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368 results for “imaging system”
Processed Vectra images for primary central nervous system lymphoma (PCNSL) patients
<ul> <li>FFPE materials</li> </ul> <p>Formalin-fixed paraffin-embedded (FFPE) tumor samples and clinical data were obtained from PCNSL patients enrolled in the HOVON105/ALLG NHL 24 intergroup, multicenter, open-label, randomized phase 3 study (NTR2437 and ACTRN12610000908033) through the HOVON Pathology Facility and Biobank. </p> <ul> <li>Muiltiplex imaging</li> </ul> <p>Multiplex immunofluorescence was performed on 4-µm-thick formalin-fixed, paraffin-embedded whole tissue sections using the Opal 7-color fluorescence immunohistochemistry (IHC) kit (Akoya biosciences, USA), as previously described. In brief, slides were deparaffinized and rehydrated, followed by a blocking step for endogenous peroxidase using 0.3% H<sub>2</sub>O<sub>2</sub>/methanol and fixation with 10% neutral buffered formalin (Leica Biosystems, Germany). Slides were washed in Milli-Q water and 0.05% Tween20 in 1x Tris-Buffered Saline (TBS-T). Antigen retrieval was done by placing the slides in 0.05% ProClin300/Tris–EDTA buffer pH 9.0 in a microwave at 100% power until boiling, followed by 15 min at 30% power. Slides were cooled in Milli-Q water, washed in 1x TBS-T and blocked with Antibody Diluent (Agilent, USA). The slides were then incubated with primary antibody diluted in Normal Antibody Diluent, followed by incubation with the broad spectrum HRP from the SuperPicture Polymer Detection Kit (Life Technologies, USA). Next, the slides were incubated with Opal TSA fluorochromes diluted in an amplification buffer (Akoya biosciences, USA). The primary and secondary antibody complex was stripped by microwave treatment with 0.05% ProClin300/Tris–EDTA buffer at pH 9.0. Finally, DAPI working solution (Akoya biosciences, USA) was applied and the slides were mounted with Prolong Diamond Anti-fade mounting medium (#P36965; Life Technologies).</p> <ul> <li>Image processing</li> </ul> <p>Stained slides were scanned using the Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya biosciences, USA). From each slide, representative tumor regions and regions at the junction of tumor and surrounding cerebral tissue were selected and multispectral imaging (MSI) images were acquired at 40x resolution. After image capture, the images were spectrally unmixed and analyzed, using supervised machine learning algorithms within Inform 4.2.2. (Akoya biosciences). Cells were assigned into ten different phenotype categories: “PAX5+PD-L1-”, “PAX5+PD-L1+”, “CD163+PD-L1-”, “CD163+PD-L1+”, “CD3+CD8-PD-1-”, “CD3+CD8+PD-1-”, “CD3+CD8-PD-1+”, “CD3+CD8+PD-1+”, “other PD-L1+” or “other”, based on the size of the cells and positivity of markers in the panel. </p> <p> </p>
Data from: Accelerated high-throughput imaging and phenotyping system for small organisms
<p>Studying the complex web of interactions in biological communities requires large multifactorial experiments with sufficient statistical power. Automation tools reduce the time and labor associated with setup, data collection, and analysis in experiments that untangle these webs. We developed tools for high-throughput experimentation (HTE) in duckweeds, small aquatic plants that are amenable to autonomous experimental preparation and image-based phenotyping. We showcase the abilities of our HTE system in a study with 6,000 experimental units grown across 2,000 treatments. These automated tools facilitated the collection and analysis of time-resolved growth data, which revealed finer dynamics of plant-microbe interactions across environmental gradients. Altogether, our HTE system can run experiments with up to 11,520 experimental units and can be adapted for other small organisms.</p>
Code and data for: Decoupling channel count from field-of-view and spatial resolution in single-sensor imaging systems for fluorescence image-guided surgery
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ThermoCyte: an inexpensive open-source temperature control system for in vitro live cell imaging
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A high-throughput multispectral imaging system for museum specimens
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Code and data for: Interpolant-based demosaicing routines for dual-mode visible/near-infrared imaging systems
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Data from: SLICE-MSI: A machine learning interface for system suitability testing of mass spectrometry imaging platforms
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Data from: Accelerated high-throughput imaging and phenotyping system for small organisms
