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42 results for “microcomputed tomography”
Application of X‑ray Microcomputed Tomography for the Static and Dynamic Characterization of the Microstructure of Oleofoams
<p>Raw, greyscale image stacks collected during a X-Ray tomography analysis on cocoa butter-based oleofoams. The dataset is divided into three subsets: aeration, storage and heating, which contain samples that have been aerated for different amounts of time, samples that have been stored for 3 and 15 months at 20 °C, and finally samples that have been heated to the melting point of the stabilizing crystals, respectively. The dataset contains instructions and the scripts for ImageJ and MATLAB (as text files) to process and measure the bubble size distribution, and the thickness of the continous phase.</p>
FIGURE 2 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography
FIGURE 2. Panoramic view of the highest level of exploitation in Owadów-Brzezinki quarry (i.e., unit III and most fossiliferous 'Corbulomima horizon' occurring in the middle of the quarry wall).
FIGURE 4 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography
FIGURE 4. Maxillary bone of osteichthyan fish Caturus sp. (ZPAL P.16/O-B/2): 1-2. reconstruction of 3-D 'virtual fossils'— the same specimen after digital processing and analysis of tomographic data (scale bars equal 10 mm). 3. vertical sections of Caturus sp. teeth. 4. just after discovery.
FIGURE 1 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography
FIGURE 1. Map of Poland (1) with the location of the Owadów-Brzezinki Quarry (2B) near Tomaszów Mazowiecki.
FIGURE 3 in Late Jurassic jaw bones of Halecomorph fish (Actinopterygii: Halecomorphi) studied with X-ray microcomputed tomography
FIGURE 3. Jaw bone of osteichthyan fish Furo sp. (ZPAL P.16/O-B/1): 1-2. 3-D model of 'virtual fossils'—a different view of the same specimen after digital processing and analysis of tomographic data. 4. vertical sections of Furo sp. teeth. 5. 3-D printed dentary – 'virtual fossils'. 6. specimen in piece of limestone (scale bars equal 10 mm).
Image Dataset for 'Digitally deconstructing leaves in 3D using X-ray microcomputed tomography and machine learning'
<p>Dataset used in the manuscript 'Digitally Deconstructing Leaves in 3D Using X-ray microcomputed Tomography and Machine Learning'. Please cite the paper presenting this dataset:</p> <p><strong>Citation:</strong> Théroux-Rancourt, G., M. R. Jenkins, C. R. Brodersen, A. McElrone, E. J. Forrestel, and J. M. Earles. 2020. Digitally deconstructing leaves in 3D using X-ray microcomputed tomography<strong> </strong>and machine learning. <em>Applications in Plant Sciences</em> 8(7): .</p> <p> </p> <p><strong>Description of the dataset</strong></p> <p>A 'Cabernet Sauvignon' grapevine (<em>Vitis vinifera</em> L.) leaf from a plant of the BOKU experimental vineyard in Tulln, Austria, was scanned using microCT at the Swiss Light Source. The original reconstructions of the scans are using the gridrec (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Gridrec_reconstruction_downsized.zip?versionId=28d98982-f69d-4eac-9dfa-efcc89c6823c">Gridrec_reconstruction_downsized.zip</a>) and the paganin, or phase-contrast, algortithm (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Phase_contrast_reconstruction_downsized.zip?versionId=bef3260d-2865-4c9b-b5e1-e692edefb691">Phase_contrast_reconstruction_downsized.zip</a>). To facilitate automated segmentation, the size of the image in the <em>x </em>and <em>y</em> dimensions have been halved, so that the size of the pixels is 0.325 µm in those dimensions, but 0.1625 µm in the <em>z</em> (slices) dimension.</p> <p>A binary image segmenting the leaf cells and the airspace for each gridrec and phase-contrast stacks are created, and both are combined together (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Binary_stack_for_local_thickness.zip?versionId=165e3938-b490-4e56-9c8e-a2084cb39d49">Binary_stack_for_local_thickness.zip</a>), a map of the local thickness is created (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Local_thickness_map.zip?versionId=ce0a7dc7-5e3f-44a4-8881-cf84b6efd87c">Local_thickness_map.zip</a>). This map gives information on the largest diameter of the pixels labeled as cells in the binary stack.</p> <p>Hand-labeled slices or ground truths were drawn on the following slices: 80, 140, 200, 260, 340, 400, 440, 540, 620, 740, 800, 860, 940, 1060, 1140, 1240, 1300, 1400, 1480, 1540, 1600, 1690, 1740, 1840 (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Hand_labelled_slices.tif?versionId=a21a13ac-fa47-4ef8-a903-ecc433787184">Hand_labelled_slices.tif</a>).