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Figure 4 in Use of open-source object detection algorithms to detect Palmer amaranth (Amoronthus polmeri) in soybean
Figure 4. Mean average precision (mAP) results of each model after training. YOLOv5 was considered the best-performing algorithm of each tested model with a mAP of 0.77.
Figure 6. Precision–recall curve for YOLOv5. Amoronthus polmeri achieved a in Use of open-source object detection algorithms to detect Palmer amaranth (Amoronthus polmeri) in soybean
Figure 6. Precision–recall curve for YOLOv5. Amoronthus polmeri achieved a slightly higher average precision (AP) (0.788) than soybean. Solid blue line represents mean average precision (mAP) computed on the test data set. The AP for each class and the mAP for the overall algorithm were representative of the area of the graph under each respective curve.
Figure 5 in Use of open-source object detection algorithms to detect Palmer amaranth (Amoronthus polmeri) in soybean
Figure 5. Change in mean average precision (mAP) @ 0.5 over each epoch during training. mAP was reported after the completion of each epoch. Training was terminated after visual inspection of curve and when mAP @ 0.5 curve was seen to "plateau."
A small body open-source dataset for image processing algorithms
<p>Crater-analog dataset acquired with a drone setup at the RIC-DFKI center. The dataset can be used to bridge the domain gap for image processing applications for lunar and small-body missions. </p>
CVEfixes Dataset: Automatically Collected Vulnerabilities and Their Fixes from Open-Source Software
<p><em>CVEfixes</em> is a comprehensive vulnerability dataset that is automatically collected and curated from Common Vulnerabilities and Exposures (CVE) records in the public <a href="https://nvd.nist.gov/">U.S. National Vulnerability Database (NVD)</a>. The goal is to support data-driven security research based on source code and source code metrics related to fixes for CVEs in the NVD by providing detailed information at different interlinked levels of abstraction, such as the commit-, file-, and method level, as well as the repository- and CVE level.</p> <p>This release, v1.0.8, covers all published CVEs up to 23 July 2024. All open-source projects that were reported in CVE records in the NVD in this time frame _and_ had publicly available git repositories were fetched and considered for the construction of this vulnerability dataset. The dataset is organized as a relational database and covers 12107 vulnerability fixing commits in 4249 open source projects for a total of 11873 CVEs in 272 different Common Weakness Enumeration (CWE) types. The dataset includes the source code before and after changing 51342 files and 138974 functions. The collection took 48 hours with 4 workers (AMD EPYC Genoa-X 9684X).</p> <p>This repository includes the SQL dump of the dataset, as well as the JSON for the CVEs and XML of the CWEs at the time of collection. The complete process has been documented in the paper <em>"CVEfixes: Automated Collection of Vulnerabilities and Their Fixes from Open-Source Software"</em>, which is published in the Proceedings of the 17th International Conference on Predictive Models and Data Analytics in Software Engineering (PROMISE '21). You will find a copy of the paper in the Doc folder. </p> <p><em><strong>Citation and Zenodo links</strong></em></p> <p>Please cite this work by referring to the published paper:</p> <ul> <li>Guru Bhandari, Amara Naseer, and Leon Moonen. 