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Data for: High-Speed 3D Imaging of Multiphase Systems: Applying SCAPE Microscopy to Analogue Experiments in Volcanology and Earth Sciences
<p>Microscale processes in three-phase suspensions (mixtures of gas, liquids, and solids) can affect the macroscale behavior of the whole suspension. To visualize these small-scale processes at high speed and in 3D, we use a recently developed imaging system: Swept Confocally-Aligned Planar Excitation (SCAPE) microscopy. This dataset contains 3D videos taken with SCAPE microscopy of experiments where different phases interact with each other. Each zipped folder contains raw data and processed data for a single experiment. "Case 1" experiments show CO2 bubbles growing on PMMA (acrylic) particles in sparkling water. The "Case 2" experiment shows water droplets suspended in canola oil and flowing through a porous medium made of packed PMMA particles. "Case 3" experiments show growth of injected air bubbles in particle suspensions (either glass beads in immersion oil, or PMMA particles in a refractive index matched liquid).</p> <p>All scaling parameters are provided in Table 1. "info.txt" files contain metadata for the processed hyperstacks.</p> <p>The experiments provided here are discussed in the following publication:<br> Oppenheimer, J.*, Patel, K.*, Lindoo, A., Hillman, E. M. C., and Lev, E.: High-Speed 3D Imaging of Multiphase Systems: Applying SCAPE Microscopy to Analogue Experiments in Volcanology and Earth Sciences. <em>Geochemistry, Geophysics, Geosystems.</em> (In press, 12/2020)</p> <p><br> </p>
The 2009 Mw6.1 L'Aquila normal fault system imaged by 64,051 high-precision foreshock and aftershock locations.
<p>The earthquake catalogue is composed by 64,051 high-precision foreshock and aftershock recorded during the Mw6.1 2009 L'Aquila (Central Italy) normal faulting seismic sequence. The catalog includes events occurred between 1<sup>st</sup> of January and 31<sup>st</sup> December 2009. The completeness magnitude is 0.7. Earthquake locations were obtained by combining an automatic picking procedure for P and S waves, together with cross-correlation and double-difference location methods. </p> <p>Seismic data were recorded at a very dense local network composed of 67 three-component seismic stations (20 permanent stations of the Italian National Network located within 80 km from the epicentral area and 47 temporary stations installed soon after the occurrence of the main shock [Margheriti et al., 2011]). </p> <p>Earthquakes were extracted by the continuous recordings by applying a detection algorithm to all stations, based on the classical STA/LTA coincidence-sum algorithm applied to the trace of the 3C covariance matrix. To these events, we applied an automatic picking algorithm (Manneken Pix) [Di Stefano et al., 2006] able to provide about 1.9 million P-wave and 503,000 S-wave accurate readings, with an estimation of the measurement errors. </p> <p>We applied a time domain cross-correlation method (Schaff and Waldhauser, 2005) to all event pairs with separation distances ≤ 5 km at all stations that recorded the pair. Seismograms were filtered in the 1-15 Hz frequency range using a 4 pole, zero phase band‐pass Butterworth filter. We selected measurements with correlation coefficients greater than 0.85, resulting in a total of ~190 million P and ~85 million S-wave delay times. </p> <p>Earthquakes were located following a two steps procedure. Initial locations for 133,236 events were computed with the Hypoellipse code [Lahr , 1989] using a 1D P-wave gradient velocity model optimized for the area [Chiaraluce et al., 2011]. In the second step, we computed relative locations by applying the large scale double-difference method described in Waldhauser and Schaff, (2008) to the catalog picks and phase delay times measured from waveform cross correlation. The entire dataset was sub-divided in 84 rectangular overlapping boxes, containing a maximum of 3000 earthquakes, orthogonal to the mean strike of the seismic sequence. Resulting relative locations from all boxes were combined into a single catalog, computing the weighted mean of double hypocenters in the overlapping regions (Waldhauser and Schaff, 2008). </p> <p>The final double-difference catalog includes 64,051 events. A subset made of 51,271 earthquakes (i.e., 80% of the whole dataset) indicates highly correlated earthquakes, having at least 10 P-waves and 5 S-waves correlated phases with at least one other event. Highly correlated events (flag=1 in the attached file) mostly occur on the major fault segments, while poorly correlated earthquakes (flag=0 in the attached file) mostly occur in the volume around the major faults.