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232 results for “Optical imaging”
Dataset for "LOROS: Laboratory Simulations of the Optical RadiOmeter composed of CHromatic Imagers (OROCHI) Experiment of the Martian Moons eXploration (MMX) Mission"
<p>This dataset hosts the image and numerical data analysed and derived in the accompanying Stabbins & Kameda article for the special issue of Progress in Earth and Planetary Science on instrumentation and preparations for the JAXA Martian Moons eXploration (MMX) mission. The paper describes and validates the performance of the Laboratory OROCHI Simulator (LOROS).</p> <p>OROCHI (Optical RadiOmeter composed of CHromatic Imagers) is a multispectral multi-view imaging system for the JAXA MMX spacecraft, that will image Phobos and Deimos across 8 visible and near-infrared spectral channels with unprecedented spatial resolution, recording data that in synergy with the other instruments of the MMX spacecraft and rover will constrain hypotheses on the origin of the Martian moons.</p> <p>LOROS is a laboratory simulator of OROCHI, constructed from commercial off-the-shelf parts.</p> <p>The dataset for the characterisation and validation of LOROS is composed of the following sub-sets:</p> <p>A. Modulation Transfer Function<br>B. Expected Reflectance of Carbonaceous Chondrite & Dark Spectralon<br>C. Radiometric Calibration<br>D. Dark Spectralon Validation</p> <div> <h2>Dataset A: Modulation Transfer Function</h2> This dataset includes the table of results of MTF measurements of the slant-edge target at 5 different random orientations in the range of ~7--10°: <div>- <code>mtf_results_07122023.csv</code></div> <br> <div>and the region-of-interest images, for each orientation and each LOROS channel, used to perform the analysis via the <a href="https://sourceforge.net/p/mtfmapper/home/Home/" target="_blank" rel="noopener">MTF Mapper software</a>:</div> <div>- <code>mtf_measurements_07122023</code></div> <br> <div>The directory tree of measurements, for the <em>n</em>th orientation, is illustrated below. Region-of-interest images are stored under <code>img</code>, and are averaged over 25 repeat images to minimise random noise, have had dark frames subtracted, and have been converted from 12-bit to 8-bit grayscale images for compatibility with the MTF Mapper software. Modulation Transfer Function (MTF) and Spatial Frequency Response (SFR) diagnostics generated by MTF Mapper are stored in the <code>results</code> directory.</div> <div> </div> <div><code>mtf_measurements_07122023</code></div> <div><code>├── mtf_knifeedge_low_07122023_*n*</code></div> <div><code>│ ├── img</code></div> <div><code>│ │ ├── 0_850_img_ave.tif</code></div> <div><code>│ │ ├── 1_475_img_ave.tif</code></div> <div><code>│ │ ├── ...</code></div> <div><code>│ ├── results</code></div> <div><code>│ │ ├── 0_850_img_ave_annotated.jpg</code></div> <div><code>│ │ ├── 0_850_img_ave_edge_mtf_values.txt</code></div> <div><code>│ │ ├── 0_850_img_ave_edge_sfr_values.txt</code></div> <div><code>│ │ ├── 1_475_img_ave_annotated.jpg</code></div> <div><code>│ │ ├── ...</code></div> <div><code>├── mtf_knifeedge_low_07122023_*n+1*</code></div> <div><code>│ ├── img</code></div> <div><code>│ │ ├── ...</code></div> <div> </div> <div>This data constitutes part of <strong>Table 1</strong> and <strong>Figure 2</strong> of the manuscript.</div> <div> <h2>Dataset B: Expected Reflectance of Carbonaceous Chondrite & Dark Spectralon</h2> This dataset includes the high-resolution ($\delta\lambda$=1 nm) reference reflectance spectra of the representative Carbonaceous Chondrite meteorite (<a href="https://westernreflectancelab.com/visor/graph/?results-selection=16136&results-item=16136&results-item=15972&results-item=231&results-item=230&graph=&form-TOTAL_FORMS=1&form-INITIAL_FORMS=0&form-MIN_NUM_FORMS=0&form-MAX_NUM_FORMS=1000&form-0-sample_name=nogoya&form-0-any_field=meteorite&form-0-id=&sort_params=-sample_name&page_selected=1&jump-to-page=" target="_blank" rel="noopener">Nogoya)</a> and the 5% reflectance Spectralon calibration target (<a