2021. CVEfixes: Automated Collection of Vulnerabilities and Their Fixes from Open-Source Software. In Proceedings of the 17th International Conference on Predictive Models and Data Analytics in Software Engineering (PROMISE '21). ACM, 10 pages. <a href="https://doi.org/10.1145/3475960.3475985">https://doi.org/10.1145/3475960.3475985</a></li> </ul> <pre><code>@inproceedings{bhandari2021:cvefixes, title = {{CVEfixes: Automated Collection of Vulnerabilities and Their Fixes from Open-Source Software}}, booktitle = {{Proceedings of the 17th International Conference on Predictive Models and Data Analytics in Software Engineering (PROMISE '21)}}, author = {Bhandari, Guru and Naseer, Amara and Moonen, Leon}, year = {2021}, pages = {10}, publisher = {{ACM}}, doi = {10.1145/3475960.3475985}, copyright = {Open Access}, isbn = {978-1-4503-8680-7}, language = {en} }</code></pre> <p>The dataset has been released on Zenodo with DOI:<a href="https://doi.org/10.5281/zenodo.4476563">10.5281/zenodo.4476563</a>. The GitHub repository containing the code to automatically collect the dataset can be found at <a href="https://github.com/secureIT-project/CVEfixes">https://github.com/secureIT-project/CVEfixes</a>, released with DOI:<a href="https://doi.org/10.5281/zenodo.5111494">10.5281/zenodo.5111494</a>.</p>
Open-Source Shared Memory implementation of the HPCG benchmark: analysis, improvements and evaluation on Cavium ThunderX2
<p>This archive contains the output files used to gerenate tables and plots in the paper "Open-Source Shared Memory implementation of the HPCG benchmark: analysis, improvements and evaluation on Cavium ThunderX2" submitted to the 9th IEEE International Workshop on "Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems" (PMBS18) held as part of ACM/IEEE Supercomputing 2018 (SC18), Dallas, TX, USA.</p>
Ecosystem-Level Determinants of Sustained Activity in Open-Source Projects: A Case Study of the PyPI Ecosystem
<pre><em>Replication pack, FSE2018 submission #164: </em><em>------------------------------------------ </em></pre> <pre><strong>**</strong>Working title:<strong>** </strong>Ecosystem-Level Factors Affecting the Survival of Open-Source Projects: A Case Study of the PyPI Ecosystem <strong>**</strong>Note:<strong>** </strong>link to data artifacts is already included in the paper. Link to the code will be included in the Camera Ready version as well. <em>Content description </em><em>=================== </em> <strong>- **</strong>ghd-0.1.0.zip<strong>** </strong>- the code archive. This code produces the dataset files described below <strong>- **</strong>settings.py<strong>** </strong>- settings template for the code archive. <strong>- **</strong>dataset_minimal_Jan_2018.zip<strong>** </strong>- the minimally sufficient version of the dataset. This dataset only includes stats aggregated by the ecosystem (PyPI) <strong>- **</strong>dataset_full_Jan_2018.tgz<strong>** </strong>- full version of the dataset, including project-level statistics. It is ~34Gb unpacked. This dataset still doesn't include PyPI packages themselves, which take around 2TB. <strong>- **</strong>build_model.r, helpers.r<strong>** </strong>- R files to process the survival data (`survival_data.csv` in <strong>**</strong>dataset_minimal_Jan_2018.zip<strong>**</strong>, `common.cache/survival_data.pypi_2008_2017-12_6.csv` in <strong>**</strong>dataset_full_Jan_2018.tgz<strong>**</strong>) <strong>- **</strong>Interview protocol.pdf<strong>** </strong>- approximate protocol used for semistructured interviews. <strong>- </strong>LICENSE - text of GPL v3, under which this dataset is published <strong>- </strong>INSTALL.md - replication guide (~2 pages)</pre> <pre><em>Replication guide </em><em>================= </em> <em>Step 0 - prerequisites </em><em>---------------------- </em> <strong>- </strong>Unix-compatible OS (Linux or OS X) <strong>- </strong>Python interpreter (2.7 was used; Python 3 compatibility is highly likely) <strong>- </strong>R 3.4 or higher (3.4.4 was used, 3.2 is known to be incompatible) Depending on detalization level (see Step 2 for more details): <strong>- </strong>up to 2Tb of disk space (see Step 2 detalization levels) <strong>- </strong>at least 16Gb of RAM (64 preferable) <strong>- </strong>few hours to few month of processing time <em>Step 1 - software </em><em>---------------- </em> <strong>- </strong>unpack <strong>**</strong>ghd-0.1.0.zip<strong>**</strong>, or clone from gitlab: git clone https://gitlab.com/user2589/ghd.git git checkout 0.1.0 `cd` into the extracted folder. All commands below assume it as a current directory. <strong>- </strong>copy `settings.py` into the extracted folder. Edit the file: <strong> * </strong>set `DATASET_PATH` to some newly created folder path <strong> * </strong>add at least one GitHub API token to `SCRAPER_GITHUB_API_TOKENS` <strong>- </strong>install docker. For Ubuntu Linux, the command is `sudo apt-get install docker-compose` <strong>- </strong>install libarchive and headers: `sudo apt-get install libarchive-dev` <strong>- </strong>(optional) to replicate on NPM, install yajl: `sudo apt-get install yajl-tools` Without this dependency, you might get an error on the next step, but it's safe to ignore. <strong>- </strong>install Python libraries: `pip install --user -r requirements.txt` . <strong>- </strong>disable all APIs except GitHub (Bitbucket and Gitlab support were not yet implemented when this study was in progress): edit `scraper/init.py`, comment out everything except GitHub support in `PROVIDERS`. <em>Step 2 - obtaining the dataset </em><em>----------------------------- </em> The ultimate goal of this step is to get output of the Python function `common.utils.survival_data()` and save it into a CSV file: # copy and paste into a Python console from common import utils survival_data = utils.survival_data('pypi', '2008', smoothing=6) survival_data.to_csv('survival_data.csv') Since full replication will take several months, here are some ways to speedup the process: <em>####Option 2.a, difficulty level: easiest </em> Just use the precomputed data. Step 1 is not necessary under this scenario. <strong>- </strong>extract <strong>**</strong>dataset_minimal_Jan_2018.zip<strong>** </strong><strong>- </strong>get `survival_data.csv`, go to the next step <em>####Option 2.b, difficulty level: easy </em> Use precomputed longitudinal feature values to build the final table. The whole process will take 15..30 minutes. <strong>- </strong>create a folder `<DATASET_PATH>/common.cache`, where `<DATASET_PATH>` is the value of the variable `DATASET_PATH` in `settings.py` <strong>- </strong>extract <strong>**</strong>dataset_minimal_Jan_2018<strong>** </strong>to the newly created folder <strong>- </strong>rename files: mv backporting.csv monthly_data.pypi_backporting.csv mv cc_degree.csv monthly_data.pypi_cc_degree.csv mv commercial.csv monthly_data.pypi_commercial.csv mv commits.csv monthly_data.pypi_commits.csv mv contributors.csv monthly_data.pypi_contributors.csv mv dc_katz.csv monthly_data.pypi_dc_katz.csv mv downstreams.csv monthly_data.pypi_downstreams.csv mv d_upstreams.csv monthly_data.pypi_d_upstreams.csv mv github_user_info.csv user_info.pypi.csv mv issues.csv monthly_data.pypi_issues.csv mv non_dev_issues.csv monthly_data.pypi_non_dev_issues.csv mv non_dev_submitters.csv monthly_data.pypi_non_dev_submitters mv package_urls.csv package_urls.pypi.csv mv q90.csv monthly_data.pypi_q90.csv # raw_dependencies.csv is not required # raw_packages_info.csv is not required # Feel free to read README.md for more details about the data mv submitters.csv monthly_data.pypi_submitters.csv # In this scenario we'll generate a new survival_data.csv mv university.csv monthly_data.pypi_university.csv mv upstreams.csv monthly_data.pypi_upstreams.csv <strong>- </strong>edit `common/decorators.py`, set `DEFAULT_EXPIRY` to some higher value, e.g. `DEFAULT_EXPIRY = float('inf') # cache never expires` Then, use the Python code above to obtain `survival_data.csv`. <em>####Option 2.c, difficulty level: medium </em> Use pre-downloaded raw data to build longitudinal feature values, and then the dataset. Despite most of the data is cached, some functions will pull up updates which might take anywhere from days to couple weeks to run. <strong>- </strong>Download <strong>**</strong>dataset_full_Jan_2018.tgz<strong>** </strong>(5.4Gb compressed, 34Gb unpacked). <strong>- </strong>edit `common/decorators.py`, set `DEFAULT_EXPIRY` to some higher value, e.g. `DEFAULT_EXPIRY = float('inf') # cache never expires` <strong>- </strong>extract the content of this archive into `<DATASET_PATH>`. <strong>- </strong>clean up `<DATASET_PATH>/common.cache` (otherwise you'll get Step 2.a. You can reproduce Step 2.b by deleting only `survival_data.pypi_2008_2017-12_6.csv`) Run