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82 results for “Mouse Imaging”
Iterative Bleaching Extends multi-pleXity (IBEX) imaging method, mouse spleen
<p>This dataset was acquired using the Iterative Bleaching Extends multi-pleXity (IBEX) imaging method described in: “IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues“, A. Radtke et al., 2020, <a href="https://doi.org/10.1073/pnas.2018488117">doi:10.1073/pnas.2018488117</a>.</p> <p>It is comprised of a three cycle IBEX experiment performed on mouse spleen sections labeled with the nuclear marker JOJO-1 and membrane label CD4 AF594. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 mm), y (0.284 mm), and z (1 mm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p> </p> <p>Markers per channel in each of the three cycles:</p> <ol> <li>spleen_panel1.nrrd (6 channels): B220 PE, CD8 BV421, IgD AF700, CD4 AF594, JOJO, Foxp3 eF660</li> <li> <p>spleen_panel2.nrrd (7 channels): CD169 PE, F480 BV421, MHCII AF700, CollIV AF488, JOJO, CD11c AF647, CD4 AF594</p> </li> <li> <p>spleen_panel3.nrrd (7 channels): CD31 PE, CD68 BV421, Ki67 AF700, CD45 AF488, CD4 AF594, JOJO, CD3 AF647</p> </li> </ol> <p>The panels can be registered using the code available on github: <a href="https://github.com/niaid/sitk-ibex">https://github.com/niaid/sitk-ibex</a></p> <p>To view these multi-channel images, in <a href="http://teem.sourceforge.net/nrrd/format.html">nrrd format</a>, use the <a href="https://imagej.net/Fiji">Fiji viewer</a>. The data is stored in XYZC order.</p>
ISS Mouse brain embryo - MIPPED images , all rounds all channels
<p>Repository containing the stitched, mipped and aligned images of all the cycles and channels used in the Mouse embryo ISS characterization from La Manno et al 2020 The repository contains:</p> <ul> <li>Stitched aligned and mipped images of all round and cycles for different samples (2A,2D, 6B,10B)</li> <li>A codebook with the code of every expected gene detecoded is included</li> <li>A preliminary decoding of the 4 samples included in the folder "decoded_spots"</li> <li>Information about channel order in a .txt</li> </ul>
Mouse olfactory bulb intrinsic signal imaging for NNMF decomposition
<p>This dataset supplements our recent paper about automatic image segmentation using Non-negative Matrix Factorisation (NMF):</p> <p>Jan Soelter, Jan Schumacher, Hartwig Spors, Michael Schmuker (2014). Automatic segmentation of odor maps in the mouse olfactory bulb using regularized non-negative matrix factorization. <em>NeuroImage</em> 98:279-288.</p> <p>http://dx.doi.org/10.1016/j.neuroimage.2014.04.041</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>
Segmentation of membrane of mouse, sea urchin and human oocytes from transmitted light images
<p>This dataset has been presented in our paper "An interpretable and versatile machine learning approach for oocyte phenotyping", in bioRxiv.</p> <p>It contains images acquired in transmitted light with different settings of mouse and human oocytes and sea urchin eggs, with the corresponding ground-truth of the membrane segmentation. Mouse oocyte images were taken before and during oocyte maturation (meiosis I). Some human oocyte images were taken during oocyte maturation (meiosis I), and some are M-II oocytes just after fertilization. Sea urchin images contains both fertilized and unfertilized eggs.</p> <p> </p>
Segmentation of oocyte zona pellucida in transmitted light images (mouse and human)