</p> <p>The attached file is a plain text with ";" separator and .csv extension.</p> <p>Here below the header is explained.</p> <p><strong>id_dd: </strong>the hypoDD unique event identifier</p> <p><strong>origin_time: </strong>date of the origin time in the format YYYY-MM-DD[T]hh:mm:ss.msec</p> <p><strong>lat</strong>: hypocenter latitude expressed in degrees </p> <p><strong>lon</strong>: hypocenter longitude east of Greenwich, expressed in degrees</p> <p><strong>dep</strong>: hypocenter depth expressed in km </p> <p><strong>mag</strong>: magnitude (pure number)</p> <p><strong>flag</strong>:<strong> </strong>1 for highly correlated earthquakes; 0 for poorly correlated earthquakes. </p> <p> </p> <p> </p> <p> </p>
Analysis of the root diameter distribution from time series images of real and simulated Cassava root systems
<p>The data was collected, simulated and analyzed in the framework of the CassavaStore project (a collaboration between IBG-2, Forschungszentrum Jülich, Germany and different institution from Thailand; for details see <a href="https://www.international-bioeconomy.org/cassavastore_eng">https://www.international-bioeconomy.org/cassavastore_eng</a>). Aim of this project is to get a better understanding of storage root development in cassava (<em>Manihot esculenta</em> Crantz) in order to optimize cassava growth with respect to variety breeding and growth management. The storage root is one of the main providers of starch in Thailand and therefore of high economic importance. Monitoring the formation of storage roots over time via quantification of the root diameter distribution of excavated root systems was one of the key aspects addressed in this project. To measure the diameters a software was developed that identifies roots in RGB images and analyzes the diameters along each identified root automatically. The published data contains 1) analyzed images from cassava roots that were acquired in a video box; 2) simulated virtual root model images with known root diameter distributions that were used to validate the analysis approach; 3) a description of the data and the folder structure.</p>
Dataset for the article "PERFORMANCE EVALUATION OF AN IMAGING RADIATION PORTAL MONITOR SYSTEM"
<p>The dataset includes root files used in generating the main figures for the article "PERFORMANCE EVALUATION OF AN IMAGING RADIATION PORTAL MONITOR SYSTEM" by Jana Vasiljević, Alf Göök and Bo Cederwal. The article will be submitted to MDPI Applied Sciences.</p> <p> </p>
Avian-eye-inspired perovskite artificial vision system for foveated and multispectral imaging
<p>Avian eyes possess a deep central fovea as a result of extensive evolution. Deep fovea efficiently refracts incident light, creating a magnified image of the target object and making it easier to track its motion. These features are essential for detecting and tracking remote objects in dynamic environments. Furthermore, avian eyes respond to a wide spectrum of light, including visible and ultraviolet light, allowing them to efficiently distinguish the target object from complex backgrounds. Despite notable advances in artificial vision systems that mimic animal vision, the exceptional object detection and targeting capabilities of avian eyes via foveated and multispectral imaging remain underexplored. Here, we present an artificial vision system that capitalizes on these aspects of avian vision. We introduce an artificial fovea and vertically-stacked perovskite photodetector arrays whose designs are optimized by theoretical simulations for the demonstration of foveated and multispectral imaging. The artificial vision system successfully identifies colored and mixed-color objects and detects remote objects through foveated imaging. The potential for use in uncrewed aerial vehicles that need to detect, track, and recognize distant targets in dynamic environments is also discussed. Our avian-eye-inspired perovskite artificial vision system marks a notable advance in bio-inspired artificial visions.</p>
Image dataset for disease quantification in barley and wheat using the Macrobot system and BluVision Macro software
<p>This dataset contains multi-spectral high-resolution macroscopic images acquired using the Macrobot system, tailored for the automated analysis of plant disease phenotyping. The dataset includes images focused on three specific diseases: </p> <ul> <li>Bipolaris sorokiniana on barley, with images captured 8 days after inoculation </li> <li>Blumeria graminis f. sp. hordei resp. tritici (wheat powdery mildew) on wheat with images captured 8 days after inoculation</li> <li>Puccinia striiformis (yellow rust) on wheat, with images taken 15 days after inoculation</li> </ul> <p>For each sample, the dataset includes individual R, G, B, UV, and backlight illumination images, along with a combined RGB preview image.</p> <p>The BluVision Macro software is compatible with this dataset, enabling precise quantification and analysis of disease severity on barley and wheat leaves. </p>