the Python code above to obtain `survival_data.csv`. <em>####Option 2.d, difficulty level: hard </em> Build the dataset from scratch. Although most of the processing is parallelized, it will take at least couple months on a reasonably powerful server (32 cores, 512G of RAM, 2Tb+ of HDD space in our setup). <strong>- </strong>ensure the `<DATASET_PATH>` is empty <strong>- </strong>add more GitHub tokens (borrow from your coworkers) to `settings.py`. Run the Python code above to obtain `survival_data.csv`. <em>Step 3 - run the regression </em><em>--------------------------- </em> install R libraries: install.packages(c("htmlTable", "OIsurv", "survival", "car", "survminer", "ggplot2", "sqldf", "pscl", "texreg", "xtable")) Use `build_model.r` (e.g. in RStudio) and produced `survival_data.csv` to build the regressions used in the paper. This process takes at least 16Gb of RAM and takes few hours to run due to the gigantic size of the dataset. </pre>
Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh
<p>Contains figures used in + the data with scripts to generate figures for the manuscript (in preparation)</p> <p>Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh</p>
Enhancing multi-mode transport emission inventories: combining open-source data with traditional approaches
<p>The primary goal of this dataset is to enhance the spatial and temporal distribution of emissions from civil aviation (NFR1.A.3.a), road transport (NFR1.A.3.b), railways (NFR1.A.3.c), and military aviation (NFR1.A.5), using Portugal as case study. For more information, please refer to the published article “Enhancing multi-mode transport emission inventories: combining open-source data with traditional approaches” (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.uclim.2024.102097" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.uclim.2024.102097</span></span></a>). This dataset contains the following folders and files:</p> <p><strong>1. Spatial_Location</strong></p> <p> 1.1. NFR1_A_3_a.gdb: Geodatabase containing the locations of Portuguese airports and aerodromes.</p> <p> 1.2. NFR1_A_3_b.gdb: Geodatabase containing the locations of Portuguese roads.</p> <p> 1.3 NFR1_A_3_c.gdb: Geodatabase containing non-electrified Portuguese railways and train station locations.</p> <p> 1.4 NFR1_A_5.gdb: Geodatabase containing the locations of Portuguese military airport facilities.</p> <p><strong>2. Temporal_Profiles</strong></p> <p><em> 2.1. Daily</em></p> <p> 2.1.1. Daily_NFR1_A_3_a.csv: This csv file contains the daily movements profiles of civil aviation sites in Portugal.</p> <p><em> 2.2. Hourly</em></p> <p> 2.2.1. Hourly_NFR1_A_3_b.txt: This txt file contains the hourly road traffic volume profiles for the road transport activities in Portugal at different locations (BigAir column).</p> <p> 2.2.2. Hourly_NFR1_A_3_c.txt: This text file contains the hourly railway profile in Portugal, categorized by line and train station.</p> <p><strong>3. Emission_Factors</strong></p> <p> 3.1. EF_NFR1_A_3_a.xlsx: This Excel file contains emission factors for civil aviation activities, categorized by technology, flight phase, fuel, and pollutant. Additionally, it includes information about engines and aircraft.</p> <p> 3.2. EF_NFR1_A_3_b.xlsx: This Excel file contains emission factors for road transport activities, categorized by vehicle type, technology, fuel, abatement, and pollutant. Emission factors for road resuspension are not provided because the papers using this dataset are still under review.</p> <p> 3.3. EF_NFR1_A_3_c.xlsx: This Excel file contains emission factors for railways activities, categorized by technology, fuel, and pollutant.</p> <p> 3.4. EF_NFR1_A_5.xlsx: This Excel file contains emission factors for military aviation activities, categorized by fuel, and pollutant.</p> <p><strong>4. Other_Info</strong></p> <p> 4.1 NFR1_A_3_b: This folder contains information organized by road segments, including fuel consumption (in the “FuelConsumption” folder), hourly meteorology (in the “Meteorology” folder), population data (in the “Population” folder), daily traffic volume (in the “TrafficVolume” folder), vehicle categories (in the “VehicleCategory” folder), and vehicle classes (in the “VehicleClasses” folder). Additionally, it includes the link between road traffic volume measurement points and the Portuguese road network (in the “sensorsVSroads” folder)</p>