href="https://www.labsphere.com/wp-content/uploads/2021/09/SpectralonStandards.pdf" target="_blank" rel="noopener">SCT5</a>):<br> <div>- <code>highres_input.csv</code></div> <br> <div>and the resampled spectra of these materials expected for OROCHI and LOROS filter wavelengths:</div> <br> <div>- <code>loros_observation.csv</code></div> <div>- <code>orochi_observation.csv</code></div> <br> <div><code>B_expected_reflectance</code></div> <div><code>├── README.md</code></div> <div><code>├── highres_input.csv</code></div> <div><code>├── loros_observation.csv</code></div> <div><code>└── orochi_observation.csv</code></div> <br> <div>This data constitutes <strong>Table 1</strong> and <strong>Figure 10</strong> of the manuscript.</div> <div> </div> <div> <div> <h2>Dataset C: Radiometric Calibration</h2> This dataset contains the image and derived data for 4 experiments with different illumination conditions for characterising the radiometric response of each of the 8 channels of LOROS.</div> <div><br> <div>This dataset contributes to <strong>Tables 2 - 4</strong> and <strong>Figures 3 - 9</strong> of the manuscript.</div> <br> <div>The final derived metrics are hosted in the spreadsheet:</div> <br> <div>- <code>measured_sensor_properties.csv</code></div> <br> <div>and image data and intermediary derived properties for each experiment are stored in the</div> <br> <div>- <code>experiments</code></div> <br> <div>directory.</div> <br> <div><code>C_radiometric_calibration</code></div> <div><code>├── README.md</code></div> <div><code>├── experiments</code></div> <div><code>│ ├── F*S5L10</code></div> <div><code>│ ├── F*S99L10</code></div> <div><code>│ ├── FGS99L2</code></div> <div><code>│ └── FGS99L10</code></div> <div><code>└── measured_sensor_properties.csv</code></div> <br> <h3><code>experiments</code> Directories</h3> In the directory of each experiment are sub-directories hosting Photon Transfer and Dark Transfer datasets, and a spreadsheet of derived metrics of these.<br> <div> </div> <div><code>C_radiometric_calibration</code></div> <div><code>├── README.md</code></div> <div><code>├── experiments</code></div> <div><code>│ ├── F*S5L10</code></div> <div><code>│ │ ├── dark_transfer_curve</code></div> <div><code>│ │ ├── photo_transfer_curve</code></div> <div><code>│ │ └── F*S5L10_derived_properties.csv</code></div> <div><code>│ └── ...</code></div> <div><code>└── measured_sensor_properties.csv</code></div> <div> </div> </div> <div> </div> <div><strong>Derived Properties</strong><br> <div> </div> <div>The spreadsheet (<code>[experiment]_derived_properties.csv</code>) collecting the properties derived from each experiment holds the following information, that has been extracted from the Photon Transfer and Dark Transfer curves as described in §4.2 of the manuscript:</div> <br> <div><code>camera # The camera number and wavelength</code></div> <div><code>k_adc # Sensitivity (e-/DN)</code></div> <div><code>full_well_e # Saturation Capacity (electrons)</code></div> <div><code>full_well_dn # Saturation Capacity (Digital Numbers)</code></div> <div><code>read_noise_e # Read Noise (electrons)</code></div> <div><code>read_noise_dn # Read Noise (Digital Numbers)</code></div> <div><code>bias_e # Offset (electrons)</code></div> <div><code>bias_dn # Offset (Digital Numbers)</code></div> <div><code>dark_current_e # Dark Current (electrons/second)</code></div> <div><code>dark_current_dn # Dark Current (Digital Numbers/second)</code></div> <div><code>DR # Dynamic Range</code></div> <div><code>lin_min # Minimum Linearity Error</code></div> <div><code>lin_max # Maximum Linearity Error</code></div> <div><code>linearity # Average Linearity Error</code></div> <div><code>snr_max # Maximum Signal-to-Noise Ratio</code></div> <div><code>t_exp_min # Minimum Exposure used in experiment (seconds)</code></div> <div><code>t_exp_max # Maximum Exposure used in experiment (seconds)</code></div> <div><code>expected_response # Expected Response (or 'Digital Flux') for OROCHI^12 at Phobos (Digital Numbers/second)</code></div> <div><code>response # Fitted Response (or 'Digital Flux') (Digital Numbers/second)</code></div> <br> <div>These values are given for each channel of LOROS, as well as the expected values for LOROS in off-the-shelf configuration (with no gain adjustment), LOROS with the gain adjustment, and OROCHI if downsampled to 12-bit resolution digital numbers.