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Dataset results
145 results for “Image processing”
Pre-processed (in Detectron2 and YOLO format) planetary images and boulder labels collected during the BOULDERING Marie Skłodowska-Curie Global fellowship
<p>This database contains 4976 planetary images of boulder fields located on Earth, Mars and Moon. The data was collected during the BOULDERING Marie Skłodowska-Curie Global fellowship between October 2021 and 2024. The data was already splitted into train, validation and test datasets, but feel free to re-organize the labels at your convenience. </p> <p>For each image, all of the boulder outlines within the image were carefully mapped in QGIS. More information about the labelling procedure can be found in the following manuscript (<a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2023JE008013">https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2023JE008013</a>). This dataset differs from the previous dataset included along with the manuscript <a href="https://zenodo.org/records/8171052">https://zenodo.org/records/8171052</a>, as it contains more mapped images, especially of boulder populations around young impact structures on the Moon (cold spots). In addition, the boulder outlines were also pre-processed so that it can be ingested directly in YOLOv8.</p> <p>A description of what is what is given in the README.txt file (in addition in how to load the custom datasets in Detectron2 and YOLO). Most of the other files are mostly self-explanatory. Please see previous dataset or manuscript for more information. If you want to have more information about specific lunar and martian planetary images, the IDs of the images are still available in the name of the file. Use this ID to find more information (e.g., M121118602_00875_image.png, ID M121118602 ca be used on https://pilot.wr.usgs.gov/). I will also upload the raw data from which this pre-processed dataset was generated (see <a href="https://zenodo.org/records/14250970">https://zenodo.org/records/14250970</a>).</p> <p>Thanks to this database, you can easily train a Detectron2 Mask R-CNN or YOLO instance segmentation models to automatically detect boulders. </p> <p><strong>How to cite:</strong></p> <p>Please refer to the "how to cite" section of the readme file of <a href="https://github.com/astroNils/YOLOv8-BeyondEarth" target="_blank" rel="noopener">https://github.com/astroNils/YOLOv8-BeyondEarth.</a></p> <p><strong>Structure:</strong></p> <pre><code>. └── boulder2024/ ├── jupyter-notebooks/ │ └── REGISTERING_BOULDER_DATASET_IN_DETECTRON2.ipynb ├── test/ │ └── images/ │ ├── <image_name>_image.png │ ├── ... │ └── labels/ │ ├── <image_name>_image.txt │ ├── ... ├── train/ │ └── images/ │ ├── <image_name>_image.png │ ├── ... │ └── labels/ │ ├── <image_name>_image.txt │ ├── ... ├── validation/ │ └── images/ │ ├── <image_name>_image.png │ ├── ... │ └── labels/ │ ├── <image_name>_image.txt │ ├── ... ├── detectron2_inst_seg_boulder_dataset.json ├── README.txt ├── yolo_inst_seg_boulder_dataset.yaml</code></pre> <p> </p> <pre><code>detectron2_inst_seg_boulder_dataset.json</code></pre> <p>is a json file containing the masks as expected by Detectron2 (see <a href="https://detectron2.readthedocs.io/en/latest/tutorials/datasets.html">https://detectron2.readthedocs.io/en/latest/tutorials/datasets.html</a> for more information on the format). In order to use this custom dataset, you need to register the dataset before using it in the training. There is an example how to do that in the jupyter-notebooks folder. You need to have detectron2, and all of its depedencies installed. </p> <pre><code>yolo_inst_seg_boulder_dataset.yaml</code></pre> <p>can be used as it is, however you need to update the paths in the .yaml file, to the test, train and validation folders. More information about the YOLO format can be found here (<a href="https://docs.ultralytics.com/datasets/segment/">https://docs.ultralytics.com/datasets/segment/</a>).</p>
Videos of the processed microscope images and time series of the petrophysical parameters from image processing and geochemical simulation and of the measured induced polarisation [Video][Dataset]
<p>Supporting Information for the manuscript <em>Microfluidics and spectral induced polarization for direct observation and petrophysical modeling of calcite dissolution</em> published in Geophysical Research Letters</p> <ul> <li><strong>Data Set S1.</strong> Porosity, water saturation, and calcite sample perimeter from image<br>processing.</li> <li><strong>Data Set S2.</strong> Porosity, water conductivity, and pH from geochemical simulation.</li> <li><strong>Data Set S3.</strong> Real and imaginary components of the complex electrical conductivity at<br>2.5 Hz and CEC from petrophysical modeling.</li> <li><strong>Movie S1.</strong> Dissolution of the calcite sample with the detected contour superimposed in<br>white on the grayscale images. Time, length scale, and flow direction are indicated. In<br>case of problems launching the file, we recommend using VLC Media Player software.</li> <li><strong>Movie S2.</strong> Segmented images of the CO2 bubbles produced by the calcite dissolution.<br>Time, length scale, and flow direction are indicated. In case of problems launching the<br>file, we recommend using VLC Media Player software.</li> </ul>
Multiplexed fluorescence imaging based on cycles, raw and processed data.