5G Campus Network QoS Dataset for Open-Source gNB Implementations
<p>This 5G campus network dataset contains 6 distinct CSV files.<br>Three for each of the testbeds located at either the Norwegian University of Science and Technology(NTNU) or the University of Wuerzburg(WUE).<br>all_Packets: contains all One-Way-Delay measurement packets. Columns: src, Timestamp, SourceIPOuter, DestinationIPOuter, SourceIPInner, DestinationIPInner, PacketSize, SeqNum, iat, trel, gnb, sdr, bw, slots, ratio, pdist, piat, psize, pnpak, rep, scenario, direction<br>Packets_with_IATs: contains all One-Way-Delay measurement packets, with the Interarrival-times already calculated and added as column. Columns: src, Timestamp, SourceIPOuter, DestinationIPOuter, SourceIPInner, DestinationIPInner, PacketSize, SeqNum, iat, trel, gnb, sdr, bw, slots, ratio, pdist, piat, psize, pnpak, rep, scenario, direction<br>all_Throughput: contains all output information from the throughput measurements conducted with iperf3. Columns: mbpsactual_uplink, mbpsactual_downlink, meanjitterms_uplink, meanjitterms_downlink, meanloss_uplink, meanloss_downlink, gnb, sdr, bw, slots, ratio, mbpsoffered_uplink, mbpsoffered_downlink, rep, scenario</p> <p>src: Source Device<br>Timestamp: Timestamp from wireshark<br>SourceIPOuter: Source IP of the outer GTP packet<br>DestinationIPOuter: Destination IP of the outer GTP packet<br>SourceIPInner: Source IP of the inner GTP packet<br>DestinationIPInner: Destination IP of the inner GTP packet<br>PacketSize: Size of the packet<br>SeqNum: Sequence number injected during traffic generation<br>iat: Interarrival-time of the packet<br>trel: relative timestamp<br>gnb: gNB implementation used<br>sdr: SDR used<br>bw: configured bandwidth<br>slots: configured DL slots<br>ratio: configured DL:UL ratio<br>pdist: chosen distribution of the packet generation (deterministic/negative-exponential time between transmission of the generated packets)<br>piat: chosen interarrival -time during packet generation<br>psize: chosen packet size mode<br>pnpak: total amount of packets generated for this measurement run<br>rep: repetition of measurement<br>scenario: measurement scenario<br>direction: direction of traffic</p> <p>mbpsactual_uplink: actual uplink throughput in MBps<br>mbpsactual_downlink: actual downlink throughput in MBps<br>meanjitterms_uplink: actual uplink jitter in ms<br>meanjitterms_downlink: actual downlink jitter in ms<br>meanloss_uplink: mean loss in uplink<br>meanloss_downlink: mean loss in downlink<br>mbpsoffered_uplink: configured uplink throughput in MBps<br>mbpsoffered_downlink: configured downlink throughput in MBps</p> <p>This dataset stems from the Paper "Parameterizing 5G New Radio: A Comparative Measurement Study on Throughput and Delay" </p>
Dataset of the paper "Self-Admitted Technical Debt Practices: A Comparison Between Industry and Open-Source"
<p>This repository contains the dataset of the manuscript "Self-Admitted Technical Debt Practices: A Comparison Between Industry and Open-Source" accepted in the Empirical Software Engineering Journal, edited by Springer</p>
Code & Data from: Development of a low cost open-source ultrasonic device for plant height measurements
