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97 results for “phase contrast”
FIGURES 1–7 in Description of a new genus and two new species of Leiodidae (Coleoptera) from Baltic amber using phase contrast synchrotron X-ray microtomography
FIGURES 1–7. External and internal morphology of Catops perkovskyi sp. n. (holotype) by PPC-SRμCT. 1, habitus dorsal view. 2, habitus lateral view. 3, antenna. 4, front leg. 5, aedeagus, lateral view. 6, aedeagus, dorsal view. 7, apex of aedeagus, dorsal view.
FIGURES 8–17 in Description of a new genus and two new species of Leiodidae (Coleoptera) from Baltic amber using phase contrast synchrotron X-ray microtomography
FIGURES 8–17. External and internal morphology of Tafforeus cainosternus sp. n. (holotype) by PPC-SRμCT. 8, habitus dorsal view. 9, habitus lateral view. 10, prosternum and procoxal cavities from behind (pp = triangular prosternal process). 11, antenna. 12, protarsus, dorsal view. 13, mesotarsus, dorsal view. 14, posterior leg (th=ventral tooth). 15, mesoventral carina (msc) and mesocoxal cavity (mcx), lateral view. 16, aedeagus, lateral view. 17, aedeagus, dorsal view.
FIGURES 8–21 in A new species of anapid spider (Araneae: Araneoidea, Anapidae) in Eocene Baltic amber, imaged using phase contrast X-ray computed micro-tomography
FIGURES 8–21. CT reconstructions of Balticoroma wheateri new species (male holotype, GPIH). (8) frontal view showing chelicerae and labral spur; (9) view of right pedipalp showing embolus; (10–14) various views of right metatarsus 1, showing y-shaped clasping structure; (15) anterior view of specimen showing the section taken through the chelicerae to produce the raw data slice in Figure 16; (16) raw data slice demonstrating that the chelicerae and clypeal extentions are clearly separated; (20–21) various views of the right pedipalp. C, chelicera; ce, clypeal extension; co, dorsal cymbial outgrowth; cy, cymbium; e, embolus; eb, embolic base; ec, embolic coil;?fc, functional conductor sensu Wunderlich (2004); ls, labral spur; t, tegulum.
FIGURE 1 in A new species of anapid spider (Araneae: Araneoidea, Anapidae) in Eocene Baltic amber, imaged using phase contrast X-ray computed micro-tomography
FIGURE 1. Microphotograph of Balticoroma wheateri new species (male holotype, GPIH). Body length = 1.8 mm.
FIGURES 2–7 in A new species of anapid spider (Araneae: Araneoidea, Anapidae) in Eocene Baltic amber, imaged using phase contrast X-ray computed micro-tomography
FIGURES 2–7. CT reconstructions of Balticoroma wheateri new species (male holotype, GPIH). (2) right lateral view; (3) left lateral view; (4) dorsal view; (5) ventral view; (6) anterior view; (7) posterior view. Body length = 1.8 mm. Mt1, metatarsus 1; ta1, tarsus 1; ti1, tibia 1.
2D phase contrast HeLa cells images with ground truth annotations
<p>Original images are from http://www.robots.ox.ac.uk/~vgg/software/cell_detection/. This software is associated with the publication "Learning to Detect Cells Using Non-overlapping Extremal Regions", MICCAI 2012. (DOI: 10.1007/978-3-642-33415-3_43)</p> <p>Here, we provide the ground truth labels of: cell centers and segmentation, which are used in the publications:</p> <ul> <li>"Learning to Segment: Training Hierarchical Segmentation under a Topological Loss", MICCAI 2015. (DOI: 10.1007/978-3-319-24574-4_32)</li> <li>"Cell Detection and Segmentation Using Correlation Clustering", MICCAI 2014. (DOI: 10.1007/978-3-319-10404-1_2)</li> </ul>
FIGURES 13–15 in Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola - group (Coleoptera: Latridiidae)
FIGURES 13–15. Fossil Latridiidae from Baltic amber: 13—Latridius jantaricus, habitus, dorsal view, specimen "12" [HPR]; 14—Latridius alexeevi, habitus, dorso-frontal view, specimen "16" [HPR]; 15—Revelieria groehni, habitus, dorsal view, specimen "046" [ACAB].
FIGURES 1–2 in Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola - group (Coleoptera: Latridiidae)
FIGURES 1–2. Corticaria amberica sp. nov., holotype "017" [ACAB]: 1—habitus, dorsal view; 2—habitus, ventral view.
FIGURES 10–12 in Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola - group (Coleoptera: Latridiidae)
FIGURES 10–12. Aedeagus: 10—Corticaria pinicola, ventral view (drawing by W.H. Rücker); 11—C. abdominalis, ventral view (drawing by W.H. Rücker); 12—C. amberica sp. nov., lateral and ventral views, reconstruction.