<p>This dataset was created from a larger acquisition in order to provide an example of reasonnable size, as a companion data set to the F1000Research paper preprint DOIXXX.</p> <ul> <li>The original raw data including metadata files are included in <strong>Microscope_Output.zip.</strong></li> <li><strong>Experiment.json</strong> and<strong> channelnames.txt </strong>are the ones generated by the acquisition software. They are the only files needed when starting from one of the processed data set below.</li> <li>The deconvolution obtained with the commercial software Microvolution is also provided in <strong>bu_deconvolution.zip.</strong> To start from Step 1(Extended Depth of Field) instead of Step 0 (deconvolution), unzip this file in your output directory and rename the folder bu_deconvolution to out.</li> <li>The extended field of view 2D images created from step 0 to step 2, provided for convenince in <strong>edfonly.zip</strong></li> <li>The final files generated by trhe Multiplex processor, including the segmentation mask , are provided in<strong> finaloutput.zip</strong>. These files can be used in a specific analysis software.</li> </ul> <p> </p>
Base images for the article "Optimization of a frosting process for soda lime silicate glass based on phosphoric acid"
<p>Raw dataset of the optimization of a frosting process for soda lime silicate glass based on phosphoric acid.</p> <p><strong>Naming scheme:</strong></p> <ul> <li>Images starting with <strong>HGr</strong> are frosted using the industrial process. These files represent the reference frosting.</li> <li>Images starting with <strong>HG</strong> are frosted manually following the industrial process.</li> <li>In all other images, the solution concentrations within the preliminary bath are noted als follows: <ul> <li><strong>[c<sub>H3PO4</sub>]-[c<sub>NH4HF2</sub>]_[specimen]_[position].jpg</strong></li> <li>For example 10-2_e_1.jpg: This specimen was treated with a preliminary bath with 10 M-% H<sub>3</sub>PO<sub>4 </sub>and 20 g/L NH<sub>4</sub>HF<sub>2</sub>. It originates from the fith specimen (e) and is the first image of this series.</li> </ul> </li> </ul> <p> </p>
Developing Digital Image Processing methods to quantify internal and interfacial convection in the Hele-Shaw cell, with applications to the laboratory ice-ocean boundary layer
<p>This dataset provides the video and image files obtained from Schlieren optical experiment 3 performed in the <span>Laboratoire de Glaciologie (GLACIOL)</span> at the Universite de libre Bruxelles. A document detailing the visual data and supporting figures is presented (DataOverview.pdf). </p>
Dataset for Fisher et al. (2023). Motion stereo at sea: Dense 3D reconstruction from image sequences monitoring conveyor systems on board fishing vessels. IET Image Processing, 17(2), pp.349-361.