<p>We here provide code and data for the study "Development of a low cost open-source ultrasonic device for plant height measurements"</p> <p>Code:<br> - Arduino code (management of the electronic circuit): "Arduino_ultrasonic_sensor.ino"<br> - OpenSCAD code (3D-printing): "3DShells_ultrasonic_sensor.scad"<br> - R code (statistical analysis of field test): "Statistical_analysis.R"</p> <p>Data:<br> - "manual_vs_sensor_controlled.csv": this file contains the comparison between the ultrasonic device and the ruler in standardized laboratory conditions. It has three columns: "manual_value", the height value measured manually; "sensor_value", the height value obtained from the ultrasonic device; "height_range", the interval to which the height value belongs (we worked with 25 cm intervals).<br> - "manual_vs_ruler_field.csv": this file contains the comparison between the ultrasonic device and the ruler in field conditions. Plant height measurements were performed on 26 sorghum genotypes. The file has four columns: "Genotype", the id of the measured genotype; "rep" the replicate (3 plants were measured for each genotype); "manual_value", the height value measured manually; "sensor_value", the height value obtained from the ultrasonic device. When using the ruler, the operator spent 15 min and 23 s to complete all measurements in the field, and 3 min and 27 s to enter all data manually in a digital file. When using the sensor, the operator spent 10 min and 52 s to complete all measurements in the field, and manual transcription was not needed since all measurements are instantaneously saved on an SD card.</p> <p>More details on the experimental data can be found in the article "Development of a low cost open-source ultrasonic device for plant height measurements".</p> <p>We also provide a tutorial to explain how to build the ultrasonic-sensor ("tutorial.docx")</p>
Research Compendium for Harrington et al. (2021): "An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code: I. Design, Tests, and Application to Exoplanet HD 189733 b"
<p>This archive is the Reproducible Research Compendium for<br> <br> An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code: I. Design, Tests, and Application to Exoplanet HD 189733 b<br> <br> by Harrington et al. (2021), published in The Planetary Science Journal.<br> <br> BART is an atmospheric parameter retrieval code. It infers the properties of planetary atmospheres from spectroscopic observations. The compendium includes all the software, documentation, configuration files, plots, and data published in the paper. The compendium is under the Reproducible Research Software License; see LICENSE file. The README provides additional information and describes the contents of each compressed .tar.gz file.</p>
Object-based image analysis for monitoring plant invasions, can we use an open-source solution?
<p><strong>Introduction</strong></p> <p>This is a practical exercise testing possibilities of open-source solutions (FOSS) for object-based image analysis (OBIA) to monitor plant invasion using unoccupied aerial system (UAS, drone).</p> <p>The material is accompanying a chapter <strong><em>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier.</em></strong></p> <p>The material is meant for readers to run the workflow and detect invasion of giant hogweed on the UAS data themselves testing different FOSS solutions.</p> <p> </p> <p><strong>Data</strong></p> <p>• a subset of UAS-borne data (consumer camera) collected in Czech Republic during the flowering of a noxious invasive plant species giant hogweed (<em>Heracleum mantegazzianum</em>)</p> <p>• training dataset</p> <p>• eCognition rulebase (proprietary OBIA software)</p> <p>• a script for SegOptim package implemented in R</p> <p> </p> <p><strong>Description</strong></p> <p>The use case represents a simple application of OBIA approach based on the SegOptim package implemented in R.</p> <p>Four bands (RGBN) UAS image subset are available, capturing the central area of a heavily invaded location (CZ) by giant hogweed (Heracleum mantegazzianum). Thanks to the proper image timing, the invasive species is clearly observable as white objects (in RGB) representing the various stage of the blossom. Considering the complex shape of the flower heads, detection based on image segmentation outperforms pixel-based classification (Müllerová et al., 2017). Simple segmentation of input imagery is performed (for simplicity only the spectral bands are considered both for segmentation and feature space definition, however additional features such as vegetation indices or textural measures may be included), followed by supervised classification using training data. Finally, a visual comparison of result detection both from proprietary (eCognition) and open-source (SegOptim) implementation is provided, confirming comparable results.