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ShareScore release 0.9.0
Dataset results
469 results for “Image analysis”
Demo dataset for publication "Development of image analysis tool to evaluate Langerhans cell migration after exposure to isothiazolinones"
<p>This dataset consists of a QuPath project and two images that can be used to test the scripts produced by the publication </p> <p>"Development of image analysis tool to evaluate Langerhans cell migration after exposure to isothiazolinones"</p>
Dataset related to article [18F]FDG PET/CT in Large Vessel Vasculitis: The Impact of Expertise and Confounders on Image Analysis
<p>[<sup>18</sup>F]FDG PET/CT in Large Vessel Vasculitis: The Impact of Expertise and Confounders on Image Analysis</p> <p> </p>
Dataset related to article "Frozen Section Analysis and Real-Time Magnetic Resonance Imaging of Surgical Specimen Oriented on 3D Printed Tongue Model to Assess Surgical Margins in Oral Tongue Carcinoma: Preliminary Results"
<p>This record contains raw data related to article “Frozen Section Analysis and Real-Time Magnetic Resonance Imaging of Surgical Specimen Oriented on 3D Printed Tongue Model to Assess Surgical Margins in Oral Tongue Carcinoma: Preliminary Results"</p> <p>Abstract</p> <p><strong>Background: </strong> A surgical margin is the apparently healthy tissue around a tumor which has been removed. In oral cavity carcinoma, a negative margin is considered ≥ 5 mm, a close margin between 1 and 5 mm, and a positive margin ≤ 1 mm. Currently, the intraoperative surgical margin status is based on the visual inspection and tissue palpation by the surgeon and intraoperative histopathological assessment of the resection margins by frozen section analysis (FSA). FSA technique is limited and susceptible to sampling errors. Definitive information on the deep resection margins requires postoperative histopathological analysis.</p> <p><strong>Methods: </strong> We described a novel approach for the assessment of intraoperative surgical margins by examining a surgical specimen oriented through a 3D-printed specific patient tongue with real-time Magnetic Resonance Imaging (MRI). We reported the preliminary results of a case series of 10 patients, prospectively enrolled, with oral tongue carcinoma who underwent surgery between February 2020 and April 2021. Two radiologists with 5 and 10 years of experience, respectively, in Head and Neck radiology in consensus evaluated specimen MRI and measured the distance between the tumor and the specimen surface. We performed intraoperative bedside FSA. To compare the performance of bedside FSA and MRI in predicting definitive margin status we computed the weighted sensitivity (SE), specificity (SP), accuracy (ACC), area under the ROC curve (AUC), F1-score, Positive Predictive Value (PPV), and Negative Predictive Value (NPV). To express the concordance between FSA and <em>ex-vivo</em> MRI we reported the jaccard index.</p> <p><strong>Results: </strong> Intraoperative bedside FSA showed SE of 90%, SP of 100%, F1 of 95%, ACC of 0.9%, PPV of 100%, NPV (not a number), and jaccard of 90%, and <em>ex-vivo</em> MRI showed SE of 100%, SP of 100%, F1 of 100%, ACC of 100%, PPV of 100%, NPV of 100%, and jaccard of 100%. These results needed to be validated in a larger sample size of 21- 44 patients.</p> <p><strong>Conclusion: </strong> The presented method allows a more accurate evaluation of surgical margin status, and the first clinical experiences underline the high potential of integrating FSA with <em>ex-vivo</em> MRI of the fresh surgical specimen.</p>
Comparison of Four-Dimensional Magnetic Resonance Imaging Analysis of Left Ventricular Fluid Dynamics and Energetics in Ischemic and Restrictive Cardiomyopathies.
<p>Riva A, Sturla F, Pica S, Camporeale A, Tondi L, Saitta S, Caimi A, Giese D, Palladini G, Milani P, Castelvecchio S, Menicanti L, Redaelli A, Lombardi M, Votta E. Comparison of Four-Dimensional Magnetic Resonance Imaging Analysis of Left Ventricular Fluid Dynamics and Energetics in Ischemic and Restrictive Cardiomyopathies. J Magn Reson Imaging. 2022 Oct;56(4):1157-1170. doi: 10.1002/jmri.28076. Epub 2022 Jan 24. PMID: 35075711; PMCID: PMC9541919.</p> <p>Abstract</p> <p><strong>Background: </strong>Time-resolved three-directional velocity-encoded (4D flow) magnetic resonance imaging (MRI) enables the quantification of left ventricular (LV) intracavitary fluid dynamics and energetics, providing mechanistic insight into LV dysfunctions. Before becoming a support to diagnosis and patient stratification, this analysis should prove capable of discriminating between clearly different LV derangements.</p> <p><strong>Purpose: </strong>To investigate the potential of 4D flow in identifying fluid dynamic and energetics derangements in ischemic and restrictive LV cardiomyopathies.</p> <p><strong>Study type: </strong>Prospective observational study.</p> <p><strong>Population: </strong>Ten patients with post-ischemic cardiomyopathy (ICM), 10 patients with cardiac light-chain cardiac amyloidosis (AL-CA), and 10 healthy controls were included.</p> <p><strong>Field strength/sequence: </strong>1.5 T/balanced steady-state free precession cine and 4D flow sequences.</p> <p><strong>Assessment: </strong>Flow was divided into four components: direct flow (DF), retained inflow, delayed ejection flow, and residual volume (RV). Demographics, LV morphology, flow components, global and regional energetics (volume-normalized kinetic energy [KE<sub>V</sub> ] and viscous energy loss [EL<sub>V</sub> ]), and pressure-derived hemodynamic force (HDF) were compared between the three groups.