds of individual trees for leaf-wood separation", <a href="https://doi.org/10.11588/data/UUMEDI">https://doi.org/10.11588/data/UUMEDI</a>, heiDATA, V1, UNF:6:9U7BGTgjjsWd1GduT1qXjA== [fileUNF]. Distributed under a Creative Commons Attribution 4.0 International Deed.</p> </div> <p>*For licensing reasons these data re not included in this repository but can be downladed from the doi provided. </p> <p> </p> <p> </p>
Enhancing Vaccination Uptake Through Points Redemption Based Financial Incentives and Digital Platforms: an Open-label Cluster Randomized Controlled Trial Utilizing Community Mobilization and Empowerm
ClinicalTrials.gov study NCT06890559. IPD Sharing: NO. Countries: 0. Publications: 0.
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
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International Brain Laboratory public data
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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.