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996 results for “mouse brain”
Data from: An experimental platform for stochastic analyses of single serotonergic fibers in the mouse brain
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Predicting the distribution of serotonergic axons: A supercomputing simulation of reflected fractional Brownian motion in a 3D-mouse brain model
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Data and code for: Spatial cell type enrichment predicts mouse brain connectivity
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BIDS-formatted example mouse brain data for SAMRI
<p>BIDS-formatted Magnetic Resonance Imaging mouse brain data example used in the SAMRI test suite.</p>
Data sets comparing Ca(2+) dynamics in whole-cell and β-escin-based perforated patch clamp recordings in adult mouse brain slices.
<p># Hess-et-al-beta-escin-2020<br> Data of the "Data in Brief" article concerning the added buffer approach with beta-escin perforated patch.</p> <p>A joint work by: Simon Hess (`simon.hess@uni-koeln.de`), Christophe Pouzat (`christophe.pouzat@math.unistra.fr`), and Peter Kloppenburg (`peter.kloppenburg@uni-koeln.de`).</p> <p>## Content</p> <p>This repository contains:</p> <p>- Directory `data_whole_cell` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the whole-cell configuration.<br> - Directory `data_beta_escin` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the β-escin perforated patch clamp configuration.</p>
Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease
<p>Connectome, traits and behavior data for APOE234 mice.</p> <ul> <li>1. connectome.zip: mouse brain structural connectivity matrices from diffusion MRI.</li> <li>2. FAGNN_Phenotype.csv: a sheet of trait information of mice used in the study.</li> </ul> <p>columns: winding numbers, total distance, normalized NE time, normalized NE distance, normalized NW time, normalized NW distance, normalized SE time, normalized SE distance, normlaized SW time, normalized SW distance, island latency to first entry, island entries, normalized thigmataxis time, and normalized thigmotaxis distance</p> <div>rows: 4 trials for each day from day 1 to day 5 with 1 probing test each at day 5 and day 8</div> <ul> <li>3. mouse_anatomy.csv: brain region information regarding the connectivity matrix.</li> <li>4. behavior.zip: behavioral data for each mouse from Morris Water Maze experiments.</li> </ul>
Raw data for "Deep mouse brain two-photon near-infrared fluorescence imaging using a superconducting nanowire single-photon detector array"
<p>Two-photon microscopy (2PM) has become an important tool in biology to study the structure and function of intact tissues in-vivo. However, adult mammalian tissues such as the mouse brain are highly scattering, thereby putting fundamental limits on the achievable imaging depth, which typically resides around 600-800um. In principle, shifting both the excitation as well as (fluorescence) emission light to the shortwave near-infrared (SWIR, 1000-1700 nm) region promises substantially deeper imaging in 2PM, yet has proven challenging in the past due to the limited availability of detectors and probes in this wavelength region. To overcome these limitations and fully capitalize on the SWIR region, in this work we introduce a novel array of superconducting nanowire single-photon detectors (SNSPDs) and associated custom detection electronics for the use in near-infrared 2PM. The SNSPD array exhibits high efficiency and dynamic range, as well as low dark-count rates over a wide wavelength range. Additionally, the electronics and software permit seamless integration into typical 2PM systems. Together with a fluorescent dye emitting at 1105 nm, we report imaging depth of > 1.1mm in the in-vivo mouse brain, limited only by available labeling density and laser power. Our work further establishes SWIR 2PM approaches and SNSPDs as promising technologies for deep tissue biological imaging. </p>
Developmental Mouse Brain scRNAseq Giotto Object
<p>Giotto object created from the single cell mouse brain atlas dataset from <a href="https://www.nature.com/articles/s41586-021-03775-x">Manno et al. 2021</a> (https://doi.org/10.1038/s41586-021-03775-x). This object contains expression information and cell annotations of developmental mouse brain cell types that are used with spatial DWLS deconvolution of Stereo-seq data in the Giotto Suite manuscript.</p> <p>The original data was downloaded from <a href="http://mousebrain.org/development/downloads.html">http://mousebrain.org/development/downloads.html </a>as a .loom file, and then loaded into Giotto.</p>
Cleared YFP-mouse brain using the PRIAMOS-clearing-method
<p>Image stack of confocal images from a cleared mouse brain (Thy1-YFP-16 , Jackson, Strain #:003709) using the PRIAMOS-method for clearing. Data contains the original Leica-format ('LIF') including all original data with the metadata, and an exported stack with 16-bit tif-images. The LIF-files can be opened using the older "LAS AF light" software, or the current software "LAS X office" from Leica Inc. Alternatively, an exported image stack of tif-images is in a zip-archive. (voxel-size: 0.11 x 0.11 x 1um^3, objective lens: HCX APO L 20x/0.95 IMM, Pinhole: 1AU)</p>
Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain
<p><span>Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action.</span></p>
Serial Coronal Sections Of An Adult Mouse Brain - Sample Dataset
<p>Experimental data: serial coronal sections of the brain of an adult mouse.</p> <p>20 um brain sections sampled every 80 um, imaged on an Olympus VS120 slide scanners with a 10x objective</p> <p>Contains label and overview images and 3 fluorescent channels:</p> <ul> <li>DAPI channel, cell nuclei</li> <li>FITC channel, autofluorescence</li> <li>Cy3 channel, fluorescent sparse mCherry labelled cells</li> </ul> <p>This dataset can be used as a test dataset for the <a href="https://biop.github.io/ijp-imagetoatlas/">Aligning Big Brain and Atlases</a> tool.</p> <p>Animal handling according to protocols approved by the Swiss animal license VD2808.2</p> <p>Two zipped QuPath project that are using the OMERO extension are also provided. One contains the full 97 section dataset, one contains a subset of 25 sections. These data are present in the German BioImaging public OMERO instance (<a href="https://omero-tim.gerbi-gmb.de">https://omero-tim.gerbi-gmb.de</a>).</p> <p> </p> <p> </p>
Ultra-high-resolution diffusion MRI atlas of CD1 embryonic mouse brains at E10.5-E15.5.
