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Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
High spatiotemporal resolution free surface detection using cost-effective video equipment and computer vision techniques in nearly stationary flow along a transparent wall in the laboratory
<p>The identification of the air-water interface in free surface flows traditionally involves intrusive techniques or costly equipment. Non-intrusive alternatives, such as computer vision, are emerging as highly effective substitutes or supplements for more invasive techniques in laboratory measurements, thanks to their straightforward implementation and cost efficiency. This research specifically delves in the conjunction of various naive techniques, exploring their collective precision in detecting the air-water interface along transparent walls in laboratory. A detection technique based on the double gradient of the image is applied and thoroughly examined. The study progresses through multiple refinement stages, culminating in a method that is both cost effective and easy to implement. This methodology allows for large-scale, high resolution measurements (200 mm × 1800 frames per video at a 0.25 mm, 50 Hz resolution), offering both spatial and temporal measurements by adeptly detecting the free surface along transparent walls.</p>
Figure 5 in Evaluation of chitosan and silver nanoparticles Against isolated pathogens from Mulberry Silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) under laboratory conditions
Figure 5. TEM micrograph of chitosan nanoparticles prepared by ionic gelation method. Table 3. Antimicrobial activity of silver nanoparticles (µl) with different concentrations against fungal and bacterial isolates.
Figure 1 in Evaluation of chitosan and silver nanoparticles Against isolated pathogens from Mulberry Silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) under laboratory conditions
Figure 1. Mean weight of healthy and infected fourth and fifth instar larvae of B. mori. Isolation and identification of bacterial isolates: Total of 7 bacterial were successfully isolated from the outer surface and the inner bоdy of silkworm larvae.
ENDGAME - Laboratory Experiment 2024-03-19 Exp. 003 - High Speed Camera data
<p>Preliminary 2D Shock-tube experiments in combination with high speed Schlieren shadow photography. </p> <p>We developed a 2D shock-tube setup using 2 glass sheets (1 cm width) separated by 2 lateral bars (gap between glass sheets 1.3 cm). We injected compressed air into the 2D setup at different overpressures (up to 8 bar). The high-pressure reservoir is connected with the 2D apparatus through a diaphragm pulse valve which allows a fast release of pressurized gas into the system. Images were collected at a frame rate of 30000 fps. The field of view of the images show the jet flow dynamics in the upper part of the 2 glass sheets and in the atmosphere.</p>
Fig. 2 in Quantifying insect predation in laboratory arenas: the effect of prey acclimation
Fig. 2. Behavioral responses of Orgyia leucostigma caterpillars that acclimated on the plant for less than 20 min (20 min), from 20 to <40 min (40 min), and from 40 to 60 min (60 min) to the attacks of Polistes fuscatus wasps. *P <0.05; ns: P> 0.05. No response = caterpillars that did not respond to predators by dropping. Drop = caterpillars that dropped from the leaf in response to the predator.
Fig. 1 in Quantifying insect predation in laboratory arenas: the effect of prey acclimation
Fig. 1. The mortality of Orgyia leucostigma caterpillars that acclimated on the plant for less than 20 min (20 min), from 20 to <40 min (40 min), and from 40 to 60 min (60 min) before exposure to Polistes fuscatus wasps. Treatments with the same letter are not significantly different (P> 0.05).
Fig. 2 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 2. Canonical analysis for pupae size parameters of males and females of laboratory and wild populations in Anastrepha ludens. The canonical analysis is represented on the first canonical axis (can 1), where the boxplots indicate the populations (laboratory and wild) and sexes (males and females) (lef). The variables of pupae size: length (mm), width (mm), and weight (mg) are indicated by vectors (right).
Fig. 1 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 1. Size distribution of laboratory and wild Anastrepha ludens and Anastrepha obliqua male and female pupae. The proportion of male and female pupae is shown in 10 pupal size classes (pupal diam mm) on the x-axis.
Fig. 3 in Pupal size distribution and sexual dimorphism in wild and laboratory populations of two species of Anastrepha (Diptera: Tephritidae) fruit flies
Fig. 3. Canonical analysis for pupae size parameters of males and females of laboratory and wild populations in Anastrepha obliqua. The canonical analysis is represented on the first canonical axis (can 1), where the boxplots indicate the populations (laboratory and wild) and sexes (males and females) (lef). The variables of pupae size: length (mm), width (mm), and weight (mg) are indicated by vectors (right).
Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
On the emergence of fault afterslip during laboratory seismic cycles
<div>This is the ReadMe file corresponding to the dataset of the study entitled:</div> <div>"On the emergence of fault afterslip during laboratory seismic cycles"</div> <div>By Noël C., Twardzik C., Dublanchet P., and Passelègue F.</div> <div> </div> <div>This Read-Me file has been last edited in October 2024</div> <div> </div> <div>This readme file describes the data repository and supplementary files accompanying the above publication. </div> <div>For any further queries please contact corentin.noel@geoazur.unice.fr</div> <div> </div> <div> </div> <div> </div> <div>Each experiment has a .txt file. The nam of the file is composed of first the sample configuration, then the confining pressure. If "down" is following, it stands for the confining pressure downphase at the end of the experiment (see method section of the manuscript). For Granite_Marble experiments, "bis" at the end of the name stands for the duplicated experiment. </div> <div> </div> <div>The data are tab separate file, each column is a variable as follow:</div> <div>Column 1: Time(s)</div> <div>Column 2: Axial average displacement (mm)</div> <div>Column 3: Axial stress (MPa)</div> <div>Column 4: Confining pressure (MPa)</div> <div>Column 5: Strain gage 1 (µstrain)</div> <div>Column 6: Strain gage 2 (µstrain)</div> <div>Column 7: Strain gage 3 (µstrain)</div> <div>Column 8: Strain gage 4 (µstrain)</div> <div>Column 9: Strain gage 5 (µstrain)</div> <div>Column 10: Strain gage 6 (µstrain)</div> <div>Column 11: Strain gage 7 (µstrain)</div> <div>Column 12: Strain gage 8 (µstrain)</div>
Linked collectors and determiners for: European Molecular Biology Laboratory Australian Mirror.
Natural history specimen data linked to collectors and determiners held within, "European Molecular Biology Laboratory Australian Mirror". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c1fc2df7-223b-4472-8998-70afb3b749ab">https://bionomia.net/dataset/c1fc2df7-223b-4472-8998-70afb3b749ab</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c1fc2df7-223b-4472-8998-70afb3b749ab">https://gbif.org/dataset/c1fc2df7-223b-4472-8998-70afb3b749ab</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Ohio State Acarology Laboratory (OSAL), Ohio State University.
Natural history specimen data linked to collectors and determiners held within, "Ohio State Acarology Laboratory (OSAL), Ohio State University". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/96b54e8c-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/96b54e8c-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/96b54e8c-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/96b54e8c-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Bee Biology and Systematics Laboratory.
Natural history specimen data linked to collectors and determiners held within, "Bee Biology and Systematics Laboratory". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/10e44c48-0839-4a20-86d5-f0e23ae2e366">https://bionomia.net/dataset/10e44c48-0839-4a20-86d5-f0e23ae2e366</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/10e44c48-0839-4a20-86d5-f0e23ae2e366">https://gbif.org/dataset/10e44c48-0839-4a20-86d5-f0e23ae2e366</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Rocky Mountain Biological Laboratory.
Natural history specimen data linked to collectors and determiners held within, "Rocky Mountain Biological Laboratory". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e82092b5-e2b0-4db8-8cca-22e11272af6b">https://bionomia.net/dataset/e82092b5-e2b0-4db8-8cca-22e11272af6b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e82092b5-e2b0-4db8-8cca-22e11272af6b">https://gbif.org/dataset/e82092b5-e2b0-4db8-8cca-22e11272af6b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Iowa Lakeside Laboratory Avian Collection.
Natural history specimen data linked to collectors and determiners held within, "Iowa Lakeside Laboratory Avian Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/738de9a9-1871-4fc9-a755-8ca3724bec46">https://bionomia.net/dataset/738de9a9-1871-4fc9-a755-8ca3724bec46</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/738de9a9-1871-4fc9-a755-8ca3724bec46">https://gbif.org/dataset/738de9a9-1871-4fc9-a755-8ca3724bec46</a>. Formatted as a Frictionless Data package.
Datasets and code for "To heal or not to heal? Part II: The moment-recurrence time behavior of Oklahoma lithologies is consistent with laboratory healing behavior"
<p>The following files are included:</p> <ul> <li>PulseWidths.csv: Pulse width measurements for each earthquake at each stations</li> <li>family_df_withMoment.csv: Average measurements of pulse width and moment for each earthquake as well as family information and timing (Datetime, recurrence time, time until next event)</li> <li>MTSpec_Prague.ipynb: A jupyter notebook with code for measuring corner frequency from spectral ratios using the joint fit procedure described in the manuscript. Produces the figures shown in the manuscript and supplement. <ul> <li>files needed to run this code are: families_df_1_25_0.95.csv, EQ_catalog_sp.csv, Catalog.txt, Repeater_Sig.csv, the waveforms supplied at Okamoto et al., 2022 (<a href="10.5281/zenodo.6658257">10.5281/zenodo.6658257</a>) <p> </p> </li> </ul> </li> </ul>
Results of inter-laboratory testing on COSC-1 cores and reference samples (density, porosity, thermal properties)
<p>The data files contain the results of comparative measurements of thermal properties of four widely used rock references and nine core samples originating from the ICDP COSC-1 borehole, using a steady-state and a transient divided-bar device, a transient plane source device, a modified Angstrom device, as well as two optical thermal conductivity scanners. In addition, the Dewar method provided benchmark values for specific heat capacity. </p> <p>participating institutions and methods (acronyms used in file headers)</p> <p>Chalmers University (CU) transient plane source (TPS)<br>Geological Survey of Sweden (SGU) optical scanning (TCS) <br>Ruhr-Universit ̈at Bochum (RUB) Dewar method, modified Angstrom (mAng), optical scanning (TCS)<br>Aarhus University (AU) transient divided bar (TDB)<br>University College Dublin (UCD) divided bar (DB)</p>
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>
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.