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60
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ShareScore release 0.9.0
Dataset results
60 results for “whole-brain”
Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI
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Whole-brain background-suppressed pCASL MRI with 1D-accelerated 3D RARE Stack-Of-Spirals Readout- Dataset 2
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Whole-brain background-suppressed pCASL MRI with 1D-accelerated 3D RARE Stack-Of-Spirals Readout- Dataset 3
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BIDS Data for "A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation"
<p>Base data package for the “"A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation” article, formatted corresponding to the Brain Imaging Data Structure.</p>
Data set for "Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas"
<p>Data set for: Liu Y, Foustoukos G, Crochet S and Petersen CCH (2022) Axonal and dendritic morphology of excitatory neurons in layer 2/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas. Front Neuroanat 15: 791015. https://doi.org/10.3389/fnana.2021.791015</p> <p>There are 2 files in this upload:</p> <p>1. The file named "<strong>2022_Liu_FrontNeuroanat.pdf</strong>" is the Open Access pdf of the online publication in Frontiers in Neuroanatomy.</p> <p>2. The file named "<strong>Liu_data_code.zip</strong>" (~1 GB) is a zipped version of a folder ‘<em>Liu_data_code</em>’, which contains the data analyzed in the study along with the Python codes used to generate the published figures. The original high resolution image stacks obtained through whole-brain two-photon serial tomography are unfortunately too large for Zenodo, and only highly-downsampled data are included in this upload, which were used for registration with the Allen CCFv3. Instructions on how to view and analyse the anatomical data are provided in the 'README.docx' file, which you will find upon unzipping the folder.</p> <p> </p>
Quail (Coturnix japonica) brain MRI template and whole-brain atlas
<p>A population average MRI brain template computed from 20 male Japanese Quails and a manually segmented atlas containing 194 regions. </p> <p>In this Version 2:</p> <ul> <li>the nomenclature in the file <em>siwiaszczyk_LUT-ITK-SNAP_v2.txt</em> was updated</li> <li>one slice of one region was completed in the file <em>siwiaszczyk_atlas_v2.nii.gz.</em></li> </ul>
Data from: Whole-brain spatial organization of hippocampal single-neuron projectomes
<p>Mapping hippocampal single-neuron projections is essential for understanding brain-wide circuit organization and diverse functions of the hippocampus, a brain structure underlying episodic memory and cognition. Here, we reconstructed 10,100 single-neuron projectomes of the mouse hippocampus, identified rostral and caudal axon pathways that preferentially innervated cortical vs. subcortical areas, and classified 43 projectome subtypes with distinct axon targeting patterns. Notably, the soma locations along hippocampal longitudinal and transverse axes determined the number of their target areas and the spatial distribution and complexity of their axon arbors within the targets. We defined selective hippocampal subdomains based on spatial transcriptomic profiles and found that many projectome subtypes were enriched in specific subdomains. Next, we defined the wiring diagram for hippocampal neurons exclusively projecting to hippocampal formation (HPF) and those projecting to both intra- and extra-HPF targets with coordinated projection strengths. Furthermore, bi-hemispheric projecting hippocampal neurons generally projected to one pair of homologous targets with ipsilateral preference. These organization principles of single-neuron projectomes provide a structural basis for understanding diverse but coordinated functions of hippocampal neurons.</p>
FlyWire: Online community for whole-brain connectomics
<p>A ground truth dataset for 3D neuron reconstruction from electron microscopy (EM) images of the fly whole-brain, created for our project FlyWire: A human-AI collaboration to map the fly connectome. For more information, please visit <a href="https://flywire.ai/">https://flywire.ai/</a>.</p> <p> </p> <p><strong>Citation</strong></p> <p><em>FlyWire: Online community for whole-brain connectomics</em><br> Dorkenwald et al.<br> bioRxiv 2020.08.30.274225; doi: https://doi.org/10.1101/2020.08.30.274225</p> <p> </p> <p><strong>Dataset description</strong></p> <ul> <li><strong>cremi_realigned.tar.gz</strong> <ul> <li>cremi_{a,b,c}_realigned.h5: re-aligned CREMI volumes (<a href="https://cremi.org/">https://cremi.org/</a>)</li> <li>cremi_b_realigned_new.h5: re-aligned CREMI B volume with de-novo annotation</li> </ul> </li> <li><strong>focused.tar.gz</strong> <ul> <li>A set of densely annotated volumes covering diverse structures in the fly brain that are underrepresented in the CREMI volumes.</li> </ul> </li> <li><strong>sparse.tar.gz</strong> <ul> <li>A set of sparsely annotated volumes covering tricky failure modes in the initial segmentation attempt. Here intracellular structures are often oversegmented conservatively to prevent merge errors at the expense of introducing some split errors. </li> </ul> </li> <li><strong>glia.tar.gz</strong> <ul> <li>Semi-automatically generated ground truth for glia detction. A set of subvolumes from the FlyWire segmentation was sampled from which human experts classified automatically generated segments into either neurons or glia, while existing merge errors were excluded from annotation.</li> </ul> </li> </ul>