<p>This dataset contains the video clips used to produce the results presented in:</p><p>Fisher, M., French, G., Gorpincenko, A., Holah, H., Clayton, L., Skirrow, R. and Mackiewicz, M., 2023. Motion stereo at sea: Dense 3D reconstruction from image sequences monitoring conveyor systems on board fishing vessels. IET Image Processing, 17(2), pp.349-361.</p>
Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process - Datasets
<p>This dataset contains supporting data for a research project aimed at analysing herbarium samples from the New England area at a large scale with deep learning techniques. Details on the methodology are shared in the acompanying paper (to be published).</p> <p>Content:</p> <ul> <li>dataset600k_withAI.csv : A dataset of over 600.000 herbarium samples with its record metadata and a corresponding AI phenological annotations with matching confidence scores. The entirety of the record headers are provided, extracted directly from the NEVP portal. In addition, the AI labels are defined by the following headers. These 8 columns represent 4 binary classifiers with the Presence/Absence of each 4 traits and corresponding confidence (as a percentage - presence/absence percentages sum to 1).<br> <ul> <li> <table> <tbody> <tr> <td>Flowering</td> <td>Not Flowering</td> <td>Budding</td> <td>Not Budding</td> <td>Fruiting</td> <td>Not Fruiting</td> <td>Reproductive</td> <td>Not Reproductive</td> </tr> </tbody> </table> </li> </ul> </li> </ul> <ul> <li>data_species_with_statuses.csv: A processed dataset summarizing flowering period shift at a species level. Two types of headers are provided. <ul> <li>First metadata concerning the flowering shift and the data used to compute that value: <ul> <li> <table> <tbody> <tr> <td>genus</td> <td>genus_species</td> <td>slope</td> <td>nb_specimens</td> <td>p_value_significance</td> <td>trend_category</td> </tr> <tr> <td>Genus of the species</td> <td>Binomial name of the species</td> <td>Regression slope defining the flowering shift as a slope</td> <td>Number of herbarium specimens used to compute the shift</td> <td>P-value significance of the slope being non-zero. ('Non Significant'/'Significant')</td> <td>Summary of the shift as a binary characteristic ('Earlier'/'Later')</td> </tr> </tbody> </table> </li> </ul> </li> <li>Second, metadata summarizing various traits associated to each species: <ul> <li> <table> <tbody> <tr> <td>lifeform_status</td> <td>native_introduced_status</td> <td>wetland_status</td> <td>seasonality_average</td> <td>seasonality_spread</td> </tr> <tr> <td>Growth form from the USDA PLANTS Database. 'Forb_Herb', 'Shrub_Tree' or 'Vine'</td> <td>'Native'/'Introduced' status from the USDA PLANTS Database.</td> <td> <p>National Wetland Plant List (NWPL) Wetland Indicator Status within the Northcentral and Northeast Region</p> <p>'OBL'/'FACW'/'FAC'/'FACU'/'UPL'</p> </td> <td>A characteristic of the flowering season of the species based on the mean Day of Year of the analysed specimens: if <=180: 'Early', else 'Late'</td> <td>A characteristic of the flowering season of the species based on the spread of the flowering season. Less than 28 days: 'Narrow', larger: 'Large'.</td> </tr> </tbody> </table> <p> </p> </li> </ul> </li> </ul> </li> <li>phylogenetic_tree.tre: The raw data used to generate the visualization of the flowering seasonality character and the detected flowering shift foreach species on a phylogenetic tree.</li> <li>phylogenetic_processed_dataset.csv: The processed dataset resuting from the phylogenetic signal analysis. For each trait, an associated significance binary value is provided.</li> </ul>
TUT Acoustic scenes 2017, Evaluation & Development datasets, processed image