<p>This dataset has been presented in our paper "An interpretable and versatile machine learning approach for oocyte phenotyping", in bioRxiv.</p> <p>It contains images acquired in transmitted light with different settings of mouse and human oocytes, with the corresponding ground-truth of the zona pellucida segmentation. Mouse oocyte images were taken before and during oocyte maturation (meiosis I). Some human oocyte images were taken during oocyte maturation (meiosis I), and some are M-II oocytes just after fertilization.</p>
Small-angle X-ray scattering datasets for imaging crossing fibers in mouse, pig, monkey, and human brain
<p>Small-angle X-ray scattering datasets for resolving crossing fibers (myelinated neuronal axon bundles), as described in</p> <p>"<strong><em>Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering</em></strong>"</p> <p>deposited in bioRxiv:</p> <p>https://doi.org/10.1101/2022.09.30.510198</p>
MALDI FTICR MS imaging data of pancreatic mouse tissue
<p>Preprocessed imaging mass spectrometry data (.imzML format) for mouse pancreatic Islets of Langerhans. Detailed information is given in the publication by Prade & Kunzke et al. "De novo discovery of metabolic heterogeneity with immunophenotype-guided imaging mass spectrometry" (currently in revision).</p>
Whole mouse embryo microCT image with nuclear staining (Bleikern)
<p>E12.5 mouse embryo stained with lead(II) acetate to contrast cell nuclei. X-ray microtomography scan as TIFF stack, 2.5um voxel size. Data used in publication</p> <p>Metscher B. (2021). A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate. Journal of Anatomy 238(4): 1036-1041.<br> https://onlinelibrary.wiley.com/doi/10.1111/joa.13351</p> <p> </p>
Images of mouse VTA and SNc sections labeled for neurotransmitter phenotype markers via RNAscope
<p>48 coronal sections from 3 male and 3 female C57Bl/6J mice were labeled for mRNAs encoding the canonical vesicular transporters for dopamine (VMAT2), GABA (VGAT), and glutamate (VGLUT2). These sections were then imaged via confocal microscopy and saved as CZI files, editable with Zeiss Zen software. These image files include 'event marker' graphics, indicating where neurons positive for one or more of the above transporters are. </p> <p>The protocols used for sample preparation, labeling, imaging, and counting are linked in the Related Works section. </p> <p>Cell count data are organized by subregion (SUBREGION counts for R.csv), anterior-posterior (e.g. VGATVTA.csv), or anterior-posterior and medial-lateral distribution (e.g. 'snc triple.csv' or 'snc vmat2 AP and ML.csv').</p> <p>The R code provided uses these csv files to visualize expression patterns across VTA and SNc. </p>
Natural Image Statistics for Mouse Vision
<p>This repository contains 232 "mouse-view" UV/Green natural scene images for the mouse vision, acquired by a custom multi-spectral camera. For details, please see the following paper:</p> <p> Natural Image Statistics for the Mouse Vision<br> Luca Abballe and Hiroki Asari<br> PLOS One (accepted)</p> <p>The preprint is also available from bioRxiv 2021.04.08.438953.</p>
Fabrication and characterization of a multimodal 3D printed mouse phantom for ionoacoustic quality assurance in image-guided pre-clinical proton radiation research
<p>Dataset related to the publication: "Fabrication and characterization of a multimodal 3D printed mouse phantom for ionoacoustic quality assurance in image-guided pre-clinical proton radiation research"</p>
3D reconstruction of an NIH/3T3 mouse fibroblast cell imaged by the SXT-100.
