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249 results for “speckle”
Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions
<p>The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (<i>Notropis jemezanus</i>) and Speckled Chub (<i>Macrhybopsis aestivalis</i>), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of <i>N. jemezanus </i>and <i>M. aestivalis </i>in the Rio Grande and Pecos River was evaluated and standing genetic variation were characterized. Genetic evidence indicates that populations of both species found in the Rio Grande and Pecos River are genetically distinct. Additionally, 159 outlier loci were identified in <i>M. aestivalis </i>suggesting possible local adaptation in the Rio Grande and Pecos River populations. Though range-wide genetic data are limited, <i>N. jemezanus </i>populations in both rivers harbor considerable genetic diversity. Mitochondrial data from both taxa are consistent with a history of secondary contact between formerly isolated populations with deeply divergent haplotypes found within the Rio Grande and Pecos River populations of <i>N. jemezanus </i>and within the Rio Grande population of <i>M. aestivalis.</i> Extensive survey efforts in the lower Rio Grande and its tributaries in Texas document significant range contraction and near extirpation of <i>N. jemezanus </i>from this part of the basin; highlighting the need for immediate action to protect the species. </p>
Speckle images from biaxial test on PMMA
<p>These images were captured during a biaxial test on a PolyMethylAcrylate cruciform sample. The actuators were driven based on the strain measured during the test using GPU integrated DIC.</p> <p>The speckle pattern was made by spraying black paint using an airbrush on a white coat of paint.</p> <p>The camera is a Ximea XiB (CB500MG-CM), the lens a canon EF 100mm, pixel size is 4.51 µm/pix</p> <p>The name of the images is "img_{count}_{time}.tiff" where {count} is the number of processed images {time} the instant the image was captured after the beginning of the test in seconds. The average time between two saved image 5.21s but is not guaranteed to be constant (std = 0.0364s). img_ref_{time}.tiff is the reference image used by the DIC algorithm.</p> <p>Not all indexes are available because only 1/100 images were saved for post-processing to limit the volume of data.</p> <p>This set of image can be used in many ways, including as a benchmark for comparing DIC algorithms. Since they are real-world images, the "real" displacement is not available.</p> <p>correl.zip contains a csv file with the results of the real-time integrated DIC used during the test. Because a few images were dropped due to limitations, make sure to use the timestamp to match the images and the csv.</p>
Speckle image stacks acquired on human skin with a high-speed camera
<p>These datasets all consist of stacks of images of various body parts of of the same 50-year-old Caucasian male subject.</p> <p>For each acquisition, the skin was first illuminated with a near-infrared LASER (wavelength 785 nm). Then, the skin was filmed with a Phantom VEO 710L camera, with an acquisition rate of 2000 to 30,000 Hz.</p> <ul> <li>Datasets <strong>WRIST_1</strong>, <strong>WRIST_2</strong> and <strong>WRIST_3</strong> were acquired by imaging the anterior surface of the left wrist, with respective acquisition frequencies of 3000, 2000 and 10,000 Hz.</li> <li>Dataset <strong>FINGERS</strong> consists of images of the end of two fingers of the left hand. It was acquired at 30,000 Hz.</li> <li>Dataset <strong>EAR</strong> consists of images of the right ear. It was acquired at 2000 Hz.</li> <li>Dataset <strong>PALM</strong> consists of images of the palm of the left hand, which was gently scraped beforehand to trigger a superficial inflammation and draw a smiley face. It was then filmed with an acquisition frequency of 10,000 Hz.</li> </ul> <p>Each dataset is stored in a HDF5 file. The data array is stored as <strong>data </strong>at the root of the tree structure. Attributes <strong>T_exp </strong>and <strong>f_acq</strong> provide respectively the exposure time (in microseconds) and the acquisition rate (in Hertz) of the dataset. The script <strong>test.py </strong>shows how data can be accessed through Python and the library h5py. It can be used as follows:</p> <pre><code class="language-bash">python test.py filename.h5</code></pre> <p>All these datasets are used and referenced in our companion article "Dynamic speckle imaging of human skin vasculature with a high-speed camera" (to be published).</p>
Ptychographic X-ray speckle tracking (PXST) scan of the Siemens star test sample
<p>The PXST scan of the Siemens star test sample measured at P11 beamtime of the PETRA III synchrotron radiation facility. The beam was focused with a pair of MLLs with focal lengths of 1.25 mm and 1.15 mm and numerical apertures of 0.014 and 0.015, in the vertical and horizontal directions, respectively. The X-ray beam photon energy was 17.5 keV.</p>
Cardiac Mechanics by Speckle Tracking as a Prognostic Predictor in Patients With Chagas Cardiomyopathy
ClinicalTrials.gov study NCT06806722. IPD Sharing: NO. Countries: 1. Publications: 2.
Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions
Open the record for dataset details and reuse information.
Complex reticulate evolution of the speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism
Open the record for dataset details and reuse information.
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
FIGURE4.Map of selected records of Siphamia species recorded in Queensland and Papua New Guinea waters in 2003–2005, including the type locality of Siphamia guttulata. Some symbols represent more than one specimen. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE4.Map of selected records of Siphamia species recorded in Queensland and Papua New Guinea waters in 2003–2005, including the type locality of Siphamia guttulata. Some symbols represent more than one specimen.