</div> <br> <div>This data constitutes <strong>Table 2</strong> of the manuscript.</div> <br> <div><strong>Dark Transfer Curve</strong></div> <br> <div>The <code>dark_transfer_curve</code> directory hosts the derived Dark Transfer Curve data (<code>derived_data</code>) and the source region-of-interest dark image pair data (<code>raw_data</code>) for each LOROS channel.</div> <br> <div><code>dark_transfer_curve</code></div> <div><code>├── derived_data</code></div> <div><code>│ ├── F*S5L10_0_850_dtc.csv</code></div> <div><code>│ ├── F*S5L10_1_475_dtc.csv</code></div> <div><code>│ ├── F*S5L10_2_400_dtc.csv</code></div> <div><code>│ ├── F*S5L10_3_550_dtc.csv</code></div> <div><code>│ ├── F*S5L10_4_725_dtc.csv</code></div> <div><code>│ ├── F*S5L10_5_950_dtc.csv</code></div> <div><code>│ ├── F*S5L10_6_650_dtc.csv</code></div> <div><code>│ └── F*S5L10_7_550_dtc.csv</code></div> <div><code>└── raw_data</code></div> <div><code>├── 0_850</code></div> <div><code>│ ├── 850_10095570us_1_calibration.tif</code></div> <div><code>│ ├── 850_10095570us_2_calibration.tif</code></div> <div><code>│ ├── 850_104us_1_calibration.tif</code></div> <div><code>│ ├── 850_104us_2_calibration.tif</code></div> <div><code>│ ├── ...</code></div> <div><code>├── 1_475</code></div> <div><code>├── 2_400</code></div> <div><code>├── 3_550</code></div> <div><code>├── 4_725</code></div> <div><code>├── 5_950</code></div> <div><code>├── 6_650</code></div> <div><code>├── 7_550</code></div> <div><code>└── camera_config.csv</code></div> <br> <div>The <code>raw_data</code> directory hosts a dark image pair for each exposure time used, and the <code>camera_config.csv</code> spreadsheet gives metadata for the system configuration, including the coordinates and dimensions of the region-of-interest for each channel.</div> <br> <div>The dark transfer curve for each experiment and each channel (<code>[experiment]_[channel]_[wavelength]_dtc</code>) gives the data derived from each raw image data, with the following values:</div> <br> <div><code>exposure # exposure duration (seconds)</code></div> <div><code>n_pix # number of pixels in the region of interest</code></div> <div><code>mean # average value of the region of interest</code></div> <div><code>std_t # total standard deviation of the region of interest</code></div> <div><code>std_rs # read+shot-noise standard deviation, copmuted from the difference of the image pair</code></div> <br> <div>This data constitutes <strong>Figures 5 and 8</strong> of the manuscript.</div> <br> <div><strong>Photon Transfer</strong></div> <br> <div>The <code>photon_transfer_curve</code> directory hosts the derived Photon Transfer Curve data (<code>derived_data</code>) and the source region-of-interest illuminated image pairs and associated dark frame image data (<code>raw_data</code>) for each LOROS channel.</div> <br> <div><code>photo_transfer_curve</code></div> <div><code>├── derived_data</code></div> <div><code>│ ├── F*S5L10_0_850_ptc.csv</code></div> <div><code>│ ├── F*S5L10_1_475_ptc.csv</code></div> <div><code>│ ├── F*S5L10_2_400_ptc.csv</code></div> <div><code>│ ├── F*S5L10_3_550_ptc.csv</code></div> <div><code>│ ├── F*S5L10_4_725_ptc.csv</code></div> <div><code>│ ├── F*S5L10_5_950_ptc.csv</code></div> <div><code>│ ├── F*S5L10_6_650_ptc.csv</code></div> <div><code>│ └── F*S5L10_7_550_ptc.csv</code></div> <div><code>└── raw_data</code></div> <div><code>├── 0_850</code></div> <div><code>│ ├── 850_104us_1_calibration.tif</code></div> <div><code>│ ├── 850_104us_2_calibration.tif</code></div> <div><code>│ ├── 850_104us_d_drk.tif</code></div> <div><code>│ ├── 850_105828us_1_calibration.tif</code></div> <div><code>│ ├── ...</code></div> <div><code>├── 1_475</code></div> <div><code>├── 2_400</code></div> <div><code>├── 3_550</code></div> <div><code>├── 4_725</code></div> <div><code>├── 5_950</code></div> <div><code>├── 6_650</code></div> <div><code>├── 7_550</code></div> <div><code>└── camera_config.csv</code></div> <br> <div>The <code>raw_data</code> directory hosts an image pair and dark frame for each exposure time used, and the <code>camera_config.csv</code> spreadsheet gives metadata for the system configuration, including the coordinates and dimensions of the region-of-interest for each channel.