<p>This dataset (*.mrc file) is a reconstructed 3D volume obtained by soft X-ray tomography on NIH/3T3 cells. The cells were grown on a 200 mesh 3.05 mm EM finder grid with a Quantifoil Holey Carbon support. The sample was vitrified by plunge-freezing in liquid ethane. The tomogram was collected with a pixel size of 28.85 nm over the tilt range from -53 to 53.5 degrees with 1.5 deg step size and 116 s exposure per tilt.</p>
Whole slide images of mouse liver serial sections - Test registration dataset
<p>15 H&E serial section of mouse liver and small intestine.</p> <p>Sampled prepared in the <a href="https://www.epfl.ch/research/facilities/histology-core-facility/">EPFL histology core facility</a> by Nathalie Müller, Gian-Filippo Mancini, and Agnès Hautier.</p> <p>All slides where imaged with a VS200 Evident slide scanner from the<a href="http://biop.epfl.ch/"> EPFL BIOP imaging facility</a>.</p>
Follicle counting in mouse ovarian images
<div>Our dataset is composed of 643 cut slices of ovaries coming from 92 mice (each mouse have between 6 and 8 cuts). Ovaries were fixed in Bouin’s solution and subsequently embedded in paraffin blocks. The entire ovaries were serially sectioned into 4μm slices using a microtome. Every fifth section was mounted on microscope slides and stained with Hematoxylin and Eosin. Ovaries have been digitized on a Panoramic 250 Flash, Slide Scanner (3DHISTECH Ltd. HUNGARY). Each section was analyzed using Calopix Viewer®. Follicles were classified according to Pedersen’s classification. Briefly, follicles were categorized as follows: primordial follicles contained an oocyte surrounded by a partial or complete layer of squamous granulosa cells; primary follicles had an oocyte sur- rounded by a single layer of cuboidal granulosa cells; and secondary follicles presented with at least two layers of granulosa cells. The size of those cuts is approximately 20000 × 20000</div>
BRAIN Journal-Cursor Movement – a Valuable Indicator in Intelligent System Design-Figure 4. Mouse trajectory – images taken from http://iographica.com 4 hours in Photoshop (left) vs. 4 hours in Eclipse (right)
<p>Studies from different fields (Arroyo & Wei, 2006), (Mäkiaho & Poranen, 2012), (Lockton, Harrison, Cain, Stanton, & Jennings, 2013), (Seelye, et al., 2015), (Hehman, Stolier, & Freeman, 2014) have shown that mouse trajectory and clicks are environment (application, device) and user specific, especially if mapped over a long working session (Figure 4). </p>
Images and supporting data for high-resolution μCT of a mouse embryo using a compact laser-driven x-ray betatron source
<p>A high resolution x-ray CT scan of an embryonic mouse sample was performed with the betatron x-ray source produced by a laser wakefield accelerator. This data deposition includes all of the raw images of the mouse sample, information regarding their indexing, featured slices of the tomogram and some further raw data regarding the x-ray source characterisation.</p>
Confocal Microscopy Imaging of Peptidoglycan Uptake in the Mouse Intestine
<p>Confocal imaging data set accompanying Fig.5 and Fig.6 for the article: Wheeler R, Dias Bastos PA, Disson O, Rifflet A, Gabanyi I, Spielbauer J, Bérard M, Lecuit M, Gomperts Boneca I. Microbiota-induced active translocation of peptidoglycan across the intestinal barrier dictates its within-host dissemination (2023) PNAS; doi: 10.1073/pnas.2209936120<br> <br> Stainings are described in detail in the the PNAS article methodology.<br> Files names beginning Fig 5A-1; DAPI, WGA, anti-E-cadherin, MDP-rhodamine<br> Files names beginning Fig 5A-2, Fig 5A-3 & Fig S5; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine<br> Files names beginning Fig 5B; DAPI, Phalloidin, <em>E.coli </em>peptidoglycan-Alexa Fluor 647 conjugate<br> Files names beginning Fig 6B; DAPI, Phalloidin, anti-Siglec-F, MDP-rhodamine (also corresponds to Supplementary data Figure 5)<br> Files names beginning Fig S5-1; DAPI, Phalloidin, anti-CgA, MDP-rhodamine<br> Files names beginning Fig S5-2; DAPI, Phalloidin, anti-NKM-16-4-2, MDP-rhodamine</p>
Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear
<p>Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear (A-1) compared with control (A-2) mouse ear. (B) PET/CT images demonstrate preferential tumor (MCF-7) accumulation of 39, compared with longer blood circulation and higher non-specific binding of 41 at 1 hour post-injection. (C) Structures of the tracers used in the preceding panels are shown.</p>
Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function: Part 2/2, Hair cell and afferent physiology from mouse utricle
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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.