FIGURE 3. Median predorsal scales of Siphamia guttulata (A—paralectotype, AMS I.16306-001, 25.7 mm SL; B—CSIRO H 7457-01, 27 mm SL) and Siphamia tubifer (C—CSIRO H 6752-02, 31 mm SL). Scale bar = 0.5 mm. Yellow arrows point to first dorsal spine, numbers or pink arrows indicate median predorsal scales. Fifth median predorsal scale of Fig. C is a scale pocket as the scale has been lost. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE 3. Median predorsal scales of Siphamia guttulata (A—paralectotype, AMS I.16306-001, 25.7 mm SL; B—CSIRO H 7457-01, 27 mm SL) and Siphamia tubifer (C—CSIRO H 6752-02, 31 mm SL). Scale bar = 0.5 mm. Yellow arrows point to first dorsal spine, numbers or pink arrows indicate median predorsal scales. Fifth median predorsal scale of Fig. C is a scale pocket as the scale has been lost.
FIGURE2. Digital radiograph of Siphamia guttulata (CSIRO H 6648-02, 25 mm SL). Blue circle highlighting two supraneurals. Scale bar = 0.5 mm. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE2. Digital radiograph of Siphamia guttulata (CSIRO H 6648-02, 25 mm SL). Blue circle highlighting two supraneurals. Scale bar = 0.5 mm.
Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.
Data from: Molecular phylogenetics and microsatellite analysis reveals cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon's Great Basin
Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs throughout western North America and is the most commonly occurring fish in Oregon. Because of the high genetic and morphological variation in this species across its range, it has been referred to as a species complex; however, no revision to its taxonomy has occurred since 1984. Here, the phylogenetics and population genetics of speckled dace are examined throughout Oregon's Great Basin to describe genetic variation and infer the geographic boundaries between distinct taxonomic entities and populations. We tested the validity of a putative subspecies, Foskett Spring speckled dace, that occurs in a single spring within Warner Valley in Southeast Oregon and is listed Federally as threatened. Dace were collected from Foskett Spring and all surrounding basins containing speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur), created phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data, and genotyped eight microsatellite loci for population-level analyses. Three highly divergent clades warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins combined. Although Foskett Spring dace were not monophyletic, substantial population structure occurs at the basin-level and separates Foskett Spring dace from other dace in the surrounding Warner Valley. Thus, we recommend ESU status for the isolated population of speckled dace in Foskett Spring. The high, previously unrecognized, taxonomic diversity within this region indicates a need for a range-wide phylogeographic study of speckled dace and an investigation of the morphological distinctiveness of the putative new species.
FIGURE 3 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 3. Arenaeus mexicanus (CCDB 2936) and diagnostic features. A, dorsal view; B, carpus view, with the inner spine (black arrow) and an outer denticle (white arrow) at the carpus; C, frontal view and the absence of a spine in the epistome region, note the concavity instead.
FIGURE 6 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 6. Bayesian tree for species of Arenaeus and selected out-groups based on the cytochrome oxidase I (COI) and large ribosomal subunit (16S) concatenated data set. Values represent Maximum Likelihood bootstrap (ML) and Bayesian (BAY) posterior probabilities, expressed as percentages (ML/BAY). ML bootstrap values <75% are not shown; BAY posterior probabilities <95% are not shown either. AL, Alagoas; GoM, Gulf of Mexico; LA, Louisiana; RN, Rio Grande do Norte; SC, Santa Catarina; SP, São Paulo.
FIGURE 2 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 2. First left gonopod of Arenaeus cribarius (CCDB 754). A, ventral view; B, tip morphology, ventral view; C, tip morphology, dorsal view; D, subterminal armature, lateral view; E, basal armature, dorsolateral view. Distal margin bent during the preparation (B and C).
FIGURE 4 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 4. First left gonopod of Arenaeus mexicanus (UNAM 3513). A, ventral view; B, tip morphology, ventrolateral view; C, tip morphology, dorsal view; D, subterminal armature, lateral view; E, basal armature, lateral view. Distal margin bent during the preparation (B and C).
FIGURE 5 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 5. An illustrated and simplified taxonomic identification key for the species of the genus Arenaeus.
FIGURE 1 in Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data
FIGURE 1. Arenaeus cribrarius (CCDB 754) and diagnostic features. A, dorsal view; B, merus-carpus joint view, with inner and outer spines (arrows) at the carpus; C, frontal view and the presence of a spine in the epistome region (arrow), between the antennules.
Sample data and algorithm implementation for ChiSCAT: Unsupervised Learning of Recurrent Cellular Micromotion Patterns from a Chaotic Speckle Pattern
<p>Sample data and algorithm implementation for the article </p> <div>Trelin, A., Kussauer, S., Weinbrenner, P., Clasen, A., David, R., Rimmbach, C., & Reinhard, F. (2024). ChiSCAT: Unsupervised Learning of Recurrent Cellular Micromotion Patterns from a Chaotic Speckle Pattern. <em>Nano Letters</em>, <em>24</em>(40), 12374-12381.</div>
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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.