</div> <br> <div>The photon transfer curve for each experiment and each channel (<code>[experiment]_[channel]_[wavelength]_ptc</code>) gives the data derived from each raw image data, with the following values across the region-of-interest:</div> <br> <div><code>exposure # exposure duration (seconds)</code></div> <div><code>n_pix # number of pixels in the region of interest</code></div> <div><code>mean # average value (Digital Numbers)</code></div> <div><code>std_t # total standard deviation (Digital Numbers)</code></div> <div><code>std_rs # read+shot-noise standard deviation (Digital Numbers), computed from the difference of the image pair</code></div> <div><code>d_mean # average value of the dark (Digital Numbers)</code></div> <div><code>d_dsnu # Dark Signal Nonuniformity (Digital Numbers)</code></div> <div><code>std_s # Shot Noise (read noise removed) (Digital Numbers)</code></div> <div><code>k_adc # Sensitivity (note this the point-wise sensitivity, rather than fitted) (electrons/Digital Number)</code></div> <div><code>linearity # Linearity Error (point-wise distance to least-squares linear fit) (%)</code></div> <div><code>snr # Signal-to-Noise Ratio, derived from shot-noise (point-wise)</code></div> <div><code>snr_t # Signal-to-Noise Ratio, derived from total noise (point-wise)</code></div> <div><code>e- # Electron count, derived from sensitivity</code></div> <div><code>e-_noise # Electron shot-noise, derived from sensitivity</code></div> <br> <div>This data constitutes <strong>Figures 3, 4, 6, 7 & 9</strong> of the manuscript.</div> <br> <div><strong>Measured Sensor Properties</strong></div> <br> <div>The <code>measured_sensor_properties.csv</code> spreadsheet collects and averages the following metrics over the 4 experiments performed, to give the values for each channel, along with the expected values for LOROS in off-the-shelf configuration, gain-adjusted LOROS, and OROCHI downsampled to 12-bit resolution.</div> <br> <div><code>SNR Max</code></div> <div><code>Dynamic Range (dB)</code></div> <div><code>Dynamic Range (bits)</code></div> <div><code>Sensitivity (e-/DN)</code></div> <div><code>Saturation Capacity (e-)</code></div> <div><code>Saturation Capacity (DN)</code></div> <div><code>Read Noise (e-)</code></div> <div><code>Read Noise (DN)</code></div> <div><code>Nonlinearity (%)</code></div> <div><code>Dark Signal@30°C (e-/s)</code></div> <div><code>Dark Signal@30°C (DN/s)</code></div> <div><code>Bias (e-)</code></div> <div><code>Bias (DN)</code></div> <div><code>DSNU1288 (DN)</code></div> <div><code>DSNU1288 (e-)</code></div> <div><code>PRNU1288 (%)</code></div> <br> <div>This data constitutes <strong>Table 3</strong> of the manuscript.</div> <div> </div> <div> <h2>Dataset D: Dark Spectralon Validation</h2> This dataset contains the raw image and derived data used to demonstrate the ability of LOROS to measure the spectral reflectance of the 5% reflectance Spectralon calibration target (<a href="https://www.labsphere.com/wp-content/uploads/2021/09/SpectralonStandards.pdf" target="_blank" rel="noopener">SCT5</a>).<br> <div>The image data is hosted in the directory:</div> <br> <div>- <code>raw_data</code></div> <br> <div>and the processed data (e.g. reflectance products) are hosted in the directory:</div> <br> <div>- <code>processed_data</code></div> <br> <div><code>D_dark_spectralon_validation</code></div> <div><code>├── processed_data</code></div> <div><code>│ ├── SCT5</code></div> <div><code>│ └── SCT99</code></div> <div><code>├── raw_data</code></div> <div><code>│ ├── SCT5</code></div> <div><code>│ ├── SCT5_dark</code></div> <div><code>│ ├── SCT99</code></div> <div><code>│ └── SCT99_dark</code></div> <div><code>└── README.md</code></div> <br> <div><strong>Raw Data</strong></div> <br> <div>The raw data directory contains images captured of <code>SCT5</code> and <code>SCT99</code> (99% reflectance white Spectralon), and accompanying dark frames, hosted in the <code>SCT5_dark</code> and <code>SCT99_dark</code> frames respectively.