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162 results for “Quantitative Imaging”
Data from: Quantitative multi-parametric magnetic resonance imaging of tumor response to photodynamic therapy
Objective: The aim of this study was to characterize response to photodynamic therapy (PDT) in a mouse cancer model using a multi-parametric quantitative MRI protocol and to identify MR parameters as potential biomarkers for early assessment of treatment outcome. Methods: CT26.WT colon carcinoma tumors were grown subcutaneously in the hind limb of BALB/c mice. Therapy consisted of intravenous injection of the photosensitizer Bremachlorin, followed by 10 min laser illumination (200 mW/cm2) of the tumor 6 h post injection. MRI at 7 T was performed at baseline, directly after PDT, as well as at 24 h, and 72 h. Tumor relaxation time constants (T1 and T2) and apparent diffusion coefficient (ADC) were quantified at each time point. Additionally, Gd-DOTA dynamic contrast-enhanced (DCE) MRI was performed to estimate transfer constants (Ktrans) and volume fractions of the extravascular extracellular space (ve) using standard Tofts-Kermode tracer kinetic modeling. At the end of the experiment, tumor viability was characterized by histology using NADH-diaphorase staining. Results: The therapy induced extensive cell death in the tumor and resulted in significant reduction in tumor growth, as compared to untreated controls. Tumor T1 and T2 relaxation times remained unchanged up to 24 h, but decreased at 72 h after treatment. Tumor ADC values significantly increased at 24 h and 72 h. DCE-MRI derived tracer kinetic parameters displayed an early response to the treatment. Directly after PDT complete vascular shutdown was observed in large parts of the tumors and reduced uptake (decreased Ktrans) in remaining tumor tissue. At 24 h, contrast uptake in most tumors was essentially absent. Out of 5 animals that were monitored for 2 weeks after treatment, 3 had tumor recurrence, in locations that showed strong contrast uptake at 72 h. Conclusion: DCE-MRI is an effective tool for visualization of vascular effects directly after PDT. Endogenous contrast parameters T1, T2, and ADC, measured at 24 to 72 h after PDT, are also potential biomarkers for evaluation of therapy outcome.
Data from: Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging
We report a method for the sensitive detection of rare chromosome breaks and translocations in interphase cells. HiBA-FISH (High-throughput break-apart FISH) combines high-throughput imaging with the measurement of the spatial separation of FISH probes flanking target genome regions of interest. As proof-of-principle, we apply hiBA-FISH to detect with high sensitivity and specificity rare chromosome breaks and translocations in the anaplastic large cell lymphoma breakpoint regions of NPM1 and ALK. This method complements existing approaches to detect translocations by overcoming the need for precise knowledge of translocation breakpoints and it extends traditional FISH by its quantitative nature.
High resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana
<p>A primary component of seedling establishment is the photomorphogenic response as seedlings emerge from the soil. This process is characterized by a reduced growth rate in the hypocotyl, increased root growth, opening of the apical hook, and expansion of the cotyledons as photosynthetic organs. While fundamental to plant success, the photomorphogenic response can be highly variable. Additionally, studies of <i>Arabidopsis thaliana</i> are made difficult by subtle differences in growth rate between individuals. High-resolution imaging and computational processing have emerged as useful tools for quantification of such phenotypes. This study sought to: 1) develop an imaging methodology which could capture changes in growth rate as seedlings transition from darkness to blue light in real time, and 2) apply this methodology to single-QTL analysis using the Cvi x L<i>er</i> RIL mapping population. Significant differences in the photomorphogenic response were observed between the parent lines and analysis of 158 RILs revealed a wide range of growth rate phenotypes. QTL analysis detected significant loci associated with dark growth rate on chromosome 5 and significant loci associated with light growth rate on chromosome 2. Candidate genes associated with these loci, such as the previously characterized <i>ER</i> locus, highlight the application of this approach for QTL analysis. Genetic analysis of Landsberg lines without the <i>erecta </i>mutation also supports a role for ER in modulating the photomorphogenic response, consistent with previous QTL analyses of this population. Strengths and limitations of this methodology are presented, as well as means of improvement.</p>
Supplementary Tables Novel Quantitative Methods to Enable Multispectral Identification of High-Purity Water Ice Exposures on Mars using High Resolution Imaging Science Experiment Images
<p>Data describing the list of images, error and uncertainty calculations for Novel Quantitative Methods to Enable Multispectral Identification of High-Purity Water Ice Exposures on Mars using High Resolution Imaging Science Experiment Images.</p>
A Mixed Cohort, Multicentre Exploratory Study of Non-invasive Quantitative Assessment of Renal Graft Function With Non-contrast Functional Magnetic Resonance Imaging
ClinicalTrials.gov study NCT07333495. IPD Sharing: NO. Countries: 1. Publications: 0.
A Novel Imaging Based Quantitative Model-aided Detection of Portal Hypertension in Patients With Cirrhosis (CHESS2104)
ClinicalTrials.gov study NCT05068492. IPD Sharing: NO. Countries: 0. Publications: 2.
