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82 results for “Mouse Imaging”
Segmentations of 3D electron microscopy image volume from an albino mouse dorsal lateral geniculate nucleus
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Data from: Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function: Part 1/2, Zebrafish data
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Data from: Microprism-based two-photon imaging of the mouse inferior colliculus reveals novel organizational principles of the auditory midbrain
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Data from: Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease
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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>
Data set for "Projection-specific activity of layer 2/3 neurons imaged in mouse primary somatosensory barrel cortex during a whisker detection task"
<p>Data set for: Vavladeli A, Daigle T, Zeng H, Crochet S, Petersen CCH (2020) Projection-specific activity of layer 2/3 neurons imaged in mouse primary somatosensory barrel cortex during a whisker detection task. FUNCTION 1: zqaa008. doi: 10.1093/function/zqaa008</p> <p>There are 2 files in this upload:</p> <p>1. The file named "2020_Vavladeli_FUNCTION.pdf" is the Open Access pdf file of the manuscript published in FUNCTION.</p> <p>2. The file named "Vavladeli_data_code.zip" (~2 GB) is a zipped version of a folder named "Vavladeli_data_code" (~2 GB), which contains the data analysed in the study along with the Matlab code used to generate the published figures. When unzipped, the folder contains 8 Matlab '.m' files with analysis code and two '.mat' data files. In order to run the analysis of the data set, you need to execute the '.m' file with the corresponding figure name.</p>
CODEX multiplexed imaging of immunotherapy in human and mouse melanomas
<p>Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to gain insights into melanoma tumors in both murine models and human samples. CODEX imaging involves an iterative process of annealing and stripping fluorophore-labeled oligonucleotide barcodes, complementing the barcodes attached to over 40 antibodies used for tissue staining. Subsequently, images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), single cell segmentation, and column marker z-normalization by tissue.</p> <p>Our datasets comprise individual cells as rows, each characterized by 40+ antibody fluorescence values quantified from various markers evaluated for each study. These markers correspond to the antibodies targeting specific proteins within the tissue, quantified at the single-cell level. The values represent per-cell/area-averaged fluorescent intensities, z-normalized along each column. Each cell is mapped with its cell type and cellular neighborhood, defined by x and y coordinates representing pixel locations in the original image. Refer to the table in the "Usage Notes" section below for further details. The CODEX multiplexed imaging data is organized into three distinct files, each representing key aspects of our research and the studies detailed in our manuscript.</p> <p>We then used this data investigate the major cellular organization of the tumor sections we imaged, with downstream spatial statistics and analyses like cellular neighborhood analysis and cell-cell interaction analysis. These data could be used to understand the cellular interactions, composition, and structure of anti-tumor melanoma responses induced by antigen-specific immunotherapy either with adoptive T cell transfer for checkpoint blockade immunotherapy. These datasets offer valuable insights for researchers interested in anti-tumor microenvironments, immune responses, and therapeutic interventions such as T cell therapies.</p> <p><em>1. Time-course of tumor microenvironment following antigen-specific T cell therapy in mice</em></p> <p>We investigate the dynamic interplay between immune responses, antigen-specific T cell interactions, and tumor progression in a murine melanoma model. We activated PMEL CD8+ T cells with cognate antigen gp100 and IL-2 for 10 days ex vivo and transferred into mice with established B16-F10 tumors. Tumors were harvested and imaged with CODEX imaging at 0-, 1-, 3-, 5-, and 12-days post-treatment (n=3-7 per time point). Our 42-plex CODEX antibody panel characterizes immune cell types, T cell phenotypes, stromal cell types, and tumor cell phenotypes, resulting in a rich dataset of 1,052,125 cells across 42 marker channels.</p> <p><em>2. Tumor microenvironment following antigen-specific T cell therapies with different phenotypes in mice</em></p> <p>We delve deeper into the modulation of the tumor microenvironment by manipulating T cell phenotypes. By comparing activated T cells stimulated with and without 2-hydroxycitrate (2HC), a metabolic inhibitor of acetyl CoA production, we explore the impact of phenotype on tumor progression. Our datasets from mice treated with 2HC T cells or T cells provide insights into the role of T cell phenotype manipulation in the tumor microenvironment (n=4-7 per group).</p> <p><em>3. Tumor microenvironment before and after checkpoint blockade in human melanoma patients of both responders and non-responders</em></p> <p>Our research extends to human melanoma patients with advanced, metastatic, stage IV tumors. We examine 12 FFPE tumor samples from six patients, each with samples taken before and after checkpoint inhibitor therapy. Our CODEX multiplexed imaging, using a panel of 58 antibodies, reveals changes in immune, stromal, and tumor compartments. We segmented 5,019,159 individual cells from the 12 CODEX images, facilitating unsupervised clustering to identify 39 major cell types based on their expression profiles. Our accompanying donor metadata table links donor IDs to essential clinical information, including treatment response, demographics, and sample details.</p>