</div> <br> <div>For each channel, 25 repeat images have been captured for the illuminated and dark frames.</div> <br> <div><strong>Processed Data</strong></div> <br> <div>The processed SCT99 and SCT5 datasets differ slightly. Both include:</div> <br> <div><code>├── img</code></div> <div><code>├── rfl</code></div> <div><code>└── rois</code></div> <br> <div>directories, with the SCT99 scene also including a <code>cal</code> directory.</div> <br> <div><code>img</code> hosts a set of <code>context</code> figures, showing the regions of interest selected, <code>fits</code> hosts the floating point mean (<code>ave</code>), standard error (<code>err</code>), standard deviation (<code>std</code>) and single-frame (<code>one</code>), all in units of Digital Number, after dark frame subtraction, flat-fielding and linearity correction. <code>uint8</code> hosts the same data rescaled to 8-bit resolution, for quick-view.</div> <br> <div><code>rfl</code> hosts the same set as <code>img</code>, after conversion to units of reflectance against the results of the SCT99 calibration (see §3.5 of the manuscript).</div> <br> <div><code>rois</code> gives plots of the mean and error of the reflectance spectrum of the region of interest, as well as the Signal-to-Noise Ratio, as well as the data for each region-of-interest (<code>roi_data</code>).</div> <br> <div><code>cal</code> also gives context figures for each channel region-of-interest, as converted to units of reflectance coefficients (1/DN/s).</div> </div> </div> </div> </div> </div>
Data Models for Dataset Drift Controls in Machine Learning With Optical Images - Datasets
<p>This dataset accompanies the paper titled</p> <p><em>Data Models for Dataset Drift Controls in Machine Learning with Images</em><br> <br> that appeared in the Transactions on Machine Learning Research<br> <br> <a href="https://openreview.net/forum?id=I4IkGmgFJz">https://openreview.net/forum?id=I4IkGmgFJz</a><br> </p> <pre><code>@article{ oala2023data, title={Data Models for Dataset Drift Controls in Machine Learning With Optical Images}, author={Luis Oala and Marco Aversa and Gabriel Nobis and Kurt Willis and Yoan Neuenschwander and Mich{\`e}le Buck and Christian Matek and Jerome Extermann and Enrico Pomarico and Wojciech Samek and Roderick Murray-Smith and Christoph Clausen and Bruno Sanguinetti}, journal={Transactions on Machine Learning Research}, issn={2835-8856}, year={2023}, url={https://openreview.net/forum?id=I4IkGmgFJz}, note={} }</code></pre> <p>We make available two datasets.</p> <p><strong>Raw-Microscopy:</strong></p> <ul> <li><strong>940 raw bright-field microscopy images</strong> of human blood smear slides for leukocyte classification (microscopy/images/raw_scale100) with corresponding labels (microscopy/labels).</li> <li><strong>5,640 variations measured at six additional different intensities </strong>(microscopy/images/raw_scale001-raw_scale0075)</li> <li><strong>11,280 images of the raw sensor data processed through twelve different pipelines</strong> (microscopy/images/processed_views)</li> </ul> <p><strong>Raw-Drone:</strong></p> <ul> <li><strong>548 raw drone camera images for car segmentation</strong> (drone/images_tiles_256/raw_scale100) with corresponding binary segmentation mask (drone/masks_tiles_256). The images and the masks are cropped from 12 raw drone camera images (drone/images_full/raw_scale100) and 12 masks (drone/masks_full) of size 3648 by 5472.</li> <li><strong>3,288 variations measured at six additional different intensities</strong> (drone/images_tiles_256/raw_scale001-raw_scale075).</li> <li><strong>6,576 images of the raw sensor data processed through twelve different pipelines</strong> (drone/images_tiles_256/processed_views).</li> </ul> <p>Detailed datasheets for the two datasets can be found in the appendices of the TMLR paper.</p> <p>The code repository for this project can be found at <a href="https://github.com/aiaudit-org/raw2logit">https://github.com/aiaudit-org/raw2logit</a></p> <p> </p>
An Agnostic Benchmark for Optical Remote Sensing Image Super-Resolution
