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109 results for “in vivo imaging”
Dataset In-vivo probabilistic atlas of human thalamic nuclei based on diffusion weighted magnetic resonance imaging
<p>This is the dataset related to the paper "In-vivo probabilistic atlas of human thalamic nuclei based on diffusion weighted magnetic resonance imaging", E. Najdenovska*, Y. Aléman-Gómez*, G. Battistella, M. Descoteaux, P. Hagmann, S. Jacquemont, P. Maeder, J.-P. Thiran, E. Fornari and M. Bach Cuadra, Sci. Data. 5:180270 doi: 10.1038/sdata.2018.270 (2018). *Equally contributed authors.</p> <p>We provide NifTI-1 files representing a digital atlas of seven thalamic subparts per hemisphere. More precisely, the files include the spatial probabilistic atlas maps for each thalamic subpart (Thalamus_Nuclei-HCP-4DSPAMs.nii.gz) and the maximum likelihood atlas (Thalamus_Nuclei-HCP-MaxProb.nii.gz) in MNI space. The region corresponding to each labeled thalamic part respectively is given in the look-up table Thalamic_Nuclei-ColorLUT.txt. The NIFTI files can be visualised with the main available tools such as tkmedit, freeview or 3D-Slicer.</p> <p>We also provide a step by step pseudo code for creating the atlas.</p>
Autofluorescence-Free In Vivo Imaging Using Polymer-Stabilized Nd3+-Doped YAG Nanocrystals
<p>Neodymium-doped yttrium aluminum garnet (YAG:Nd<sup>3+</sup>) has been widely developed during roughly the last sixty years and has been an outstanding fluorescent material. It has been considered as the gold standard among multipurpose solid-state lasers. Yet, the successful downsizing of this system into the nano regimen has been elusive, so far. Indeed, the synthesis of a garnet structure at the nanoscale, with enough crystalline quality for optical applications was found to be quite challenging. Here, we present an improved solvothermal synthesis method producing YAG:Nd<sup>3+</sup> nanocrystals of remarkably good structural quality. Adequate surface functionalization using asymmetric double-hydrophilic block copolymers, constituted of a metal-binding block and a neutral water soluble block, provides stabilized YAG:Nd<sup>3+</sup> nanocrystals with a long term colloidal stability in aqueous suspensions. These newly stabilized nanoprobes keep the spectroscopic quality (long lifetimes, narrow emission lines, and large Stokes shift) characteristic of bulk YAG:Nd<sup>3+</sup>. The narrow emission lines of YAG:Nd<sup>3+</sup> nanocrystals are exploited by differential infrared fluorescence imaging, thus achieving an autofluorescence-free <em>in vivo</em> readout. In addition, nanothermometry measurements, based on the ratiometric fluorescence of the stabilized YAG:Nd<sup>3+</sup> nanocrystals, are demonstrated. The progress here reported paves the way for the implementation of this new stabilized YAG:Nd<sup>3+</sup> system in the preclinical arena.</p>
Quantification of ROIs corresponding to MQs from fluorescence in vivo imaging experiments
<p>We injected DIr labelled macrophages into mice carring immunolgical hot and cold KPC pancreatic tumors and quantified the recruitment to the tumor sites and lungs of the injected cells at different days after injection using fluorescence imaging. We hypotesized that macrophages would be recruited into tumor tissue and in prevalence into cold tumors.</p>
Raw gel images accompanying the publication: Koralewska et al, NAR 2024, Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo, DOI 10.1093/nar/gkae284
<p>A set of raw gel images used in the article: Koralewska <em>et al</em>. Short 2’-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production <em>in vitro</em> and <em>in vivo, </em>NAR 2024, DOI 10.1093/nar/gkae284.</p>
Instantaneous In Vivo Imaging of Acute Myocardial Infarct by NIR‐II Luminescent Nanodots
<p>Fast and precise localization of ischemic tissues in the myocardium after an acute infarct is required by clinicians as the first step toward accurate and efficient treatment. Nowadays, diagnosis of a heart attack at early times is based on biochemical blood analysis (detection of cardiac enzymes) or by ultrasound‐assisted imaging. Alternative approaches are investigated to overcome the limitations of these classical techniques (time‐consuming procedures or low spatial resolution). As occurs in many other fields of biomedicine, cardiological preclinical imaging can also benefit from the fast development of nanotechnology. Indeed, bio‐functionalized near‐infrared‐emitting nanoparticles are herein used for in vivo imaging of the heart after an acute myocardial infarct. Taking advantage of the superior acquisition speed of near‐infrared fluorescence imaging, and of the efficient selective targeting of the near‐infrared‐emitting nanoparticles, in vivo images of the infarcted heart are obtained only a few minutes after the acute infarction event. This work opens an avenue toward cost‐effective, fast, and accurate in vivo imaging of the ischemic myocardium after an acute infarct.</p>
Raw diffraction images of polyhedra in-vivo crystals
