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74 results for “Vascular imaging”
Datasets of Vascular Networks Extracted from Retinal Images of Hypertensive Retinopathy and Glaucoma Patients
<p>This dataset contains high resolution images of blood vessels extracted from Digital Retinal Images for Optic Nerve Segmentation Database (DRIONS-DB). It contains 110 blood vessels of individuals of which 23.1% are patients with chronic glaucoma while the remaining 76.9% are hypertensive retinopathy patients. </p>
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d).
Text-fig. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f).
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g).
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>
Data from: Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease
Open the record for dataset details and reuse information.
Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT
<p>µCT dataset of a mouse kidney injected with contrast agent XlinCA and scanned with 3.3 µm voxel size. Detailed sample preparation and image acquisition protocols are published as <a href="https://doi.org/10.1017/S1431927620001725">"Simultaneous three-dimensional vascular and tubular imaging of whole mouse kidneys with X-ray µCT"</a> in <em>Microscopy and Microanalysis</em>.</p> <p>Segmentations of the vascular and tubular lumina along with the renal tissue are provided as masks. The three different segmented features were combined into a single dataset and encoded as different gray values:</p> <p>0: Background<br> 51: Tubules<br> 204: Tissue<br> 255: Blood vessels</p> <p>The Supplemental Video features a computer graphics visualization of the segmented masks. Blood vessel lumina are rendered in red, tissue in transparent blue and tubular lumina in yellow.</p>
Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer
<p>All data supporting the publication: "Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer."</p><p>1. Fully_Processed_OME.TIFF: This folder contains the OME.TIFF files with all markers after compensation and hot pixel removal for visualization of the data. These can be opened with QuPath and other software. </p><p>2. PDAC_IMC_Seurat_FINAL.rds: Seurat object of all cells included in the analysis with cell type and neighborhood annotations, and unintegrated and rPCA-integrated UMAP reductions. </p><p>3. Raw_Data_TIFF_Files: All raw individual TIFF files from the image acquisition</p><p>4. ROI_Selection: Brightfield and IHC images of individual samples showing where the ROIs for each sample are collected </p><p>5. Segmentation_Files: All relevant segmentation files from Mesmer for nuclear and whole cell segmentation. </p><p>6. H&E Images for each case scanned at 40x </p>
REAVER Vascular Networks Fluorescent Image Dataset
<p><strong>Fluorescent Images of Vessel Networks from Various Murine Tissues</strong></p> <p> </p> <p><strong>Purpose</strong>: Image dataset of vascular networks with a diverse range of vessel architectures. Dataset is used to evaluate performance of several image processing programs (AngioQuant<sup>1</sup>, AngioTool<sup>2</sup>, RAVE<sup>3</sup>, REAVER). Manual analysis from ImageJ is used as ground truth to compare other programs against.</p> <ul> <li><strong>Labeling</strong>: IB4-Lectin with Alexa Flour 647</li> <li><strong>Modality</strong>: Confocal Microscope Nikon 80i CLSM</li> <li><strong>Objective</strong>: Mixture of 20x and 60x objective images</li> <li><strong>Image Format</strong>: Images originally acquired in Nikon IDS format, converted to 8-bit greyscale TIFs found in “_Original_Images” folder.</li> <li><strong>Questions</strong>: Email <a href="mailto:bac7wj@virginia.edu">bac7wj@virginia.edu</a> for inquiries.</li> </ul> <p> </p> <p><strong>External Links</strong></p> <ol> <li><strong>Manuscript</strong>:</li> <li><strong>Code repository: </strong><a href="https://github.com/bacorliss/REAVER_public">https://github.com/bacorliss/REAVER_public</a> for code to analyze this data (MATLAB 2019a).</li> </ol> <p> </p> <p><strong>Dataset Summary:</strong></p> <p>Each image folder contains 36 images. For each image:</p> <ol> <li>The first channel (red) is the segmented image with values of 0 or 255 (false or true).</li> <li>The second channel (green) is the skeleton image with values of 0 or 255 (false or true).</li> <li>The third channel (blue) is empty except for the Manual images where the third channel contains the original raw image.</li> </ol> <p> </p> <p><strong>Subfolders</strong></p> <ol> <li><strong>_Original_Images</strong>: contains raw input images.</li> <li><strong>AngioQuant_Auto</strong>: contains output images from automated analysis in AngioQuant.</li> <li><strong>AngioTool_Auto</strong>: contains output images from automated analysis in AngioTool.</li> <li><strong>ImageJ_Auto</strong>: contains output images from automated analysis in ImageJ.</li> <li><strong>ImageJ_Manual</strong>: contains output images from manual analysis in ImageJ.</li> <li><strong>RAVE_Auto</strong>: contains output images from automated analysis in RAVE.</li> <li><strong>REAVER_Auto</strong>: contains output images from automated analysis in REAVER.