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>
Mouse CA1 Calcium Imaging and Behavioural Dataset in 3x3 Geometric Morph Paradigm
<p>The following dataset was collected by Dr. J. Quinn Lee, Dr. Alexandra T. Keinath, and Erica Cianfarano in the laboratory of Dr. Mark P. Brandon. All methods and details are described in the original research article reporting these data published in <em>Neuron</em>: Lee, Keinath, Cianfarano, and Brandon (2025) Identifying representational structure in CA1 to benchmark theoretical models of cognitive mapping. Any use of the following dataset must cite the original publication in Neuron. The code base to reproduce all analyses and figures can be found at: <a href="https://github.com/jquinnlee/georepca1">https://github.com/jquinnlee/georepca1</a></p> <p dir="auto">The dataset (Python joblib files or MATLAB .mat files in the zipped "data" folder) are given names of animal IDs from the original study that can be downloaded from Zenodo and contain the following fields in each file:</p> <p dir="auto">SFPs: spatial footprints (also known as ROI) for every registered cell, centered over each cell. Shape - Dimx, dimy, number of SFPs (ROIs), number of days. If cell is not registered it will be nan along dimx and dimy for a given day.</p> <p dir="auto">blocked: location of blocked (occluded) partitions in 3x3 design of environment. Location of partitions are shown in paper, but are organized in the following way – [[0, 1, 2], [3, 4, 5], [6, 7, 8]]. If no partitions are blocked, value is -1.</p> <p dir="auto">centroids: centroid of spatial footprint. Shape – number of cells, x-y location, number of days.</p> <p dir="auto">envs: environment shape identified with string name</p> <p dir="auto">maps: three types of maps generated from the dataset. “sampling” is the occupancy of animal in each spatial bin, shape – xbins, ybins, number of days. “smoothed” is the event rate map smoothed with 2.5 cm gaussian kernel, shape – xbins, ybins, number of cells, number of days. “unsmoothed” is the same event rate map data without smoothing.</p> <p dir="auto">position: x-y position data for all days. List shape number of days, with shape on each day indicating x-y position in first dimension, and number of temporal bins / frames in second dimension.</p> <p dir="auto">trace: rise-extracted calcium traces, where “1” indicates a significant event. See paper for details on processing pipeline. If cell is not registered on given day, will appear as nan the same shape.</p> <p dir="auto">Precomputed results can also be downloaded in the zipped "results" folder to avoid recomputing main results from scratch using the Github code base linked above.</p>
Open data repository, An et al., Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images
<p>Open data repository of journal article "Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images" by Jeehye An <em>et al. </em>At time of publication of this dataset, the manuscript is still under revision.</p> <p>This dataset contains mouse T2 weighted MRI data, and manually and automated segmented ischemic stroke lesion masks for developing and evaluating a deep learning-based automated lesion segmentation. All files are in NIFTI format.<br> </p>
Imaging the onset of oscillatory signaling dynamics during mouse embryo gastrulation
<p>A fundamental requirement for embryonic development is the coordination of signaling activities in space and time. A notable example in vertebrate embryos is found during somitogenesis, where gene expression oscillations linked to the segmentation clock are synchronized across cells in the presomitic mesoderm (PSM) and result in tissue-level wave patterns. To examine their onset during mouse embryo development, we studied the dynamics of the segmentation clock gene Lfng during gastrulation. To this end, we established an imaging setup using selective plane illumination microscopy (SPIM) that enables culture and simultaneous imaging of up to four embryos (SPIM-for- 4). Using SPIM-for-4, combined with genetically encoded signaling reporters, we detected the onset of Lfng oscillations within newly formed mesoderm at presomite stages. Functionally, using chemical inhibition and genetic mutants, we found that initial synchrony and first ~6-8 oscillation cycles occurred even when Notch-signaling was impaired, revealing similarities to previous findings made in zebrafish embryos. Finally, we show that a spatial period gradient is already present at the onset of oscillatory activity, providing a potential mechanism accounting for our observation that wave patterns build up gradually over the first oscillation cycles.</p>
Development of an imaging toolbox to assess the therapeutic potential and biodistribution of macrophages in a mouse model of multiple organ dysfunction
<p>Data set to accompany manuscript entitled "Development of an imaging toolbox to assess the therapeutic potential and biodistribution of regenerative therapies in a mouse model of multiple organ dysfunction " which can be found on BioRxiv.</p>
Tau deposition is associated with imaging patterns of calcifications and immunhistochemical markers of osteogenesis in the P301L mouse model of human tauopathy
