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996 results for “mouse brain”
Cellular-resolution X-ray microtomography of an entire mouse brain: supporting data, scripts and parameters
<h2><strong>Abstract </strong></h2> <p><strong>Purpose:</strong> Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge.</p> <p><strong>Approach:</strong> Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 × 8 offset acquisitions were stitched to reconstruct a 15,000^3 voxel volume. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs.</p> <p><strong>Results: </strong>We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 μm voxel size. The data were block-wise transformed to a common coordinate system then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer.</p> <p><strong>Conclusions:</strong> This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers.</p> <h2>Data</h2> <p>File <code>b32_atlas_registration.zip</code> contains the input data, parameter files and output data of affine and non-rigid registration of the 32 x 32 x 32 voxels downsampled microtomography image to the Allen Mouse Brain Common Coordinate Framework v3.</p> <p>File <code>create_sharded_Neuroglacer_format.pdf</code> will provide instructions how to create gZip-compressed, sharded, pre-computed Neuroglancer format via the open source software <a href="https://github.com/seung-lab/igneous">igneous</a>. This is currently still missing.</p> <h2>Processing</h2> <p>Reconstruction of extended field microtomography images mit projection stitching in horizontal and vertical direction was achieved with our software pipeline <a href="https://github.com/unibas-bmc/mosaicreconstruction">mosaicreconstruction</a>.</p> <p>The 32 x 32 x 32 voxels downsampled microtomography image was registered with the open source software <a href="https://elastix.lumc.nl/">elastix (and transformix)</a>. The <code>elastix.log</code> file states the used command line options. Directory names require adapting for reproducing the results. </p> <p>As terabyte large images and the non-rigid transformation parmeters do not fit into memory, we developed a distributed hierarchical approach with sub-volume transformations for the high resolution level, see <a href="https://github.com/unibas-bmc/LargeVolumeTransformix">LargeVolumeTransformix</a>. The high resolution tomography volume (moving volume) was warped to the atlas (fixed volume) by dividing the fixed space into 12 × 12 × 12 target subregions, such that the axes-aligned extended moving image subregion, the moving image transformed subregion, and the transformation parameters all fit in memory for an isotropic target voxel resolution of 0.65 μm.</p>
Phosphorylated mTOR targets in the E13.5 mouse brain
<p>Staining of p-S6 S240/244 and p-4EBP1/2 T37/46 in embryonic day 13.5 whole mouse brain, cleared using iDISCO+ </p>
Anndata object of 10x Mouse Brain 5k data set for scDGD training
<p>This data from 10x (5k Adult Mouse Brain Nuclei Isolated with Chromium Nuclei Isolation Kit, Single Cell Gene Expression Dataset by Cell Ranger 7.0.0, 2022) is comprised of 7377 cells from the adult mouse brain with 32285 features. Cell type annotations were approximated using CellTpyist with the `Developing_Mouse_Brain` reference model and majority voting. This resulted in 7 distinct cell types.</p>
NEATmap: a high-efficiency deep learning approach for whole mouse brain neuronal activity trace mapping
<p>Here are some demo datasets for validating the NEATmap pipeline for high-efficiency whole brain c-Fos<sup>+</sup> cell automated segmentation and quantitative analysis, including:</p> <ol> <li>BrainImage_group.zip.001-007: Validation of NEATmap for automated segmentation and quantitative analysis of mouse whole-brain c-Fos activity images (in Forced Swimming Test).</li> <li>Segmentation_result.zip: Figure 1a, Supplementary Videos 1 and 2 show dual-channel brain slices and segmentation results. They can be merged using Imaris to validate the segmentation results of NEATmap.</li> <li>RawImage_example.zip: High-resolution 3D images of mouse brain slices showing c-Fos<sup>+</sup> cells in Figure 1e.</li> </ol> <p>Due to the total size of the mouse whole-brain image datasets (both raw and processed) included in all the tests exceeding 10 Terabytes, uploading it to a public data repository is impractical. In this work, we provide a dataset of dual-channel (c-Fos<sup>+</sup> channel and autofluorescence channel in forced swimming test experimental group) whole-brain images of mouse for the validation of NEATmap automated segmentation method.</p>
Neual activities of 126 mouse brain areas under itch-scratching cycles
<p>The data in a Cell Report paper: "An Atlas of Itch-associated Neural Dynamics in the Mouse Brain".</p> <p>The paper will be online about on Nov 1st, 2023.</p>
Multi-contrast MRI and histology datasets used to train and validate MRH networks to generate virtual mouse brain histology
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Proximity labeling of tau interactions in primary neurons and mouse brain
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Data from: Isoflurane anesthesia alters <sup>31</sup>P magnetic resonance spectroscopy markers compared to awake mouse brain
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3D dataset of tissue cleared MADM mouse brain