</li> </ol> <p> </p> <p><strong>Image Metadata and Output data</strong></p> <p>Each image folder has a .mat file called “Results.mat” containing the results of analysis in the form of the following variables all of which are 1x36 arrays (one entry for each image) unless specified otherwise:</p> <ol> <li><strong>branchpoint_RC</strong>: A 1x36 struct containing the row-column values for each branchpoint in the i<sup>th</sup> image (when organized in alphabetic order which is the order given everywhere else); Effectively the same as “BranchpointsByName.mat”</li> <li><strong>mean_diameter</strong>: The mean diameter of vessels in the image</li> <li><strong>num_branchpts</strong>: The number of branchpoints in the image</li> <li><strong>threshold_false_neg</strong>: The number of false negative pixels – a pixel is a false negative if the program has it as “false” and the manual image has the pixel as “true”</li> <li><strong>threshold_false_pos</strong>: The number of false positive pixels – a pixel is a false positive if the program has it as “true” and the manual image has the pixel as “false”</li> <li><strong>threshold_true_neg</strong>: The number of true negative pixels – a pixel is a true negative if the program has it as “false” and the manual image has the pixel as “false”</li> <li><strong>threshold_true_pos</strong>: The number of true positive pixels – a pixel is a false positive if the program has it as “true” and the manual image has the pixel as “true”</li> <li><strong>umppix</strong>: The length of the edge of one pixel in micrometers</li> <li><strong>vessel_area</strong>: The number of “true” pixels in the segmented image</li> <li><strong>vessel_length</strong>: The number of “true” pixels in the skeleton image</li> </ol> <p> </p> <p><strong>Dataset Output Data</strong></p> <p>The file “image_quantification.csv” in the base folder contains the aggregated results from each image folder. Each row contains the results for a given (Program, Image) pair. The columns are described below:</p> <ol> <li><strong>Program</strong>: Designates the program used to calculate the data for that row</li> <li><strong>Tissue_Type</strong>: Gives the tissue type for the image</li> <li><strong>Image_Name</strong>: Gives the specific name of the given image</li> <li><strong>Vessel_Length</strong>: The number of “true” pixels in the skeleton image</li> <li><strong>Vessel_Area</strong>: The number of “true” pixels in the segmented image</li> <li><strong>Mean_Diameter</strong>: The mean diameter of vessels in the image</li> <li><strong>Num_Branchpoints</strong>: The number of branchpoints in the image</li> <li><strong>Sensitivity</strong>: (Number of True Positive pixels) / (Number of True Positive pixels + Number of False Negative pixels)</li> <li><strong>Specificity</strong>: (Number of True Negative pixels) / (Number of True Negative pixels + Number of False Positive pixels)</li> <li><strong>Accuracy</strong>: (Number of True Positive pixels + Number of True Negative pixels) / (Total number of pixels)</li> <li><strong>umppix</strong>: The length of the edge of one pixel in micrometers</li> <li><strong>pix_dim</strong>: The edge length in pixels of the square image</li> </ol> <p> </p> <p><strong>References</strong></p> <p>1. Niemisto, A., Dunmire, V., Yli-Harja, O., Wei Zhang & Shmulevich, I. Robust quantification of in vitro angiogenesis through image analysis. <em>IEEE Trans. Med. Imaging</em> <strong>24</strong>, 549–553 (2005).</p> <p>2. Zudaire, E., Gambardella, L., Kurcz, C. & Vermeren, S. A Computational Tool for Quantitative Analysis of Vascular Networks. <em>PLOS ONE</em> <strong>6</strong>, e27385 (2011).</p> <p>3. Seaman, M. E., Peirce, S. M. & Kelly, K. Rapid Analysis of Vessel Elements (RAVE): A Tool for Studying Physiologic, Pathologic and Tumor Angiogenesis. <em>PLoS ONE</em> <strong>6</strong>, e20807 (2011).</p>
Optical Frequency Domain Imaging (OFDI) and Vascular Healing After Stent Placement
ClinicalTrials.gov study NCT01794949. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Targeted PET/CT and PET/MRI Imaging of Vascular Inflammation
ClinicalTrials.gov study NCT02995642. IPD Sharing: NO. Countries: 1. Publications: 2.
Vascular Inflammation Imaging Using Somatostatin Receptor Positron Emission Tomography
ClinicalTrials.gov study NCT02021188. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Diagnostic Imaging of Vascular Malformations Using MSOT and ULM
ClinicalTrials.gov study NCT06994260. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Cerebral Vascular Malformations: From Multimodal Imaging, to Endovascular, Surgical or Combined Treatment
ClinicalTrials.gov study NCT05729295. IPD Sharing: NO. Countries: 1. Publications: 1.
The Process of Blood Collection With a Vascular Imaging Device
ClinicalTrials.gov study NCT05678504. IPD Sharing: NO. Countries: 1. Publications: 10.
VIP: Vascular Imaging Project. Study on the Progression of Cardiovascular Disease in Renal Transplant Recipients
ClinicalTrials.gov study NCT00169910. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Amyloid and Glucose PET Imaging in Alzheimer and Vascular Cognitive Impairment Patients With Significant White Matter Disease
ClinicalTrials.gov study NCT02330510. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Vascular Endothelial Growth Factor (VEGF) Imaging Before and During Everolimus Treatment for Renal Cell Carcinoma
ClinicalTrials.gov study NCT01028638. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Investigation of Vascular Inflammation in Migraine Using Molecular Nano-imaging and Black Blood Imaging MRI
ClinicalTrials.gov study NCT02549898. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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.