<p>Diffraction images of wild type cypovirus polyhedra in-vivo crystals (WTPhC) and the mutant (Δ3-PhC) related to PDB codes 5GQM and 5GQN, respectively.</p> <p>Small-wedge (5°/crystal) datasets were collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. The datasets for 5GQN were collected automatically using ZOO system.</p> <p>The crystals belonged to space group <em>I</em>23 with unit cell parameter a~103 Å. 14 and 41 datasets were merged at 1.68 and 1.55 Å resolution in the published result (Abe <em>et al</em>. <em>ACS Nano</em> 2017; PDB codes: 5GQM & 5GQN, respectively) using KAMO; see https://github.com/keitaroyam/yamtbx/wiki/Processing-Polyhedra-data-(5GQM-&-5GQN)</p> <p>NOTE</p> <ul> <li> <p>flatfield correction was not applied to the images and you need to apply it using the correction table saved in master.h5 files.</p> </li> <li> <p>master.h5 files were modified; see https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</p> </li> <li> <p>Most frames have ice (rings).</p> </li> </ul>
In vivo parameter maps for: Unconstrained quantitative magnetization transfer imaging: disentangling T1 of the free and semi-solid spin pools
<p>Quantitative magnetization transfer and relaxometry maps as described in the Paper <em>Unconstrained quantitative magnetization transfer imaging: disentangling T1 of the free and semi-solid spin pools</em>.</p> <p>.</p>
Volumetric and morphological analysis of the clades based on the in vivo confetti imaging
<p>This dataset contains a script in programming language that describes the analytical pipeline for image processing of the in vivo data from the Confetti mice skin. The algorithm describes volumetric analysis, 3D reconstruction, density analysis, as well multiple other morphological parameters. </p>
Data: Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography.
<p>This data set includes all the raw data collected for the following article: "Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography."</p>
Micro-CT Imaging Dataset on ex-vivo Ovine Functional Spinal Segments as Healthy, Injured and Treated with Cement Discoplasty
<p>General information:</p> <p>- This dataset contains micro-CT images and mechanical test data from ovine functional spinal units (FSU). <br> - The micro-CT data was produced using a Bruker SkyScan 1172. The settings for the scans are given in the '.log' files in each folder. <br> - The compression testing was conducted on an MTS 858 Mini Bionix T/II. The settings for each test can be found in test '.txt' files.<br> - In short, every FSU was mechanically tested in compression under different conditions. Before and after every test, the FSUs were scanned to ensure there was no damage<br> to the sample. More information can be found in the related publication: <br> - The mechanical testing data is arranged in folders with consecutive cycles. It is highly recommended to use the last three cycles for analysis. </p> <p>Data set notation:</p> <p>- All the datasets are noted by Sheep number. Sh7 = Sheep 7; Sh8 = Sheep 8; Sh9 = Sheep 9. In the publication, the numbers were switched to 1,2,3 respectively.<br> - files denoted with '_rec' contain the reconstruction of the projection images. <br> - 'Tested' or 'After test' files refers to the scan after mechanical testing. </p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: In vitro data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG2_Histone_vs_free_GFP <ul> <li>data for Sparks et al Figure 2</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG3_in_vitro_dose_response <ul> <li>data for Sparks et al Figure 3#</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_SuppFIG2_endoscope_spectral_cross_talk <ul> <li>data for Sparks et al Supplementary Figure 2</li> <li>Supplementary information</li> </ul> </li> </ul> <p><strong>Cell lines</strong></p> <p>IGROV-1 cell lines were cultured in CO<sub>2</sub> dependent media with 10% fetal bovine serum and 1% Pen Strep at 37 ˚C. Before experiments, cells were grown to 80% confluence. For measuring doxorubicin uptake by fluorescence an IGROV-1 cell line stably expressing GFP fused to Histone-1 (H1) was made using the PiggyBac transposon system. As a control to show that effect of doxorubicin on GFP depends on whether it is fused to H1 or not, a stable whole cell expression of GFP by lentiviral transfection and selection by Geneticin was made. For bioluminescence imaging of xenograft tumors, all IGROV-1 cell lines were made to stably express firefly luciferase.</p> <p>To investigate the effect of doxorubicin on other histones, IGROV-1 cells were transiently transfected with a Histone-2B-GFP plasmid (gift from Kurt Anderson) using the Lipofectamine® 2000 reagent.</p> <p>IGROV-1 cells were obtained from Crick institute cell services and confirmed as IGROV-1 by Short Tandem Repeats (STR) profiling and no mycoplasma was detected.</p> <p><strong>In vitro experiments</strong></p> <p>IGROV-1 cells were grown to 80% confluence in 75 ml flasks before being re-plated in 12 or 24 well plates or 35 ml glass bottomed dishes and allowed to attach to the surface for 24 hours before experiments.