</p> <p>Based on #github("joaofgoncalves/SegOptim")</p> <p> </p> <p><strong>References</strong></p> <p>Gonçalves, J., Pôças, I., Marcos, B., Mücher, C. A., & Honrado, J. P. (2019). SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data. <em>International Journal of Applied Earth Observation and Geoinformation</em>, <em>76</em>, 218-230.</p> <p>Müllerová, J., Brůna, J., Bartaloš, T., Dvořák, P., Vítková, M. & Pyšek, P. (2017b). Timing Is Important: Unmanned Aircraft vs. Satellite Imagery in Plant Invasion Monitoring. Frontiers in Plant Science 8:1–13.</p> <p>Accompanying material for</p> <p>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier</p>
FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking
<p>This is the software described in our article 'FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking' and the used datasets for image analysis. It is intended as a easy to use software for tracking of cytoskeletal fibers offering both source code and GUI-based executable. Datasets are sorted according to figures in the article with folders containing raw images, analysis results and resulting figure files. The source folder also includes a tutorial and installation notes.</p> <p>For a system running Ubuntu 21.04 there is a slightly modified command line needed: java --module-path /usr/share/openjfx/lib –add-modules=javafx.base,javafx.controls,javafx.fxml,javafx.graphics,javafx.media,javafx.swing,javafx.web -jar GUIFocalAdhesionOnly.jar</p>
Open-source design files for harvesting energy from overhead power line cables
<p>OpenSource_CalculationFile_MEH.xlsx : this is an excel file that provides a calculation tool to select a magnetic core for harvesting energy from powerlines.</p> <p>OpenSource_Schematic_MEH.pdf : this is a schematic file that provides a detailed design of the charging circuit.</p>
Data Supplement: GIRFReco.jl: An Open-Source Pipeline for Spiral Magnetic Resonance Image (MRI) Reconstruction in Julia
<p><strong>Dataset for GIRFReco.jl Paper</strong><br> <br> Please download this and extract to an appropriate location prior to running the demonstration code in GIRFReco.jl. The extracted folder will serve as the root directory in the demo code.</p>
Example sonifications from the Astronify open-source Python package.
<p>The file named "10_galexFlare.wav" is a sonification of a stellar flare observed by the GALEX space telescope. This sonification uses a linear stretch on the pitch range 100-10,000 Hz, with a note duration of 0.8 seconds and 0.04 seconds between notes. The file named "1_kepler12b.wav" is a sonification of a transiting exoplanet observed by the Kepler space telescope. This sonification uses a linear stretch on the pitch range 100-10,000 Hz, with a note duration of 0.5 seconds and 0.01 seconds between notes.</p>
Alert Type Frequency Assessment of Open-Source Static Analysis Tools and Codebases
<p>This includes all data needed to replicate and validate our frequency analysis of static analysis (SA) alerts produced using open-source SA tools on several OSS codebases. It includes instructions how to get and run the SA tools, a Dockerfile to conveniently get and use the SA tools, raw SA tool output, some python scripts to parse that output, parsed SA data and aggregate analyses, and SA data augmented with CERT coding rule and CWE data. </p> <p>The SA tools used:</p> <ul> <li>clang-tidy version 15.07 </li> <li>cppcheck version 2.9 </li> <li>CERT Rosecheckers </li> </ul> <p>The codebases analyzed:</p> <ul> <li>zeek version 5.1.1</li> <li>git version 2.39.0</li> <li>dos2unix version 7.4.3</li> </ul>
Bee Tracker – an open-source machine-learning based video analysis software for the assessment of nesting and foraging performance of cavity-nesting solitary bees
Open the record for dataset details and reuse information.
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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.