Role of Magnetic Resonance Fingerprinting and Quantitative MR Imaging in Breast Cancer
ClinicalTrials.gov study NCT03650803. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Image-Based Quantitative Assessment of Acute Radiation-Induced Changes in Glioma
ClinicalTrials.gov study NCT03168919. IPD Sharing: NO. Countries: 1. Publications: 0.
Effect of Ranolazine on Myocardial Perfusion Assessed by Serial Quantitative Exercise SPECT Imaging
ClinicalTrials.gov study NCT01221272. IPD Sharing: Not stated. Countries: 8. Publications: 0.
High resolution imaging as a tool for identifying quantitative trait loci that regulate photomorphogenesis in Arabidopsis thaliana
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Data from: Quantitative analysis of fundus-image sequences reveals phase of spontaneous venous pulsations
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Data from: Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging
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Non-human primate white matter development during the first year of life as assessed by diffusion tensor imaging and quantitative relaxometry
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Data from: An ultrasound image-based dynamic fusion modeling method for predicting the quantitative impact of in vivo liver motion on intraoperative HIFU therapies: investigations in a porcine model
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Data from: Quantitative multi-parametric magnetic resonance imaging of tumor response to photodynamic therapy
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Data from: Robust extraction of quantitative structural information from high-variance histological images of livers from necropsied Soay sheep
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Data from: Rapid quantitative pharmacodynamic imaging by a novel method: theory, simulation testing and proof of principle
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Quantitative live-cell imaging of secretion activity reveals dynamic immune responses
GEO Series GSE253100. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
Light and transmission electron microscopic images for quantitative lung morphology of mechanically ventilated rat lungs.
<p>The joint American Thoracic Socity (ATS) and European Respiratory Society (ERS) guidelines recommend design-based stereology for quantitative morphology of lung structures in health and disease (DOI:<a href="https://doi.org/10.1164/rccm.200809-1522ST"> 10.1164/rccm.200809-1522ST</a>). Design-based stereology is founded on stochatic geometry and rigorous sampling protocols to obtain a set of images which is representative for the whole organ so that the generated data are accurate (unbiased) and sufficiently precise. Regarding quantitative light and electron microscopic analyses lungs were fixed by airway instillation fixation using 1.5 % glutaraldehyde, 1.5% paraformaldehyde in 0.15M HEPES buffer at a hydrostatic pressure of 25 cmH<sub>2</sub>O. Afterwards lungs were subjected to a systematic uniform random sampling for light and transmission electron microscopy based on established protocols (DOI: 10.1016/j.aanat.2013.04.011). Regarding light microscopy, 3 to 4 tissue samples were taken randomly per lung, embedded in plastic (Technovit 8100), sectioned (thickness of 1.5 µm) and stained with toluidine blue. Whole slides were scanned (AxioScanZ.1) and subjected to a systematic uniform area sampling process using newCAST-stereology software (Visiopharm, Hoersholm, Denmark) to image 10% of the section. Depending on the size of the section the goal was to obtain at least 60 (in general >100) randomized light microscopic images per lung for quantitative assessment. Moreover, 6 tissue blocks were randomly taken for transmission electron microscopy, embedded in epoy resin (Epon) and sectioned with a thickness of 80nm. Using an electron microscope (FEI Morgagni transmission electron microscope, Eindhoven, The Netherlands), a systematic uniform area samplinbg was performed and at least 100 micrographs were randomly taken per lung. The dataset in this publication contains the representative light and transmission electron microscopic images of lungs from six different experimental groups (male Fisher 344 rats, aged 11-13 weeks). Healthy rat lung were either not mechanically ventilated (H/ No ventil) or mechanically ventilated with positive end-exspiratory pressure (PEEP) = 1 cmH2O (group H/PEEP1) or PEEP = 5 cmH2O (group H/PEEP5). In addition, lungs suffering from occult lung injury due to bleomycin instillation were also either not mechanically ventilated (B/No ventil) or ventiled with PEEP = 1 cmH2O (B/PEEP1) or PEEP = 5 cmH2O (B/PEEP5). The respiratory rate was 90/min and the tidal volume was 10ml/ kg bodyweight.</p>
Dataset of A2780 and G361 cells - efect of FITC phototoxicity, quantitative phase imaging (2/2)