<p>In remote sensing, image super-resolution (ISR) is a technique used to create high-resolution (HR) images from low-resolution (R) satellite images, giving a more detailed view of the Earth’s surface. However, with the constant development and introduction of new ISR algorithms, it can be challenging to stay updated on the latest advancements and evaluate their performance objectively. To address this issue, we introduce SRcheck, a Python package that provides an easy-to-use interface for comparing and benchmarking various ISR methods. SRcheck includes a range of datasets that consist of high-resolution and low-resolution image pairs, as well as a set of quantitative metrics for evaluating the performance of SISR algorithms.</p>
Automatic Choroid Vascularity Index Calculation in Optical Coherence Tomography Images with Low Contrast Sclerocho-roidal Junction Using Deep Learning
<p>This project aims to calculate Choroid Vascularity Index (CVI) in optical coherenece tomography (OCT) images, using loss modified U-Net. The method is detailed in "Automatic Choroid Vascularity Index Calculation in Optical Coherence Tomography Images low contrast sclerochoroidal junction Using Deep Learning". The dataset consists of Enhanced-depth imaging optical coherence tomography images from two patient groups.</p> <p>• First dataset is including Raster OCT B-scans from patients with diabetic retinopathy.</p> <p>• Second dataset is including EDI-HD OCT B-scans from patients with pachychoroid spectrum.</p>
Optical Image Correlation Data for 2023 Kahramanmaras Earthquakes
<p>Horizontal surface deformation maps generated from pixel tracking of Sentinel-2 optical satellite images using COSI-Corr.</p>
Dataset of "Challenging Point Scanning across Electron Microscopy and Optical Imaging using Computational Imaging"
<p>Dataset containing the jupyter notebook with codes for the simulation of the structured illumination patterns used for image reconstruction (the simulation parameters have been optimized to make sure that the patterns were almost identical to the experimental ones), the reconstruction algorithms. Moreover, there are three experimental dataset saved as txxt file, where each line contains the six biases applied to the electron modulator and the intensity measured by the single pixel detector that we used.</p>
Dataset of "Single-Pixel Imaging in Space and Time with Optically Modulated Free Electrons"
<p>This dataset contains the simulated spatial images and temporal profiles reconstructed using the Electron Single-Pixel Imaging where free-electrons are shaped by light pulses. The reconstruction is performed using two different basis (Hadamard and Fourier) and for three different light frequency cutoffs. Some of these data and images are published in https://doi.org/10.1021/acsphotonics.3c00047. </p>
Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images - dataset
<p>This dataset includes 4 files with segmentation results for 4 different ODT reconstructions of SH-SY5Y neuroblastoma cell. The segmentation results contain:</p> <ol> <li>3D binary masks of biological cells obtained through Cellpose [1] and <a href="https://github.com/biopto/ODT-SAS.git">ODT-SAS</a>;</li> <li>3D binary masks of organelles: nucleoli and lipid structures (LS) obtained through slice-by-slice manual segmentation and ODT-SAS.</li> </ol> <p>All files are .*mat files.</p> <p>The files <em>REC_SH-SY5Y_1.mat, REC_SH-SY5Y_2.mat</em> and<em> REC_SH-SY5Y_3.mat</em> consist of 7 variables:</p> <p>RECON – tomographic reconstruction of SH-SY5Y neuroblastoma cell;<br> n_imm – refractive index of object immersion medium;<br> dx – object space sample size in XY [<span class="math-tex">\(\mu m\)</span>];<br> rayXY – xy-coordinates of illumination vectors;</p> <p>maskManual – table with manually determined 3D binary masks of organelles;<br> maskCellpose – 3D binary mask of biological cell obtained through Cellpose;<br> maskODTSAS – table with 3D binary masks of biological cell and their organelles obtained through ODT-SAS.</p> <p>File <em>REC_SH-SY5Y_4.mat</em> includes masks for the ODT-SAS and Cellpose segmentation of three closely packed cells and consists of 5 variables: RECON, n_imm, dx, maskCellpose and maskODTSAS.<br> <br> Access a particular 3D binary mask from 'maskManual' and 'maskODTSAS' tables, using the following names: 'Cell', 'Nucleoli', 'LS'.<br> For example:</p> <pre><code>cellMask = maskODTSAS.Cell{1};</code></pre> <p><br> [1] Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106.</p> <p> </p>