</p> <p><strong>Statistical tests: </strong>Intergroup differences in flow components were tested by one-way analysis of variance (ANOVA); differences in energetic variables and peak HDF were tested by two-way ANOVA. A P-value of <0.05 was considered significant.</p> <p><strong>Results: </strong>ICM patients exhibited the following statistically significant alterations vs. controls: reduced KE<sub>V</sub> , mostly in the basal region, in systole (-44%) and in diastole (-37%); altered flow components, with reduced DF (-33%) and increased RV (+26%); and reduced basal-apical HDF component on average by 63% at peak systole. AL-CA patients exhibited the following alterations vs. controls: significantly reduced KE<sub>V</sub> at the E-wave peak in the basal segment (-34%); albeit nonstatistically significant, increased peaks and altered time-course of the HDF basal-apical component in diastole and slightly reduced HDF components in systole.</p> <p><strong>Data conclusion: </strong>The analysis of multiple 4D flow-derived parameters highlighted fluid dynamic alterations associated with systolic and diastolic dysfunctions in ICM and AL-CA patients, respectively.</p>
Introduction to Biomedical Image Analysis (for Beginners)
<p>Small dataset of the zebrafish brain vasculature acquired at 3 days post fertilization (dpf) with a Zeiss Z.2 light-sheet microscope. Transgenic reporter line used: blood vessels <em>Tg(kdrl:HRAS-mCherry)</em><sup><em>s916</em></sup> labels EC membrane (Chi et al., 2008).</p> <p>Data were acquired by Elisabeth Kugler at the University of Sheffield conforming to UK Home Office regulations and were performed under Home Office Project Licence 70/8588 held by TJAC. - Data are part of the publication: Kugler et al., 2019 as well as Dr Kugler's thesis.</p> <p>Dataset consists only of 3 samples and is used as a sample dataset to train students in biomedical image analysis.</p> <p>Image Acquisition Details:<br> Datasets in Sheffield were obtained using a Zeiss Z.1 light sheet microscope with a water-dipping detection objective (Plan-Apochromat 20×/1.0 Corr nd = 1.38) and a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data were acquired with activated pivot scan, dual-sided illumination and online fusion; properties of acquired data are as follows: 0.7× zoom, 16bit image depth, 1,920 × 1,920px image size and minimum z-stack interval (approx. 0.33 × 0.33× 0.5 μm). Green and red fluorophores were excited using 488 nm and 561 nm laser, respectively. Used filters in sequential tracks for multi-colour images were LP560 for both and BP505-545 and LP585, respectively. Samples were embedded in 1% or 2% LMP-agarose containing 200 mg/l Tricaine (MS-222, Sigma). The image acquisition chamber was filled with E3 plus Tricaine (200 mg/ml) and maintained at 28°C.</p>
Analysis of an optical imaging system prototype for autonomously monitoring zooplankton in an aquaculture facility
<p>This upload consists of a zip file containing all the images used in the zooplankton training library. Individual folders of each zooplankton class contain all the images in the training library for that respective class. Each image is labeled with its actual classification. The labeled images provide a reproducible source to test and retest various classification algorithms and image decomposition approaches.</p>
dataset for image analysis for ML
<p>image dataset for image analysis for ML</p>
Which are the most frequently involved peripheral joints in calcium pyrophosphate crystal deposition at imaging? A Systematic Literature Review and meta-analysis by the OMERACT Ultrasound – CPPD subgroup
<p><strong>Objectives</strong>: To identify the prevalence of calcium pyrophosphate crystal deposition (CPPD) using ultrasound and conventional radiology at peripheral joints in patients with suspected or definite CPPD.</p> <p><strong>Methods: </strong>A systematic literature search was performed in PubMed and Embase using pre-defined search strategies from inception to April 2021 to identify studies that evaluated conventional radiology and ultrasound in detecting CPPD at peripheral joints, including definite or suspected CPPD [Research question 1 (RQ1) and Research Question 2 (RQ2), respectively]. For the meta-analysis, the first, second, and third sub-analysis included studies with the knee, and knee or wrist as the index joint for CPPD (without restrictions on the reference standard) and synovial fluid analysis or histology as a reference standard (without restrictions on the index joint), respectively.</p> <p><strong>Results: </strong>One-thousand eight hundred and twenty-seven manuscripts were identified, of which 94 articles were finally included. Twenty-two and seventy-two papers were included in RQ1 and RQ2, respectively. The knee had the highest prevalence for RQ1 and RQ2 by both conventional radiology and ultrasound, followed by the wrist with the highest prevalence for RQ1. The hand had the lowest CPPD prevalence. The third sub-analysis showed a higher CPPD prevalence on ultrasound than conventional radiology at the knee (only data available).</p> <p><strong>Conclusion: </strong>Among all peripheral joints, the knees and wrists could be regarded as the target joints for CPPD detection by imaging. Furthermore, ultrasound seems to detect a higher number of calcium pyrophosphate deposits than conventional radiology, even when using a more restrictive reference standard.</p>
Image analysis hatching
<p>Images for developing a machine learning approach for hatching</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.