Data from: Direct segmentation of cortical cytoarchitectonic domains using ultra-high-resolution whole-brain diffusion MRI
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Whole-brain mapping in adult zebrafish and identification of the functional brain network underlying the novel tank test
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Data from: Whole-brain spatial organization of hippocampal single-neuron projectomes
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[Dataset for] Whole-brain meso-vein imaging in living humans using fast 7 T MRI
<p>This dataset is associated with:</p> <ul> <li>Gulban, Stirnberg, Tse, Pizzuti, Koiso, Archila-Melendez, Huber, Bollmann, Goebel, Kay, Ivanov, 2025. Whole-brain meso-vein imaging in living humans using fast 7 T MRI (Preprint).</li> </ul> <p>This dataset is also used in:</p> <ul> <li>Pizzuti, Bazin, Ivanov, Dresbach, Peter, Goebel, Gulban, 2024. Multimodal laminar characterization of visual areas along the cortical hierarchy (Preprint).</li> </ul> <p>More data are going to be be added as we progress with our manuscripts though their publications or upon request (please contact Omer Faruk Gulban).</p>
Data from: In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution (PART I)
<p>This whole-brain in vivo diffusion MRI dataset was acquired at 760 µm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. It was acquired using state-of-the-art acquisition hardware and advanced reconstruction to achieve high SNR at such resolution, including a high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition, and parallel imaging reconstruction with advanced ghost reduction algorithms. With its unprecedented high resolution, SNR and image quality, it could help explore the fine-scale structures of in vivo human brain, and further advance the understanding of human brain connectivity. This dataset can also be used as a test bed for further technical development of new modeling, sub-sampling strategies, denoising and processing algorithms for in vivo high resolution dMRI. Whole brain anatomical T<sub>1</sub>-weighted and T<sub>2</sub>-weighted images at submillimeter scale, field maps and the code for preprocessing pipeline are also made available in the repository.</p>
Whole-Brain 3D MRF and MRI Multi-Scanner, Scan-Rescan Dataset at 3T
<p>This repository contains a multi-scanner, scan-rescan dataset comprising thirty (30) whole-brain 3D MRI acquisitions. Each scan acquisition (n = 30) includes whole-brain quantitative MRI maps (MRF T1, MRF T2, and ADC) and weighted MR images (T1w MPRAGE, T2w SPACE, and T2w FLAIR). Five healthy subjects (deidentified) were scanned over three scanners (all 3T field strength). Each subject was scanned twice per scanner, for a total of 30 scans (5 subjects × 3 scanners × 2 scans). All data was acquired at University Hospitals Cleveland Medical Center and Case Western Reserve University.</p> <p> </p> <p>This dataset was used in the analysis for the following research article published in Investigative Radiology: "<strong><a href="https://journals.lww.com/investigativeradiology/fulltext/9900/physics_informed_discretization_for_reproducible.159.aspx">Physics-Informed Discretization for Reproducible and Robust Radiomic Feature Extraction Using Quantitative MRI</a></strong>" and request this article be referenced in all research works that use this dataset.</p>
Stereotactic Radiation Therapy With or Without Whole-Brain Radiation Therapy in Treating Patients With Brain Metastases
ClinicalTrials.gov study NCT00377156. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Memantine in Preventing Side Effects in Patients Undergoing Whole-Brain Radiation Therapy for Brain Metastases From Solid Tumors
ClinicalTrials.gov study NCT00566852. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Avoiding the Hippocampus During Whole-Brain Radiation Therapy in Treating Patients With Brain Metastases
ClinicalTrials.gov study NCT01227954. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Stereotactic Radiosurgery or Whole-Brain Radiation Therapy in Treating Patients With Brain Metastases That Have Been Removed By Surgery
ClinicalTrials.gov study NCT01372774. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Whole-Brain Radiation Therapy or Stereotactic Radiosurgery With or Without Lapatinib Ditosylate in Treating Patients With Brain Metastasis From HER2-Positive Breast Cancer
ClinicalTrials.gov study NCT01622868. IPD Sharing: Not stated. Countries: 3. Publications: 0.
Whole-Brain Radiation Therapy With or Without Hippocampal Avoidance in Limited Stage or Extensive Stage Small Cell Lung Cancer
ClinicalTrials.gov study NCT02635009. IPD Sharing: Not stated. Countries: 2. Publications: 2.
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.