<p>Part of article Feith, M,Vičar, T., Gumulec, J., Raudenská, M. Wingren, AG, Masařík, M., Balvan, J. Quantitative Phase Dynamics of Cancer Cell Populations Affected by Blue Light, <em>Appl. Sci.</em> <strong>2020</strong>, <em>10</em></p> <p>Increased exposition to blue light may induce many changes in cell behavior and significantly affect the critical characteristics of cells. Here we show that multimodal holographic microscopy (MHM) within advanced image analysis is capable of correctly distinguishing between changes in cell motility, cell dry mass, cell density, and cell death induced by blue light. We focused on the effect of blue light with a wavelength of 485 nm on morphological and dynamical parameters of four cell lines, malignant PC-3, A2780, G361 cell lines, and the benign PNT1A cell line. We used MHM with blue light doses 24 mJ/cm<sup>2</sup>, 208 mJ/cm<sup>2 </sup>and two kinds of expositions (500 and 1000 ms) to acquire real-time quantitative phase information about cellular parameters. It has been shown that specific doses of the blue light significantly influence cell motility, cell dry mass and cell density. These changes were often specific for the malignant status of tested cells. Blue light dose 208 mJ/cm<sup>2 </sup>× 1000 ms affected malignant cell motility but did not change the motility of benign cell line PNT1A. This light dose also significantly decreased proliferation activity in all tested cell lines but was not so deleterious for benign cell line PNT1A as for malignant cells. Light dose 208 mJ/cm<sup>2 </sup>× 1000 ms oppositely affected cell mass in A2780 and PC-3 cells and induced different types of cell death in A2780 and G361 cell lines. Cells obtained the least damage on lower doses of light with shorter time of exposition.</p> <p><strong>Materials and Methods </strong></p> <p><em>Cell Lines</em></p> <p>The PC-3, A2780, PNT1A, and G361 cell lines were purchased from HPA Culture Collections (Salisbury, UK). PC-3 prostate cancer cell line was derived from bone metastasis of a 4-grade prostatic adenocarcinoma of a 62-year-old Caucasian male The A2780 cell line was derived from the ovarian carcinoma of a nontreated patient according to ECACC. PNT1A cell line was established from prostatic epithelial tissue of healthy 35-years old male and immortalized by plasmid transfection containing the SV40 genome with defective replication origin. The G361 cell line was established from a malignant melanoma of a 31-year-old male Caucasian. The G361 cells produce melanin for up to 50 population doublings. As the aim of this study is to compare the effect of blue light on the cell lines differing by morphology, transformation state, sensitivity to cell death, and origin, we decided to use the cell lines listed above. PC-3 cells are larger in comparison with small A2780 cells. Benign PNT1A cell line differs from malignant PC-3, and all four cell lines are derived from diverse tissues of origin. Furthermore, melanoma G361 cells expressing melanin may differ in the reaction of cells to blue light exposure.</p> <p></p> <p><em>Cell Cultivation</em></p> <p>All four cell lines were cultivated in 25 cm<sup>2</sup> flasks with 5 ml of media at 37 °C in a humidified incubator (60%) with 5% CO<sub>2 </sub>(Sanyo, Osaka City, Japan). Cell lines A2780, PNT1A and G361 were cultured in RPMI-1640 medium with phenol red indicator, L–glutamine, FBS and antibiotics penicillin/streptomycin (Sigma Aldrich Co., St. Louise, MO, USA). For the PC-3 cell line cultivation, Ham´s F-12 medium with FBS and antibiotics (Sigma Aldrich Co., St. Louis, MO, USA) was used. The same supplementation with antibiotics (penicillin 100 U/mL and streptomycin 0.1 mg/mL) and 10% FBS was used in both media. The cell medium was changed two times per week. Cell subculturing was done with 10% of trypsin solution (PAA, Pasching, Austria) with previous washing with EDTA (0.02% in PBS buffer).</p> <p><em>QPI and Holographic Microscopy and Fluorescence Setting</em></p> <p>QPI was performed by using a Q-PHASE multimodal holographic microscope (Telight, Brno, CZ). The Q-PHASE is equipped with fluorescence module using a halogen lamp as a non-coherent source of blue light. In this work, the module was used as a source of blue light for treatment of observed cell lines. The 485 nm light waves are emitted by the fluorescence light source of the attached module. Before the imaging experiment, cells were cultivated overnight in a concentration of 7000 cells/mL in flow chamber µ-Slide I Lauer Family (Ibidi, Martinsried, Germany). During the measurements, the chamber with cells was incubated in 37 °C humidified, 5% CO<sub>2</sub> atmosphere in H201–for Mad City Labs Z100/Z500 piezo Z-stages (Okolab, Ottaviano NA, Italy). Images and holograms were captured with lens Nikon Plan 10/0.3 and CCD camera (XIMEA MR4021 MC-VELETA, Münster, Germany) respectively. The fluorescence mode used was a plasma light source (Sutter Instrument Lambda XL Novato, CA, USA). Cells were irradiated with a 485 nm light with a 25 nm bandwidth. Light doses 0 mJ/cm<sup>2</sup>, 24 mJ/cm<sup>2</sup> and 208 mJ/cm<sup>2 </sup>were achieved by the combination of time exposition and light intensity.</p> <p>The images were acquired automatically from seven positions every 3 min for 24 h. Holographic images were collected by custom software and raw data were numerically reconstructed. The numerical reconstruction was performed by custom software where the established methods of the fast Fourier-transform and phase unwrapping are implemented. The output from the software is an unwrapped phase image. This image has high intrinsic contrast and can be processed by an available image processing software. The unwrapped phase image is integrated phase shift through the cell and it is proportional to integrated cell dry mass density.</p>
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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.