<p>Unseparated Pulse Energy Spectrogram</p> <p>Processed audio data.</p> <p>Sound source separation is a <strong>preliminary</strong> for <strong>acoustic scene classification</strong>. It can be argued that rare sound detection can be performed without separation, but in most cases it also depends on it.</p> <p>I have come up with the theory that the full <strong>time-domain</strong>, or if assumptions are made on the amplitude-waveform or the phase-profile, even the <strong>sequence</strong> of events can be <strong>discarded</strong> for acoustic scene classification.</p> <p>For short time frame bins, a <strong>statistical representation</strong> should be enough to correctly identify the scene. Even more so, if deep learning methods are applied.</p> <p>I have also come up with the theory that <strong>energy</strong> scalograms are applied <strong>pulse-length</strong> or waveform/profile-length wise. This can enhance the input representation for machine learning.</p> <p>Furthermore I have used derivatives of the time signal and applied similar signal processing methods to them. For visualisation I have added them to the original scalogram in different colors. The use of <strong>derivatives</strong> is very much <strong>distorted</strong>, if the sound is not separated.</p>
Data processing scripts and images from e-MERLIN project CY6213 used in Ghirlanda et al. 2019, Science
<p>Data processing scripts and images from e-MERLIN project CY6213 used in Ghirlanda et al. 2019, Science</p> <p> </p> <ul> <li>info.txt contains a general description of how the data was processed and the main results.</li> <li>pipeline.tar contains the data pipeline used to process the e-MERLIN observations</li> <li>imaging.py is the script used to produce the final images</li> <li>CY6213_images.tar contain the final images of the target source (not corrected by calibration factor, described in the imaging script).</li> </ul> <p> </p>
Dataset of image processing - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress
<p>The data set contains the analysis data files from the image analysis workflow developed to quantify cortical microtubules rearrangements in the case of tensile stress (<a href="https://github.com/VergerLab/MT_Angle2Ablation_Workflow">https://github.com/VergerLab/MT_Angle2Ablation_Workflow</a>), generated form a specific dataset (https://doi.org/10.5878/17te-jg54). The files include the intermediary images processed at each step of the image analysis workflow in imageJ, the log files produced by the imageJ macro describing the input and the output images and the text files containing the quantified values. </p>
Literature Datasets for the publication "Systematic Review: Prevalence and Practices of Immunofluorescent Cell Image Processing"
<p>This dataset contains the CSV files returned from PubMed searches used to complete a Systematic Review of Image Processing Publication Practices for methods applied to immunofluorescent images of all CNS cells. <br> <br> The file names are organized "date_supplementarytablenumber" followed by the appropriate search terms. </p>
The image processing of Milani: challenges after DART impact
<p>This dataset contain data for the paper The image processing of Milani challenges after DART impact, presented at ESA-GNC Sopot, Poland, June 2023 </p> <p>The .zip folder Dataset is made of 4 subfolders <br> -CoefficientsPCE With the PCEFull9.mat file with all the coefficients of the aPC basis and PCE listed in the paper<br> <br> -TestResults With the ResultsAll.mat file that contains the predicted and true values of phase angle over the test set illustrated in the paper and the MakePlot.m script in Matlab. You can use this data to compare your method directly with the results we have obtained in this work. The script generate a simple histogram plot and compute the mean, std, Q67, and Q95 values. </p> <p> -D1_with_sz_1p00s0ImagesDataset directory within this folder contains all data obtaind during the rendering phase of the 5k samples of Didymos using the polar scale of the Didymos Reference model by ESA (old values before impact).</p> <p> -D1_with_sz_0p78s0 ImagesDataset directory within this folder contains all data obtaind during the rendering phase of the 5k samples of Didymos using the polar scale of the Didymos Reference model by JHUAPL (updated values after impact). This directory also contains the pre-processed input-output pairs for the WCOB, NN, and PCE (X_features, Y) and CELM, and CNN (X_images, Y) methods. </p> <p>You can either decide to use the same pre-processed data we have used for training, validation, and testing or you can work with the raw data (the one from the ImagesDataset folder) to generate your own dataset. </p> <p>Feel free to drop a line vie email in case you need clarification at mattia.pugliatti@polimi.it or pugliatti.mattia@gmail.com</p>