Unidimensional Phenotypes using Concurrent Imaging Collected Via a High-Throughput Imaging System
<p>SIPID and SIMID are dataset repositories used to compute Single-Aspect Phenotypes. SAPP has 28 samples and SAPM has 12 samples. Each dataset contains:</p> <ol> <li>Two species physically different. Buckwheat is a thin plant with a variety sizes of leaves and Sunflower is a bushy plant that contains flowering;</li> <li>the most commonly used induced environments in plant phenotyping such as a control and drought-induced; </li> <li>a temporal resolution that begins with the plants vegetative stage and ends with the plant fully matured;</li> <li>modalities (infrared, visible, near infrared) that are commonly used in plant phenotyping analysis; and </li> <li>multiple perspectives that are becoming widely acquired in plant phenotyping analysis due to its potential for three dimensional analysis.</li> </ol> <p>We thank Vincent Stoeger for acquiring the dataset using LemnaTec at the University of Nebraska-Lincoln.</p> <p>If you use this dataset, please cite this paper:</p>
data set for Design of architectural environment integration of cyber-physical systems based on image segmentation and retrieval technology
<p>This data set is used to implement the project Design of architectural environment integration of cyber-physical systems based on image segmentation and retrieval technology</p>
Search strategies for generic justification for a slot scanning, biplanar X-ray imaging system (EOS™ imaging system) for the diagnosis and assessment of orthopaedic conditions.
<p>The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The search strategies address the following research questions:</p> <p>RQ 1 To determine the test accuracy, clinical benefits and safety of slot scanning devices (EOS system) compared to conventional X-ray imaging for diagnosis of scoliosis and evaluation or monitoring of scoliosis patients.</p> <p>RQ 2 To determine the test accuracy, clinical benefits and safety of slot scanning devices (EOS system) compared to current practice for evaluation, monitoring or diagnosis of patients with other known or suspected orthopaedic conditions.</p>
Data from: 3-D deconvolution of human skin immune architecture with Multiplex Annotated Tissue Imaging System (MANTIS)
<p><span class="pre-line-wrapping ng-binding">Routine clinical assays, such as conventional immunohistochemistry, often fail to resolve the regional heterogeneity of complex inflammatory skin conditions. Here we introduce MANTIS (Multiplexed Annotated Tissue Imaging System), a flexible analytic pipeline compatible with routine practice, specifically designed for spatially-resolved immune phenotyping of the skin in experimental or clinical samples. Based on phenotype attribution matrices coupled to alpha-shape algorithms, MANTIS projects a representative digital immune landscape, while enabling automated detection of major inflammatory clusters and concomitant single-cell data quantification of biomarkers. We observed that severe pathological lesions from systemic lupus erythematosus, Kawasaki syndrome, or COVID-19-associated skin manifestations share common quantitative immune features, while displaying a non-random distribution of cells with the formation of disease-specific dermal immune structures. Given its accuracy and flexibility, MANTIS is designed to solve the spatial organization of complex immune environments to better apprehend the pathophysiology of skin manifestations.</span></p>
Software Architecture Reconstruction for Microservice Systems Using GraalVM Native Image
<p>This Dataset contains the System Architecture Reconstruction for Train-Ticket microservice benchmark.</p> <p>It includes: Manual Analysis, GraalVM Analysis, and Source code Analysis.</p> <p>It's described in a paper with title: Software Architecture Reconstruction for Microservice Systems Using GraalVM Native Image</p> <p> </p>
Novel Optical Surface Image Guidance System for Beam-Gated Online Adaptive SBRT Delivery in Mobile Lower Lung and Upper Abdominal Malignancies
ClinicalTrials.gov study NCT05030454. IPD Sharing: YES. Countries: 1. Publications: 1.
ScienceDex guides
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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.