</p> <p>To study how the fluorescence of GFP labelled H1 labelled IGROV-1 cells changes with doxorubicin treatment, fluorescence intensity and lifetime distributions were measured from cells after 3 hours of incubation with doxorubicin of varying concentrations (0, 0.18, 0.9, 1.8, 9, 18 µM) by serial dilutions of a stock solution with PBS. After 3 of hours, cells were washed in PBS then fixed for 20 minutes in 4% PFA. Cells were then imaged in PBS. Doxorubicin hydrochloride (Sigma-Aldrich, D1515-10 mg) was dissolved in PBS to a concentration of 9 mM and stored at -20˚C.</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: in vivo data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG_6_IP_intranodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG4_5_6_IP_IV_chemo_comparison <ul> <li>data for Sparks et al Figures 4,5 & 6</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_FIG6_IP__internodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'Intra-tumor heterogeneity'</em></li> </ul> </li> </ul> <p><strong>In vivo experiments</strong></p> <p>Murine xenografts were prepared by intraperitoneal (IP) injection of IGROV-1 cancer cells. IGROV-1 cells were grown to 80% confluence before being trypsinized and re‑suspended in PBS at a concentration of cells per ml. cells were injected into ICRF nude mice. After 14 days post-injection, the presence of intraperitoneal tumors was confirmed by bioluminescence imaging. Briefly, an IVIS bioluminescence imaging system was used to image isoflurane anesthetized mice. 100 µl of D-luciferin (luciferase substrate) at 30mg ml<sup>-1</sup> was injected IP 10 minutes before recording of bioluminescence images. The presence of peritoneal tumors was confirmed if bioluminescence signals from the peritoneum were above background noise 10-30 minutes after D‑luciferin injections. Following confirmation of tumors, in vivo fluorescence imaging experiments were carried out after 21 days. To study differences in drug uptake between intravenous or intraperitoneal delivery, prior to imaging mice were subject to IP or IV doxorubicin-based chemotherapy for 1.5, 3 or 24 hours. Imaging involved terminal procedures, mice were anesthetized then peritoneal tumors were exposed by minor surgery and inspected with the CEM.</p> <p>All animal model procedures were approved by The Francis Crick Institute Biological Ethics Committee and UK Home Office authority provided by Project License 70/8380.</p> <p> </p> <p> </p>
Images, graphs and tables from the article: Biological performance of a bioabsorbable Poly (L-Lactic Acid) produced in polymerization unit: in vivo studies -
<p>The images, graphs and tables attached correspond to the study performed in the thesis project on the in vivo biocompatibility of the PLLA polymer produced.</p>
Biological performance of a bioabsorbable Poly (L-Lactic Acid) produced in polymerization unit: in vivo studies - HEMATOXYLIN&EOSIN, MASSON AND CT SCAN IMAGES
<p>CT, hematoxylin & eosin and masson staining images of the animals in the experimental biocompatibility study.</p> <p>Groups at 6 months post implantation and groups at 9 months post implantation.</p> <p>In addition to the subgroups lesion with PLLA and lesion without PLLA</p>
Ex vivo [18F]Fenoprofen PET imaging
<p>Coronal slice, maximum intensity projection (MIP) static PET image, and CT image of representative TPA-treated ear (A, C and E) or normal ear (B, D and F) harvested from the mice injected intravenously with [<sup>18</sup>F]Fenoprofen. (G) Dynamic PET time-activity curve (tac) of organ ROIs in nude mice injected with a rapid intravenous bolus of [<sup>18</sup>F]Fenoprofen, imaged for 30 minutes post-injection. (H) Uptake of [<sup>18</sup>F]Fenoprofen in TPA-treated or normal ear measured by ROIs hand-drawn on static <em>ex vivo</em> PET images. (I) Uptake of [<sup>18</sup>F]Fenoprofen in TPA-treated or normal ear measured by gamma counting.</p>
In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
<p>Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these events <i>in vivo</i>. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous and oral routes. BLI permitted temporal tracking of orally administered retroviruses along the gastrointestinal tract as they traversed the lumen through Peyer's Patches to reach the draining mesenteric sac. Importantly, capture and acquisition of lymph-, blood- and milk-borne retroviruses spanning three routes, was promoted by a common host factor, the I-type lectin CD169, expressed on sentinel macrophages. These results highlight how retroviruses co-opt the immune surveillance function of tissue resident sentinel macrophages for establishing infection.</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>
Novel in Vivo Synaptic Imaging in Experienced Meditators
ClinicalTrials.gov study NCT05418608. IPD Sharing: YES. Countries: 1. Publications: 22.
Non-Linear Imaging of Skin In Vivo
ClinicalTrials.gov study NCT05410964. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Imaging Synaptic Density in Cocaine and Opiate Addiction In Vivo Using 11UCB-J PET
ClinicalTrials.gov study NCT03527485. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
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.