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Data from: Sex-specific developmental alterations in DYRK1A expression in the brain of a Down syndrome mouse model
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Sex‐dimorphic effects of biogenesis of lysosome‐related organelles complex‐1 deficiency on mouse perinatal brain development
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mouse brain sagittal
Drawing uploaded to scidraw.io on: 28 May 2020
mouse head brain
Drawing uploaded to scidraw.io on: 28 May 2020
mouse head brain
Drawing uploaded to scidraw.io on: 28 May 2020
Automated identification of the mouse brain's spatial compartments from in situ sequencing data
<p>Example data [1] for testing in situ sequencing graph-based decoding pipeline and decoding results for reproducing publication analyses. Image decoding pipeline and notebooks are available at: <a href="https://github.com/wahlby-lab/graph-iss">https://github.com/wahlby-lab/graph-iss</a></p> <p>------------</p> <p>[1] Ke, Rongqin, et al. "In situ sequencing for RNA analysis in preserved tissue and cells." <em>Nature methods</em> 10.9 (2013): 857.</p>
Decreased content of ascorbic acid (vitamin C) in the brain of knockout mouse models of Na+, K+- ATPase-related neurologic disorders
<p><strong><span><span><span><span><span><span><span><span><span><span><span>Raw data, a2Ca3-dKO phenotype and dystonic spell of a3-HT</span></span></span></span></span></span></span></span></span></span></span></strong></p> <p><strong><span><span><span><span><span><span><span><span><span><span><span>We found brain haemorrhage phenotype of Atp1a2 and Atp1a3 doule knockout (α2α3-dKO) foetuses. Here we present two kinds of α2α3-dKO line, α2-Nα3-dKO andα2-Cα3-dKO, both show brain haemorrhage upon birth. They were similar to that of homozygous knockout of the gene encoding ascorbic acid (ASC orNvitamin C) transporter, SVCT2 (SVCT2-KO). We made SVCT2-knockout mouse line by CRIPR/CAS9 method. We present SVCT2-KO, showing brain hemorrage as α2α3-dKO. The α2α3-dKO and SVCT2-KO brain showed significantly decreased level of ASC compared with the wild-type (WT) and single knockout (here, raw data). We found that the ASC content in the basal ganglia and cerebellum was significantly lower in the adult <i>Atp1a3 </i>heterozygous knockout mouse (α3-HT) than in the WT (here, raw data). We did not observe increased oxidative stress in them (here raw data). Interestingly, we observed a significant decrease in the ASC level in the basal ganglia and cerebellum of α3-HTin the peripartum period, during which mice are under physiological stress(here, raw data). Here, we show dystonic spell of α3-HT in peripartum. These observations indicate that the α2 and α3 subunits independently contribute to the ASC level in the foetal brain and that the α3 subunit contributes to ASC transport in the adult basal ganglia and cerebellum. We propose that decreases in ASC levels may affect neural network development and are linked to the pathophysiology of <i>ATP1A2- </i>and <i>ATP1A3</i>-related neurologic disorders.</span></span></span></span></span></span></span></span></span></span></span></strong></p>
Human umbilical cord mesenchymal stem cell-derived exosomes combined with mouse nerve growth factor can more effectively ameliorate the motor disorder and brain pathological injury in mice with cerebral palsy
<p>Supplementary Table 1.The statistics of the pole-climbing experiments and the horizontal network test</p> <p>Supplementary Table 2.Results of Kruskal–Wallis test as presented in pole-climbing experiments and the horizontal network test.</p> <p>Supplementary Figure 1. Identification of human umbilical cord mesenchymal stem cell exosomes (hUC-MSCs-exos)</p> <p>Supplementary Figure 2. Results of horizontal network test and pole-climbing experiments.</p> <p> </p>
Human umbilical cord mesenchymal stem cell-derived exosomes combined with mouse nerve growth factor can more effectively ameliorate themotor disorder and brain pathological injury inmice with cerebral palsy
<p>This research design.</p>
Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain
<p>Previously, we showed that cholinergic interneurons of the dorsal striatum lose cilia in mice harboring the Parkinson's disease associated, kinase activating, R1441C LRRK2 mutation (<a href="https://www.biorxiv.org/content/10.1101/2021.03.02.433576v1#ref-8">Dhekne et al., 2018</a>). Here we show that this phenotype is also seen in two mouse strains carrying the most common human G2019S LRRK2 mutation. Heterozygous loss of the PPM1H phosphatase that is specific for LRRK2-phosphorylated Rab GTPases (<a href="https://www.biorxiv.org/content/10.1101/2021.03.02.433576v1#ref-3">Berndsen et al., 2019</a>) yields the same cilia loss phenotype, strongly supporting a connection between Rab GTPase phosphorylation and cilia loss. In addition, astrocytes throughout the striatum show a ciliation defect in LRRK2 and PPM1H<sup>-/+</sup> mutant models. Hedgehog signaling requires cilia, and loss of cilia correlates here with a loss in induction of Hedgehog signaling as monitored by in situ hybridization of <em>Gli1</em> transcripts. These data support a model in which LRRK2 and PPM1H mutant mice struggle to receive and respond to critical Hedgehog signals in the nigral-striatal pathway.</p>
DeepCAD-RT dataset: mouse brain neutrophils
<p>DeepCAD-RT dataset: mouse brain neutrophils</p>
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.