Supplementary data for: Comparison of optical flow derivation techniques for retrieving tropospheric winds from satellite image sequences
Open the record for dataset details and reuse information.
Optical projection tomography images of Invitrogen™ beads
<p>Optical projection tomography (OPT) dataset from samples consisting of optical beads embedded in hydrogel.</p> <p>Used beads were commercially available from Thermo Fischer Scientific Inc.: Invitrogen™ Countbright™ (catalog number F8844) and Invitrogen™ FluoSpheres 505/515 (catalog number C36950). Beads were prepared in 2\% agarose gel and placed inside fluorinated ethylene propylene tube having inside diameter of 1 mm.</p>
RGB and Thermal Integral Image dataset for Search and Rescue with Airborne Optical Sectioning.
<p>The `Integral Images` folder contains labels and augmented AOS integral images (both RGB and Thermal) used for training, validation and testing (`data`).</p> <p>The integral images are computed using the complete data that were recorded during 18 flights at 6 different sites over 10 different days.</p> <p> </p> <p>The dataset mirrors [YOLO (8GB)](https://zenodo.org/record/3894774/files/YOLO.zip?download=1) (`data`) for integral (`SARAOS/AOS`) images, however, now additionally contain corresponding RGB integral images in addition to corresponding thermal integral images.</p>
Dataset - Generalization of deep recurrent optical flow estimation for particle-image velocimetry data
<p>This is the official test datasets of "Generalization of deep recurrent optical flow estimation for particle-image velocimetry data" published in Measurement Science and Technology. Particle-Image Velocimetry (PIV) is one of the key techniques in modern experimental fluid mechanics to determine the velocity components of flow fields in a wide range of complex engineering problems. Current PIV processing tools are mainly handcrafted models based on cross-correlations computed across interrogation windows. Although widely used, these existing tools have a number of well-known shortcomings, including limited spatial output resolution and peak-locking biases. Recently, new approaches for PIV processing leveraging a novel neural network architecture for optical flow estimation called Recurrent All-Pairs Field Transforms (RAFT) have been developed. These have matched or exceeded the performance of classical, handcrafted models. While the RAFT-PIV method is a promising approach, it is important for the broader fluids community to more completely understand its empirical behavior and performance. To this end, in this study, we thoroughly investigate the performance of RAFT-PIV under varying image and lighting conditions. IWe consider applications spanning synthetic and experimental data, with a breadth and depth going far beyond currently available empirical results. The results for the wide variation of experiments included in this dataset shed new light on the capabilities of deep learning for PIV processing. This dataset is given as binary TFRECORD format.</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Code availability</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Data availability for polymer measurements</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Data availability of TiO2/SiO2 grid measurements</p>
Testing a new optical strain gage for full-field strain measurement: Raw images