<p>This dataset is assciated with the paper "A Spatiotemporal Continuum of Embryonic Mouse Brain Development Built on Diffusion MR Microscopy for Probing Dynamic Gene-Neuroanatomy" on PNAS. For each stage, average FA (fractional anisotropy) and DEC (directionally encoded colormap) images (n=5) are provided. <br> <br> </p>
Multi-contrast MRI and histology datasets used to train and validate MRH networks to generate virtual mouse brain histology
<p><span>H MRI maps brain structure and function non-invasively through versatile contrasts that exploit inhomogeneity in tissue micro-environments. Inferring histopathological information from MRI findings, however, remains challenging due to absence of direct links between MRI signals and cellular structures. Here, we provided deep convolutional neural networks, called MRH-Nets, developed using co-registered multi-contrast MRI and histological data of the mouse brain, can estimate histological staining intensity directly from MRI signals at each voxel. The results provide three-dimensional maps of axons and myelin with tissue contrasts that closely mimics target histology and enhanced sensitivity and specificity compared to conventional MRI markers. </span><span> </span>The dataset contains multi-contrast MRI and histology used for the training and testing and the acquisition parameters. The datasets have been carefully registered to mouse brain images from the Allen Mouse Brain Atlas (https://mouse.brain-map.org). The source codes for MRH-Nets can be found at <a href="https://github.com/liangzifei/MRH-Net">https://github.com/liangzifei/MRH-Net</a>.</p>
Impact of CD4 T cells on intratumoral CD8 T cell exhaustion and responsiveness to PD-1 blockade therapy in mouse brain tumors
<p>scRNA-seq data (Cellranger filtered feature-barcode matrices) and scVDJ-seq data (Cellranger filtered_contig_annotations.csv files) for publication listed above.</p>
Mouse Brain snRNASeq Demo Dataset for Cellxgene VIP
<p>snRNASeq data generated at Biogen from 3 control mouse brains. Each brain picked 3 brain regions.</p> <p>Animal IDs 1, 4 and 7</p> <p>Brain region codes:<br> W: WhiteMatter<br> H: Hippo<br> G: GreyMatter</p> <p>10X standard mm10 (3.0.0) reference was used, on cellranger 5.0.0 with --include-introns on.<br> </p>
Mouse Brain Visium Demo Dataset for Cellxgene VIP
<p>Visium data generated from 3 control mouse full half brains</p> <p>Animal IDs 13, 14 and 53</p> <p>10X standard mm10 (2020-A) reference and spaceranger 1.1.0 was used<br> </p>
Mouse Brain snRNASeq and Visium Demo Dataset for CelEry
<p>## snRNASeq data generated from control mouse brain 3 brain regions.</p> <p>Animal IDs 7</p> <p>Brain region codes:<br> 7W-1: WhiteMatter<br> 7H-1: Hippo<br> 7G-1: GreyMatter</p> <p>10X standard mm10 (3.0.0) reference was used, on cellranger 5.0.0 with --include-introns on.</p> <p><br> ## Visium data generated from the same animal control mouse full half brains</p> <p>Animal IDs 14 (075B slice)</p> <p>10X standard mm10 (2020-A) reference and spaceranger 1.1.0 was used<br> </p>
Proximity labeling of tau interactions in primary neurons and mouse brain
<p><span>Microtubule-associated protein tau is a central factor in Alzheimer's disease and other tauopathies. However, physiological functions of tau are unclear. Here, we used proximity labelling proteomics to chart functional tau interactomes in primary neurons and mouse brai<span>n <span>in vivo</span></span><span>. Here, we use proximity labelling with the biotin ligase BioID2 to map interactomes of tau in neurons. Data sets relate to mass spectrometry and protein identification of biotinylated proteins in primary neurons and in mouse brain after delivery of BioID2-tau fusion protein or BioID2 control protein by adeno-associated virus (AAV). Mouse brain samples are either from P35 wild-type mice with intracranial AAV delivery at P0 or from tau knockout mice at P60 after hippocampal delivery of AAV. Details on BioID2 fusion protein expression, biotin supplementation and sample extraction can be obtained in the associated publication.<br></span></span></p>
Xenium benchmarking- xenium formatted to AnnData 1 (mouse_brain)
<p>This repository contains Xenium datasets formated to AnnData format for benchmarking the characteristics and performance of Xenium (Marco Salas et al., 2024). Please visit https://github.com/Moldia/Xenium_benchmarking to obtain further information about the datasets. On summary, AnnData contains the expression of profiled cells with some metadata, including spatial position. In adata.obs['spots'] we also include the position of decoded reads as well as some additional metadata and quality. </p> <p> </p> <p>This repository is the part 1/4 of all repositories containing the datasets used in the study already formated to AnnData</p>
Mini In Situ Sequencing mouse brain dataset using Cartana technology
<div> <div> <div> <p>A subset of an ISS dataset is being utilized here to showcase the data format without replicating the ISS decoding procedure (for this first version).</p> <p>There are in total 3 data objects:</p> <ol> <li>A 5-channel raw microscope image</li> <li>The corresponding single cell segmentation image (label image)</li> <li>The correspdoning single-cell gene expression data object (.h5ad)</li> </ol> </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.