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2,007 results for “Image Studies”
Supplementary 1: Underwater photogrammetry for close-range 3D imaging of dry-sensitive objects: The case study of cephalopod beaks
<ul> <li>Technical advances in 3D imaging have contributed to quantifying and understanding biological variability and complexity. However, small, dry-sensitive objects are not easy to reconstruct using common and easily available techniques such as photogrammetry, surface scanning, or micro-CT scanning. Here we use cephalopod beaks as an example as their size, thickness, transparency, and dry-sensitive nature make them particularly challenging. We developed a new, underwater, photogrammetry protocol in order to add these types of biological structures to the panel of photogrammetric possibilities.</li> <li>We used a camera with a macro-photography mode in a waterproof housing fixed in a tank with clear water. The beak was painted and fixed on a colored rotating support. Three angles of view, two acquisitions, and around 300 pictures per specimen were taken in order to reconstruct a full 3D-model. These models were compared to others obtained with micro-CT scanning to verify their accuracy.</li> <li>The models can be obtained quickly and cheaply compared to micro-CT scanning, and have sufficient precision for quantitative inter-specific morphological analyses. Our work shows that underwater photogrammetry is a fast, non-invasive, efficient, and accurate way to reconstruct 3D models of dry-sensitive objects while conserving their shape. While the reconstruction of the shape is accurate, some internal parts cannot be reconstructed with photogrammetry as they are not visible. In contrast, these structures are visible using reconstructions based on micro-CT scanning. The mean difference between both methods is very small (10<sup>-5</sup> to 10<sup>-4</sup> mm) and is significantly lower than differences between meshes of different individuals.</li> <li>This photogrammetry protocol is portable, easy-to-use, fast, and reproducible. Micro-CT scanning, in contrast, is time-consuming, expensive and non-portable. This protocol can be applied to reconstruct the 3D shape of many other dry-sensitive objects such as shells of shellfish, cartilage, plants and other chitinous materials.</li> </ul>
raycast: multi-view object detection in UAV image clouds (case-study data)
<p>This package contains image data for conducting multi- and single-view sewer inlet detection in UAV image clouds. The package consists in: - individual UAV images, taken with high overlap and corrected for lens distortion - orthophoto of the case study area, clipped to road boundaries.</p>
Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC–MS in pharmacokinetic study of metformin
<p>Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC-MS in a pharmacokinetic study of metformin</p> <p><a href="https://doi.org/10.4155/bio-2017-0190">https://doi.org/10.4155/bio-2017-0190</a></p> <p>MALDI MSI datasets</p>
Figure 6 in Using digital images in the study of fluctuating asymmetry in the spur-thighed tortoise Testudo graeca
Figure 6. Regression plot with extreme variation in humeral scute area (HSA) for differences in left–right sides of the plastron due to malformations indicated by white arrows (SCL: straight carapace length; dashed line: standard deviation).
Figure 3 in Using digital images in the study of fluctuating asymmetry in the spur-thighed tortoise Testudo graeca
Figure 3. The deviation from bilateral symmetry in females and males for area (A) in mm2 and height (H) and width (W) in mm (LSP: left side of plastron, RSP: right side of plastron).
CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies
<p><strong>Abstract:</strong></p> <p>We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.</p> <p>Code submission: <a href="https://github.com/alessandro-bertero/FUCCIplex">https://github.com/alessandro-bertero/FUCCIplex.git</a></p> <p><strong>Dataset description:</strong></p> <ol> <li>This dataset includes all data and the additional files to recreate the sc-RNAseq analysis in our manuscript. The Rmd files include the Seurat QC pipeline to preprocess the counts data from cellranger (<strong>QC_Seurat_gitgub_polished.RmD</strong>) and the monocle pipeline to re-create the clusters and pseudotime analysis (<strong>monocle_github_polished.Rmd</strong>).</li> <li><strong>Data obtained from Cellranger 7.2 pipeline</strong> are also available here including all the 3 files, usually placed in the path "outs/count/filtered_feature_bc_matrix" by cellrancer. This includes: <strong>barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz</strong> (alternatively the h5 file filtered_feature_bc_matrix.h5 can be loaded directly in Seurat v5).</li> <li>We also added few RData files to recreate our graphs and follow our pipeline smoothly. <strong>240111_seurat_before_clean.RData, 240111_seurat_clean.RData</strong> and <strong>240111_seurat_processed.RData</strong> are the files created by the codes in QC_Seurat_gitgub_polished.RmD pipeline. Then, <strong>240118_monocle_cds_clustered_proteincoding_PSEUDOTIME_clean_gene_info.RData</strong> is the file set created by the<strong> </strong>monocle_github_polished.Rmd pipeline.</li> </ol> <p>We also suggest to use this pipeline within a docker container by pulling our docker image with R studio:</p> <p><strong>docker pull hedgelab/rstudio-hedgelab:latest</strong></p>
Data from: Studying developmental variation with Geometric Morphometric Image Analysis (GMIA)
The ways in which embryo development can vary across individuals of a population determine how genetic variation translates into adult phenotypic variation. The study of developmental variation has been hampered by the lack of quantitative methods for the joint analysis of embryo shape and the spatial distribution of cellular activity within the developing embryo geometry. By drawing from the strength of geometric morphometrics and pixel/voxel-based image analysis, we present a new approach for the biometric analysis of two-dimensional and three-dimensional embryonic images. Well-differentiated structures are described in terms of their shape, whereas structures with diffuse boundaries, such as emerging cell condensations or molecular gradients, are described as spatial patterns of intensities. We applied this approach to microscopic images of the tail fins of larval and juvenile rainbow trout. Inter-individual variation of shape and cell density was found highly spatially structured across the tail fin and temporally dynamic throughout the investigated period.
