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34 results for “Orientation imaging”
Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function
<p>Dataset for Ono et al., 2024.<br>Contains all source data from the Tarchini laboratory, including illustrative images and raw data for quantification, as well as the data file containing statistical analysis. It also contains the data file produced by the Cullen laboratory reporting behavioral data. </p>
Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
<p>Starving <em>Myxococcus xanthus</em> bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern as well as C-signal-dependent gene expression in TCs and spores were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.</p>
Replication Data for: (111)-oriented, single crystal diamond tips for nanoscale scanning probe imaging of out-of-plane magnetic fields
<p>Data repository for: <strong>(111)-oriented, single crystal diamond tips for nanoscale scanning probe imaging of out-of-plane magnetic fields</strong></p> <p><em>Data description.pdf </em>describes the uploaded data.<br> <em>Data.xlsx</em> is the data represented in the paper.</p>
Salient objects dominate the central fixation bias when orienting towards images
<p>Data and stimulus material from:</p> <p>Wolf, C., & Lappe, M. (2021). Salient objects dominate the central fixation bias when orienting towards images. Journal of Vision</p> <p>For questions please contact chr.wolf[at]wwu.de</p>
Fiber Orientation Estimation from X-ray Dark Field Images of Fiber Reinforced Polymers using Constrained Spherical Deconvolution: Data
<p>The data was simulated in GATEv8.0. The macro's and other files for the simulation can be found in the folders: Sim_50_40, Sim80_60 and Sim90_70. Here, the different files to perform the simulation are given, as well as the output data, found in the folders Flats and Projs (flatfields and projections) in the form of a csv-file. The csv-file contains 5000 rows (one for each image), and each row contains a flattened 450x450 image.</p> <p>The files for visualization of the fiber directions are given in the folder MRtrix. This folder contains the reconstructed scatter magnitudes and their respective directions in a mat-file. On this set of directions the constrained spherical deconvolution is applied using the sf_dirs.mif, sf_mask.mif, sf_response.mif and data.mif files. This returns the orientation density function in each voxel as output (odf_csd_14.mif). An alternative approach is performing a Funk-Radon transform on the coefficients of the scatter function (data_coeffs_10.mif) to obtain odf_frt_10.mif.</p> <p>Using a peak finding algorithm the fiber orientations are extracted from these odf-files and written to peaks_x.mif files, with or without a threshold (10% of largest amplitude).</p>
Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
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Data from: A tilt after-effect for images of buildings: evidence of selectivity for the orientation of everyday scenes
The tilt after-effect (TAE) is thought to be a manifestation of gain control in mechanisms selective for spatial orientation in visual stimuli. It has been demonstrated with luminance-defined stripes, contrast-defined stripes, orientation-defined stripes and even with natural images. Of course, all images can be decomposed into a sum of stripes, so it should not be surprising to find a TAE when adapting and test images contain stripes that differ by 15° or so. We show this latter condition is not necessary for the TAE with natural images: adaptation to slightly tilted and vertically filtered houses produced a 'repulsive' bias in the perceived orientation of horizontally filtered houses. These results suggest gain control in mechanisms selective for spatial orientation in natural images.
Text-fig. 23. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Longitudinal section (orthoslice yz0827) showing fruitlet with apical stigmatic region and a single seed enclosed within the fruitlet wall that has a thick epidermal cuticle; note the tiny embryo (emb) internal to the micropyle (mi) and oriented toward the base of the fruitlet; b) Transverse section through apical part of two fruitlets (orthoslice xy0810) showing the fruitlet wall (fr) composed of small thin-walled cells covered by an epidermis of isodiametric cells (ep) with a thick outer cuticle (cu); c) Longitudinal section (orthoslice xz0370) through basal part of fruitlet perpendicular to section in (a) showing the micropyle (mi), embryo (emb) composed of tiny cells, and the thick cuticle (cu) covering the bulging cells of the fruitlet epidermis. Specimen, Catefica 50-S174907 (a–c). Scale bars = 300 Μm (a–c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 23. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Longitudinal section (orthoslice yz0827) showing fruitlet with apical stigmatic region and a single seed enclosed within the fruitlet wall that has a thick epidermal cuticle; note the tiny embryo (emb) internal to the micropyle (mi) and oriented toward the base of the fruitlet; b) Transverse section through apical part of two fruitlets (orthoslice xy0810) showing the fruitlet wall (fr) composed of small thin-walled cells covered by an epidermis of isodiametric cells (ep) with a thick outer cuticle (cu); c) Longitudinal section (orthoslice xz0370) through basal part of fruitlet perpendicular to section in (a) showing the micropyle (mi), embryo (emb) composed of tiny cells, and the thick cuticle (cu) covering the bulging cells of the fruitlet epidermis. Specimen, Catefica 50-S174907 (a–c). Scale bars = 300 Μm (a–c).
Fig. 2. Habitus images for Diognetus species from Nepal. A–C – D in Revision of the plant bug genus Diognetus, with descriptions of thirteen new species from the Oriental and Eastern Palearctic Regions (Hemiptera: Heteroptera: Miridae)
Fig. 2. Habitus images for Diognetus species from Nepal. A–C – D. bagmaticus sp. nov.; D – a female identical to D. dhamphus sp. nov. (from Langtang Himal National Park, Rasuwa, NMTU); E – D. duwalorum sp. nov., holotype J; F–G, D. puspae sp. nov., sucking on banana fruit; H – a female identical to D. intonsus Distant, 1904 (from Langtang Himal National Park).
Data for: Artificial squares, rectangles and Xray images in random rotational orientations, centered and in different sizes
<p>SORFAC-CT (Cylindrical-Topology Self-Organizing Reference-Free Alignment and Classification; pronounced sôr-fakt or sôr-fak-si-ti) is an efficient method of reference-free rotational image alignment. SORFAC-CT circumvents the dependence of subjective user- or computer-generated external or internal reference images used by other reference-based techniques. Alignment is performed using a Kohonen self-organizing map (SOM), configured on a cylindrical array of artificial neurons. Although alternative alignment protocols often depend on an expert to adjust many ad hoc parameters, SORFAC-CT instead achieves the minimization of one objectively calculated target function by varying only two free parameters. Because SOMs preserve the topological properties of the training (dataset) images, the relative in-plane rotational orientations of dataset images are obtained directly from the array's intrinsic cylindrical coordinate system by noting each mapped dataset image's respective azimuthal angle coordinate placement around the cylinder. Dataset images are not rotated into alignment with internally or externally generated reference images. Instead, SORFAC-CT starts with a cylindrical array of proto-models consisting of random pixel values. The proto-models gradually morph to become the rotational class models by an unsupervised process. The dataset images are then mapped to the class models according to greatest similarity; the alignment angles directly read off the cylinder. This was tested on datasets including square, rectangular and hexagonal geometrical shapes in six different sizes, to introduce heterogeneity. It was also tested using noisy 2-dimensional projections of the AQP-1 x-ray model. The results were near-perfect alignments that could be improved by increasing cylinder circumference, until the resolution limits of the dataset images are reached.</p>
Data from: A tilt after-effect for images of buildings: evidence of selectivity for the orientation of everyday scenes
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Data for: Artificial squares, rectangles and Xray images in random rotational orientations, centered and in different sizes
Open the record for dataset details and reuse information.
Effectiveness of an Electronic Training Program for Orienting and Interpreting [18F]Flutemetamol Positron Emission Tomography (PET) Images
ClinicalTrials.gov study NCT01672827. IPD Sharing: Not stated. Countries: 0. Publications: 0.
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>
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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.