<p>Brain calcifications are associated with several neurodegenerative proteinopathies. Here, we report a new phenotype of imaging pattern of intracranial calcifications in transgenic P301L mice overexpressing 4 repeat human tau. P301L mice (Thy1.2) of 3, 5, 9 and 18-25 months-of-age and age-matched non-transgenic littermates (n = 4-11 per group) were assessed using <em>in vivo / ex vivo</em> magnetic resonance imaging with a gradient recalled echo sequence and micro computed tomography. Susceptibility weighted images computed from the gradient recalled echo data revealed regional hypointensities in the hippocampus, cortex, caudate nucleus and thalamus of P301L mice, in which corresponding phase images indicated diamagnetic lesions. In the hippocampus, occurrence of diamagnetic susceptibility calcifications increased with age. Concomitantly micro computed tomography detected hyperdense lesions. Immunochemical staining of brain sections revealed osteocalcin positive nodules, which is a marker of osteogenic maturation. Furthermore, we found vessel-associated and intra-neuronal osteocalcin positivity co-localizing with phosphorylated tau (AT8 and AT100) in the hippocampus. In contrast, osteocalcin containing nodules were vessel-associated, indicating ossified vessels, in the thalamus in absence of phosphorylated tau. In summary, we demonstrated imaging pattern of intracranial calcifications, early spheroid formation containing proteins associated with ossification along with phosphorylated tau in the P301L mouse model of human tauopathy.</p> <p> </p>
Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function
<p>Dataset for Ono et al., 2024.<br>Contains all source data from the Tarchini laboratory, including illustrative images and raw data for quantification, as well as the data file containing statistical analysis. It also contains the data file produced by the Cullen laboratory reporting behavioral data. </p>
Implantation of abdominal imaging windows on the mouse kidney
<p>This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen).</p> <p>Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation.</p> <p>This upload contains the full version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.</p>
Supplementary data to "Protocol to image, segment and quantify cortical contractions in maturing mouse oocytes"
<p>This dataset contains supplementary materials for the "Protocol to image, segment and quantify cortical contractions in maturing mouse oocytes" manuscript.</p> <p>This dataset contains two timelapse images of maturing oocytes (control_oocyte.tif and ArpC4_KO_oocyte.tif) with the corresponding Region of Interest files for FIJI (control_oocyte_UnetCortex.zip and ArpC4_KO_oocyte_UnetCortex.zip). The .csv files contain raw measurements produced by Radioak plugin for FIJI, and the .xlsx files contain the quantifications based on the raw data. The units in .csv and .xlsx files are microns.</p> <p> In the timelapse images the time resolution is 1 min, each pixel is 0.1135 micrometers.</p>
DAPI images, molecules and segmentation boundaries for: A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space
<div> </div> <p><strong>Data Description</strong></p> <ol> <li><strong>Stitched & rotated DAPI images</strong> - tiff file format filename indicates sample and optical z-slice position, i.e. embryo3_z5.tif is the DAPI image for embryo 3 in optical z-slice 5. Also provided in PNG format.</li> <li><strong>Detected molecules and cell segmentation in MoleculeExperiment objects</strong> - RDS files to read data using the MoleculeExperiment format in R/Bioconductor. Filename embryo3_z5.Rds indicates MoleculeExperiment RDS file for embryo 3 in optical z-slice 5. Coordinates are provided in microns. Note that z-slices 2 and 5 are only provided for embryos 1,2,3 as they were originally provided in Lohoff et al, Nature Biotechnology, 2023.</li> <li><strong>Pixels-to-microns conversion</strong> - pixelSize.R Simple R script/text to indicate the size of each pixel in the DAPI images, this is to align the coordinate systems between the DAPI images and molecules.<br><br> <div> <h4>Project Abstract</h4> </div> <p>At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics and a scRNA-seq atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.</p> </li> </ol>
MALDI imaging of mouse kidney peptides - test dataset
<p>This imzML test file is concise but meaningful as a training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p> <p>One 6 µm thick section of formalin-fixed paraffin-embedded mouse kidney (from 6 month old, male, C57 black 6 mice) was mounted onto an indium-tin oxide (ITO) glass slide, deparaffinized and subjected to antigen retrieval in citric acid (pH 6, 100°C, 1h). Before and after antigen retrieval the sample was washed with 10mM ammonium bicarbonate buffer. After air drying, four 1 µl spots of Bombesin (0.01 mg/ml) were placed around the tissue to control digestion.<strong> </strong>Trypsin was sprayed onto the tissue with the iMatrix Sprayer and the sample was incubated for 2 h at 50°C in a humid chamber. Internal Calibrants (Angiotensin I, Substance P, [Glu]-Fibrinopeptide B, ACTH 18-39) were mixed with α-Cyano-4-hydroxycinnamic acid (CHCA) matrix and sprayed onto the sample.</p> <p>The sample was measured with the Applied Biosystems/MDS SCIEX 4800 MALDI TOF/TOF™ Analyzer in reflector positive ion mode and a spatial resolution of 150 µm. The acquired Analyze7.5 file was loaded into Cardinal and filtered to reduce file size and decrease analysis time: Filtering was done for m/z values between 1220 and 1625 as well as pixel that represent about half of the kidney and one Bombesin digestion control spot. The data was exported in the common data format imzML.</p> <p> </p>
Mouse Organoids imaged with Dual Oblique Plane Microscopy
<p>This is a dataset to demonstrate segmenting colonies of 3D cells. The primary focus is segmenting mouse organoids images using timelapse dual oblique plane microscopy. There is also a set of data mouse embryonic stem cells imaged using spinning disk confocal microscopy.</p>
Code and imaging data for: Mouse epidermal chromatin architecture
<p>Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline that leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of keratin-10 nascent RNA, which marks the onset of stem cell differentiation, we find that keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.</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.