DATASETS - Integration of Non-Destructive Acoustic Imaging investigation with Photogrammetric and Morphological Analysis to Study the "Graecia Vetus" in the Chigi Palace of Ariccia
<p>Datasets of an integrated investigation on the monochrome painting "Graecia Vetus" located in the Ariosto Room in the historical Chigi Palace of Ariccia.</p> <p>Three datasets including:</p> <p>- <strong>Dense Cloud from the surface morphological investigation of the surface by Photogrammetric Survey:</strong></p> <p>1. Zip file containing the "*.obj", "*.mtl", "*.jpg" files to open the Model.</p> <p><strong>- Four matrices from structural damage investigation of the painting by Frequency Resolved Acoustic Imaging:</strong></p> <p>1. Integrated Acoustic Image (IAI) in the wideband (500 - 12,000) Hz;</p> <p>2. Frequency Resolved Acoustic Image (FRAI) in the narrow frequency band 1/3 octave band centred at 1000 Hz;</p> <p>3. Frequency Resolved Acoustic Image (FRAI) in the narrow frequency band 1/3 octave band centred at 6300 Hz;</p> <p>4. Frequency Resolved Acoustic Image (FRAI) in the narrow frequency band 1/3 octave band centred at 10,000 Hz.</p> <p><strong>- One profile and one matrix from structural damage investigation of the wall by Sonic Tests with Impact Hammer:</strong></p> <p>1. Relative variation of pulse velocity along the horizontal axis;</p> <p>2. Tomographic map of the relative variation of pulse velocity inside the wall</p>
Supplementary material 1 from: Tulek B (2023) Investigation of cultural ecosystem services supply in a river landscape: a case study in the Lower Rhine area using social media images. One Ecosystem 8: e97259. https://doi.org/10.3897/oneeco.8.e97259
Appendix 1
Supplementary material 2 from: Tulek B (2023) Investigation of cultural ecosystem services supply in a river landscape: a case study in the Lower Rhine area using social media images. One Ecosystem 8: e97259. https://doi.org/10.3897/oneeco.8.e97259
Appendix 2
Figure 7 in A Case Study of Wavelets and SVM Application in Coffee Agriculture: Detecting Cicadas Based on Their Acoustic and Image Patterns
Figure 7. The SVM structure used in application two. Similar to AP1, the weights determined during the superoised part of the training are {w0, w1, …, wX̅1}. The output element linearly combines the outputs of the hidden layer with the weights.
A Study to Evaluate the Use of Supine MRI Images in Breast Conserving Surgery
ClinicalTrials.gov study NCT01929395. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Studying Skeletal Muscle, Heart, and Diaphragm Imaging in Boys With Duchenne Muscular Dystrophy
ClinicalTrials.gov study NCT01451281. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Randomised Double-Blind, Placebo-Controlled, Parallel Group Study in Patients With Active Rheumatoid Arthritis:Magnetic Resonance Imaging Sub-Study
ClinicalTrials.gov study NCT02092961. IPD Sharing: Not stated. Countries: 11. Publications: 0.
A Pilot Study Evaluating the Potential of 18F Fluorodeoxyglucose PET-CT Imaging in Diagnosing Cardiac Rejection.
ClinicalTrials.gov study NCT06519240. IPD Sharing: NO. Countries: 0. Publications: 1.
Cardiovascular Inflammation Reduction Trial - Inflammation Imaging Study
ClinicalTrials.gov study NCT02576067. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Operator Radiation Exposure During Image-Guided Robotic-Assisted Bronchoscopy: A Multicenter Prospective Cohort Study
ClinicalTrials.gov study NCT07318402. IPD Sharing: YES. Countries: 1. Publications: 0.
A Feasibility Study of a Modular Video Augmentation System for Image-Guided Skull Base Surgery
ClinicalTrials.gov study NCT01591954. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study to Evaluate the Effect of VX-661 in Combination With Ivacaftor on Chest Imaging Endpoints in Subjects With Cystic Fibrosis, Homozygous for the F508del CFTR Mutation
ClinicalTrials.gov study NCT02730208. IPD Sharing: Not stated. Countries: 1. Publications: 0.
PET/CT Imaging Companion Study To ACTG A5314
ClinicalTrials.gov study NCT02312219. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.