</p> <p>Using the hand-labeled slices and the different images, a random-forest model was trained, which allowed to automatically segment the remaining slices of the stack (<a href="https://zenodo.org/api/files/bbca544a-15d0-40f3-8cc9-a3ee3c08fd7e/Fullstack_Prediction_Example-6_training_slices-6_testing_slices.zip?versionId=02b69e65-da85-492e-9b72-9b2b3ccd085f">Fullstack_Prediction_Example-6_training_slices-6...</a>).</p> <p>The source code for the segmentation program is available <a href="https://github.com/plant-microct-tools/leaf-traits-microct/tree/master">here</a>, and the source code for the testing used in the paper is available <a href="https://github.com/plant-microct-tools/leaf-traits-microct/tree/nb-slices-eval">here</a>.</p>
Anatomy of the neural endocranium and stapes of Diadectes absitus (Diadectomorpha) from the early Permian of Germany based on the high‐resolution X‐ray microcomputed tomography
<p>A detailed anatomy of the braincase and stapes of the subadult specimen of <i>Diadectes absitus</i> from early Permian sediments of Germany based on the high-resolution X-ray microcomputed tomography are described for the first time. In contrast to previous studies of <i>Diadectes</i>, the bones of the braincase (opisthotic, prootic, supraoccipital, basioccipital, exoccipital, basisphenoid, sphenethmoid), and parasphenoid of <i>D. absitus</i> are not co-ossified, but suturally defined. This has allowed for a reconstruction of a complete braincase with all sutures between the individual bones. The opisthotic, prootic, and supraocciptal contain a well-preserved endosseous labyrinth. The 3D-reconstruction of its cavities shows a well-preserved vestibule, three semicircular canals, and well-developed cochlear recess. In addition, a shallow subarcuate fossa is present on the ventral surface of the supraoccipital, which lies medial to the anterior semicircular canal. A typical feature of the diadectid braincase is the presence of the otic tube leading from the fenestra vestibuli to the vestibule. A revision of the topology of this structure is presented here. Here we describe new structures of the stapes, especially in its proximal portion, as well as its position to the fenestra vestibuli. These structures are described for the first time not only in <i>D. absitus</i>, but for the genus.</p>
Anatomy of the neural endocranium and stapes of Diadectes absitus (Diadectomorpha) from the early Permian of Germany based on the high‐resolution X‐ray microcomputed tomography
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Data from: Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high-resolution x-ray microcomputed tomography, and the origin of the amniote crown group
The origin of amniotes was a key event in vertebrate evolution, enabling tetrapods to break their ties with water and invade terrestrial environments. Two pivotal clades of early tetrapods, the diadectomorphs and the seymouriamorphs, have played an unsurpassed role in debates about the ancestry of amniotes for over a century, but their skeletal morphology has provided conflicting evidence for their affinities. Using high-resolution X-ray microcomputed tomography, we reveal the three-dimensional architecture of the well preserved endosseous labyrinth of the inner ear in representative species belonging to both groups. Data from the inner ear are coded in a new cladistic matrix of stem and primitive crown amniotes. Both maximum parsimony and Bayesian inference analyses retrieve seymouriamorphs as derived non-crown amniotes and diadectomorphs as sister group to synapsids. If confirmed, this sister group relationship invites re-examination of character polarity near the roots of the crown amniote radiation. Major changes in the endosseous labyrinth and adjacent braincase regions are mapped across the transition from non-amniote to amniote tetrapods, and include: a ventral shift of the cochlear recess relative to the vestibule and the semicircular canals; cochlear recess (primitively housed exclusively within the opisthotic) accommodated within both the prootic and the opisthotic; development of a distinct fossa subarcuata. The inner ear of seymouriamorphs foreshadows conditions of more derived groups, whereas that of diadectomorphs shows a mosaic of plesiomorphic and apomorphic traits, some of which are unambiguously amniote-like, including a distinct and pyramid-like cochlear recess.