<pre>This dataset contains images obtained during two different tests performed to assess the response of a new optical strain gage developped for full-field strain measurement.</pre> <pre><strong>File contents:<br></strong> - SMA: Folder containing images obtained with a SMA specimen<br> - SMA_Paint_Ref: contains 100 images in the reference state. These were taken with the optimal parameters for the painted and engraved half (lower half in the images).<br> - SMA_Paint_Def: contains 100 images in the deformed state. <br> - SMA_Gage_Ref: contains 100 images in the reference state. These were taken with the optimal parameters for the gage (upper half in the images).<br> - SMA_Gage_Def: contains 100 images in the deformed state. <br> - Wood: Folder containing images obtained with a wood specimen<br> - Wood_Paint_Ref: contains 100 images in the reference state.<br> - Wood_Paint_Def: contains 100 images in the deformed state. <br> - Wood_Gage_Ref: contains 100 images in the reference state.<br> - Wood_Gage_Def: contains 100 images in the deformed state. <br><br>These images can be processed with the Python code available in the OpenLSA library: https://gitlab.ip.uca.fr/expmech/openlsa .</pre> <p>An example is provided in this library.</p>
PL maps, optical images and PLQY analyses
<p>Large data set of PL maps, optical images and PLQY analyses</p>
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
<p>Source data of paper "Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging" published on Nature Methods.</p>
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
<p>Source data of paper "Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging" published on Nature Methods.</p>
Global daily Aerosol Optical Depth measurements from Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA's Aqua and Terra satellites
<p>This repository contains input MODIS AOD data prepared for “Subways and Urban Air Polution” by Gendron-Carrier, Gonzalez-Navarro, Polloni and Turner (American Economic Journal: Applied Economics, <a href="https://doi.org/10.1257/app.20180168">https://doi.org/10.1257/app.20180168</a>). The main replication archive is available at <a href="https://doi.org/10.3886/E126401V1">https://doi.org/10.3886/E126401V1</a> .</p> <p>Description of input MODIS AOD data</p> <p>The Moderate Resolution Imaging Spectroradiometers aboard the Terra and Aqua earth-observing satellites provide daily measures of the aerosol optical depth of the atmosphere at a 3km spatial resolution everywhere in the world. Data is available in ‘granules’ which describe five minutes of satellite time. These granules are available, more or less continuously, from February 24, 2000 for the Terra satellite and from July 4, 2002 for Aqua. During September of 2018, we downloaded all available granules for Terra and Aqua until August 31, 2018 and subsequently consolidated them into daily rasters describing global AOD. In August 2020, we processed additional Terra data. This archive therefore contains daily rasters for Aqua (from 2002-07-04 to 2018-08-31) and Terra (from 2000-02-24 to 2020-07-31). We note that February 2005 data are missing for the Aqua satellite.</p> <p> </p> <p>We use source products MOD04_3K (<a href="https://doi.org/10.5067/MODIS/MOD04_L2.006">https://doi.org/10.5067/MODIS/MOD04_L2.006</a>) and MYD04_3K (<a href="https://doi.org/10.5067/MODIS/MYD04_L2.006">https://doi.org/10.5067/MODIS/MYD04_L2.006</a>). The product files are stored in Hierarchical Data Format (HDF) and we use the "Optical Depth Land And Ocean" layer, which is stored as a Scientific Data Set (SDS) within the HDF file, as our measure of aerosol optical depth. The "Optical Depth Land And Ocean" dataset contains only the AOD retrievals of high quality. We convert all HDF formatted granules to GIS compatible formats using the HDF-EOS To GeoTIFF Conversion Tool (HEG) provided by NASA’s Earth Observing System Program. We consolidate GeoTIFF granules into a global raster for each day using ArcGIS. First, we keep only AOD values that do contain information. The missing value is -9999 in AOD retrievals. Second, we create a raster catalog with all the granules for a given day and calculate the average AOD value using the Raster Catalog to Raster Dataset tool. The code used to accomplish this is included for reference purposes in “dofiles/old_work” of the main replication archive at <a href="https://doi.org/10.3886/E126401V1">https://doi.org/10.3886/E126401V1</a>.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.