Dataset of processed Sentinel-2 images for chlorophyll-a estimation in high-altitude lakes in the Sierra Nevada, Spain
<p>This dataset contains Sentinel 2 satellite images clipped to 5 high-altitude lakes in the Sierra Nevada Mountain Range, Spain. The images were processed with the following atmospheric correction algorithms:</p><ul><li><a href="https://c2rcc.org/">C2RCC</a> (<a href="https://ui.adsabs.harvard.edu/abs/2016ESASP.740E..54B/abstract">Brockmann et al. 2016</a>)</li><li><a href="https://github.com/MarcYin/SIAC">SIAC</a> (<a href=" https://doi.org/10.5194/gmd-15-7933-2022">Yin et al. 2022)</a></li><li><a href="https://github.com/acolite/acolite/releases/tag/20221114.0">ACOLITE</a> (<a href="https://doi.org/10.1016/j.rse.2018.07.015">Vanhellemont & Ruddick, 2018</a>)</li><li><a href="https://grass.osgeo.org/grass83/manuals/i.atcorr.html">6SV</a> (<a href="https://doi.org/10.1109/36.581987">Vermote et al. 2006</a>)</li></ul><p><strong>Included Lakes and and their IDs:</strong></p><ul><li>Laguna de la Caldera (ID = P-2)</li><li>Laguna-embalse de las Yeguas (ID = D-6)</li><li>Laguna de Río Seco (ID = P-8)</li><li>Laguna Larga (ID = G-7)</li><li>Laguna de la Mosca (ID = G-11)</li></ul>
Dataset and software for processing of hyperspectral images of different CDW materials
<h2>Overview</h2> <p>The provided scripts are designed to process hyperspectral images of construction and demolition waste (CDW) materials, extract relevant features, and train a machine-learning model for material classification. The scripts perform the following tasks:</p> <ol> <li><strong>Feature Extraction</strong>: Extract spectral features from hyperspectral data.</li> <li><strong>Background Removal and Subset Extraction</strong>: Remove backgrounds from images and extract subsets for analysis.</li> <li><strong>Data Visualization</strong>: Generate plots to visualize the extracted features and reflectance curves.</li> <li><strong>Machine Learning Model Training</strong>: Using the extracted features, train and evaluate a multilayer perceptron (MLP) classifier.</li> </ol> <h2>Prerequisites</h2> <p>Before running the scripts, ensure that you have the following:</p> <ul> <li><strong>Python 3.x</strong> installed on your system.</li> <li>Required Python packages: <ul> <li><code>numpy</code></li> <li><code>matplotlib</code></li> <li><code>scipy</code></li> <li><code>pandas</code></li> <li><code>scikit-learn</code></li> <li><code>seaborn</code></li> <li><code>rembg</code> (for background removal)</li> <li><code>Pillow</code> (PIL)</li> </ul> </li> <li><strong>Hyperspectral data files</strong> in <code>.mat</code> format containing calibrated hyperspectral cubes and wavelength information.</li> <li>A directory structure to organize input and output files as described in each script.</li> </ul> <h2>Scripts Description</h2> <h3>1. <code>hyperspectral_features_v2.py</code></h3> <h4><strong>Purpose</strong></h4> <p>This script processes individual hyperspectral image files to extract spectral features from a central subset of the image. It generates RGB images from the hyperspectral data, plots the mean reflectance spectra, and outputs a LaTeX-formatted table containing the extracted features.</p> <h4><strong>Functionality</strong></h4> <ul> <li><strong>Loading Data</strong>: Reads <code>.mat</code> files containing hyperspectral data from a specified input directory.</li> <li><strong>Feature Calculation</strong>: <ul> <li>Calculates mean reflectance within a central window of the image.</li> <li>Extracts spectral features such as peak wavelength and area under the reflectance curve.</li> <li>Records reflectance values at selected wavelengths, including standard RGB channels and additional wavelengths.</li> </ul> </li> <li><strong>RGB Image Generation</strong>: Creates RGB images using specific wavelengths corresponding to the red, green, and blue channels.</li> <li><strong>Spectra Plotting</strong>: Plots the mean reflectance spectra for each sample.</li> <li><strong>LaTeX Table Generation</strong>: Produces a LaTeX-formatted table of the extracted features for inclusion in a report or paper.