X-ray microcomputed tomography (μCT) datasets of hydrogen (H2) drainage and imbibition in a layered sandstone at reservoir pressure and temperature conditions.
<p>This dataset contains raw (unfiltered), filtered, and segmented image stacks of the dry and wet scans (containing fluids) for two pore-scale X-ray H<sub>2</sub> flow experiments in a layered Clashach sandstone sample at 50°C and 10 MPa. Please refer to the readme file '00_Readme.pdf' for details about the dataset.</p>
Data from: Inner ear morphology of diadectomorphs and seymouriamorphs (Tetrapoda) uncovered by high‐resolution x‐ray microcomputed tomography, and the origin of the amniote crown group
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Data from: Description of a soft-bodied invertebrate with microcomputed tomography and revision of the genus Chtonobdella (Hirudinea: Haemadipsidae)
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Figure 6 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 6 Paraba bresslaui (Schirch 1929), µCT-derived images of cephalic extremity of holotype A, B perspective view of 3D rendering C virtual transverse section showing anteriormost eyes, pixel size: 1.9 µm D virtual transverse section showing eye and sensory pit, pixel size: 1.9 µm E horizontal virtual section showing rows of sensory pits, pixel size: 1.9 µm.
Figure 29 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 29 Pseudogeoplana wetzeli (Schirch 1929), syntype A. A Virtual section of pharynx, pixel size: 4.77 µm B photomicrograph of sagittal section of pharynx C photomicrograph of tangential section of outer epithelium of pharynx and its muscle, in sagittal plane D photomicrograph of sagittal section of outer epithelium of pharynx and its underlying muscle.
Figure 3 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 3 Obama itatiayana (Schirch 1929). Syntype C AµCT-derived image. Virtual sagittal section of pharynx and copulatory region, pixel size: 6.3 µm B photomicrograph of sagittal section of pharynx C photomicrograph of sagittal section of copulatory apparatus.
Figure 28 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 28 Pseudogeoplana wetzeli (Schirch 1929). Photomicrographs of syntype A. A Horizontal section of anterior extremity B horizontal section of ovarian region C horizontal section of testicular region D transverse section of anterior extremity.
Figure 22 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 22 Dolichoplanasp. Specimen MNRJ 8922. Virtual sagittal section of pharynx, pixel size: 11.92 µm.
Figure 9 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 9 Paraba bresslaui (Schirch 1929), holotype A virtual horizontal section of copulatory apparatus, pixel size: 7.99 µm B virtual sagittal section of copulatory apparatus, pixel size: 7.99 µm C horizontal section of ovarian region, pixel size: 7.99 µm.
Figure 5 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 5 Paraba bresslaui (Schirch 1929), holotype A dorsal view B original drawing by Schirch (1929)C ventral view D dorsal view with original label E anterior extremity.
Figure 17 from: Silva MS, Carbayo F (2020) X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes). ZooKeys 910: 1-42. https://doi.org/10.3897/zookeys.910.39486
Figure 17 Pseudogeoplana arpi (Schirch 1929), photomicrographs of syntype B A transverse section of anterior extremity B transverse section of pre-pharyngeal region C transverse section of anterior extremity D horizontal section of testicular region.
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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.