</li> </ul> <h4><strong>Usage Instructions</strong></h4> <ol> <li> <p><strong>Prepare Input Data</strong>:</p> <ul> <li>Place your <code>.mat</code> files containing the hyperspectral data in the appropriate input directory (e.g., <code>input/mortar</code>).</li> </ul> </li> <li> <p><strong>Run the Script</strong>:</p> <ul> <li>Modify the <code>materials</code> list at the end of the script to include the materials you want to process (e.g., <code>materials = ['mortar']</code>).</li> <li>Execute the script: <div> <div>bash</div> <div> <div> <div> </div> </div> </div> </div> </li> </ul> </li> </ol>
OHS data provided by Competition in Hyperspectral Remote Sensing Image Intelligent Processing Application
<p>Images from Chinese Orbita Hyperspectral Satellites (OHS) provided by <em>the Competition in Hyperspectral Remote Sensing Image Intelligent Processing Application</em> are shared. All the images have been radiometric calibrated and atmospheric corrected by the author.</p> <p>Paper: J. He, J. Li, Q. Yuan, H. Shen, and L. Zhang, "Spectral Response Function-Guided Deep Optimization-Driven Network for Spectral Super-Resolution," <em>IEEE Transactions on Neural Networks and Learning Systems (IEEE TNNLS)</em>, 2021.</p> <p>More information about the author can be found at https://jianghe96.github.io/</p> <p>If this dataset is helpful please cite as:</p> <pre>@article{he2021spectral, title={Spectral Response Function-Guided Deep Optimization-Driven Network for Spectral Super-Resolution}, author={He, Jiang and Li, Jie and Yuan, Qiangqiang and Shen, Huanfeng and Zhang, Liangpei}, journal={IEEE Transactions on Neural Networks and Learning Systems}, year={2021}, }</pre>
How to Build an Image Processing Pipeline for Automating Multiparameter Histocytometry Analysis
<p>Image files for evaluation of an upcoming Current Protocols submission, as well as associated reference files.</p>
Comprehensive Automatic Processing and Analysis of Adaptive Optics Flood Illumination Retinal Images
<p>A collaborative research group has established this database to support AO-FIO image utilization and evaluation of photoreceptor detection. <br> Please cite the following publication when using the database:</p> <p>Eva Valterova, Jan D. Unterlauft, Mike Francke, Toralf Kirsten, Radim Kolar, and Franziska G. Rauscher, "Comprehensive automatic processing and analysis of adaptive optics flood illumination retinal images on healthy subjects," Biomed. Opt. Express <strong>14</strong>, 945-970 (2023)<br> <br> The database can be utilized in connection with our application MATADOR for AO-FIO image registration and analysis, which is freely available on:</p> <p>https://github.com/evavalterova/MATADOR.git</p> <p>The database includes</p> <ul> <li>over 200 flood illumination adaptive optics images of 10 normal healthy subjects. Each folder includes 10 images of the right eye (denoted by OD) and 10 images of the left eye (denoted by OS) with their preliminary determined retinal position during image acquisition.</li> <li>foveal and peripheral patches. Each consists of 40 cropped regions from the set of 200 images. In each cropped region are manually labeled positions of photoreceptors by three evaluators.</li> <li>axial lengths of 10 subjects in ".xlsx" file<br> </li> </ul>
Raw images and processed datasets related to the journal article Robust Assessment of Post-Localisation Hardening Behaviour in Eurofer97 using Inverse Finite Element Methods
Open the record for dataset details and reuse information.
Precalculated results for "An image processing pipeline for electron cryo-tomography in RELION-5"
<p>RELION workspace containing the results presented in the article "An image processing pipeline for electron cryo-tomography in RELION-5"</p>
ImageJ-processed Images from the BBBC022 dataset
<p>Processed microscopy images from the Cell Painting dataset BBBC022. 5 fluorescence channel images converted to RGB images with ImageJ and resized to 224x224 pixels. The CSV files contain the metadata (b22_dataset.csv all data points, b22_dataset_mesh_nonans.csv only MeSH annotated data points).</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.