FIGURES 3–5 in Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola - group (Coleoptera: Latridiidae)
FIGURES 3–5. Corticaria amberica sp. nov., holotype "017" [ACAB], phase-contrast synchrotron microtomography renderings (BESSY II, Helmholtz-Zentrum, Berlin): 3—habitus, dorsal, ventral and lateral views; 4—location of aedeagus inside abdomen; 5—aedeagus, lateral and ventral views.
FIGURES 6–9 in Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola - group (Coleoptera: Latridiidae)
FIGURES 6–9. Corticaria amberica sp. nov., paratypes: 6—habitus, dorsal view, paratype "0024/2000" [WRUE]; 7— habitus, dorso-frontal view, paratype "612" [GPIH]; 8—habitus, ventral view, paratype "8216" [GPIH]; 9—habitus, dorsal view, paratype "8059" [HPR].
Example Phase Contrast data acquired on a Philips scanner
<p>Example of phase contrast (left and right) sequences acquired on a Philips scanner and their respective renal artery mask.</p>
3d virtual histology of the human hippocampus based on phase-contrast computed-tomography
<p>This data package contains:<br> - exemplary data sets of multiscale imaging of the human hippocampus as raw-files (gray values, segmentation masks)<br> - object properties as xlsx-files (for all data sets)<br> - analysis scripts (based on matlab, R, python)</p>
Time-Resolved X-ray Phase-Contrast Video Imaging of Continuous Anti-Solvent Crystallisation
<p>X-ray phase-contrast video showing early crystal growth in a continuous anti-solvent crystalliser. Data was collected on the Diamond Light source I13-2 beamline. For further information see the paper:</p> <p>@article{das_pallipurath_leng_wanelik_mcginty_miller_kathyola_chang_al-madhagi_marathae_et<br> al._2020,<br> place={Cambridge},<br> title={Time-Resolved X-ray Phase-Contrast Imaging (XPCI) of Nucleation and Crystal Growth in the Anti-Solvent Crystallization of Lovastatin},<br> DOI={10.26434/chemrxiv.12911168.v1},<br> journal={ChemRxiv},<br> publisher={Cambridge Open Engage},<br> author={Das, Gunjan and Pallipurath, Anuradha and Leng, Joanna and Wanelik, Kazimir<br> and McGinty, John and Miller, Russell and Kathyola, Thokozile and Chang,<br> Sin-Yuen and Al-Madhagi, Laila H. and Marathae, Shashidhara and et<br> al.},<br> year={2020},<br> note={This content is a preprint and has not been peer-reviewed.}<br> }</p>
On the effect of precession for magnetic differential phase contrast imaging
<p>4D-STEM datasets and processing scripts used for the journal publication "<strong>On the effect of precession for magnetic differential phase contrast imaging</strong>".</p> <p>DOI link to publication: <a href="https://doi.org/10.1016/j.micron.2024.103761">10.1016/j.micron.2024.103761</a></p> <p> </p> <p><strong>Prerequisites</strong></p> <p>The scripts presented below were created using open-source Python packages with specific versions:</p> <ul> <li>hyperspy 1.7.1</li> <li>pyxem 0.14.2</li> <li>fpd 0.2.5 (with scikit-image 0.18)</li> <li>jupyterlab 4.0.7</li> </ul> <p>There is no guarantee that other versions of the listed packages will run the code.</p> <p><strong>Data files</strong></p> <p>In total five zipped (.7z extension) files are included in this repository. The files contain data from the different samples studied with different precession electron diffraction calibrations where applicable. The three samples studied are LSMO, and the corresponding 4D-STEM datasets taken away from a high-symmetry zone axis (<em>LSMO_LZ_data.7z</em>) and on the zone axis (<em>LSMO_HZ_data.7z</em>), FeAl sample (<em>FeAl_data.7z</em>), and scans from an Au TEM alignment grid (<em>AuGrid_data.7z</em>). The <em>precession_azimuths.7z</em> files contains the precession azimuthal circles from the three precession calibrations performed.</p> <p><strong>Processing scripts</strong></p> <p>Three scripts are included in the IPython notebook format (.ipynb extension). The <em>Precession_azimuth_plot.ipynb</em> script plots the precession azimuth for comparison. The <em>Segmentation_script.ipynb</em> is used to process the precession path segmented 4D-STEM datasets, and the <em>DPC_processing.ipynb</em> includes code to perform center of mass and phase correlation processing on the 4D-STEM data to extract differential phase contrast signals.</p>
Figure 13 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 13. Rooted maximum likelihood tree of the Orchomene s.l. complex COI. Bootstrap support is shown for each branch. Hirondellea gigas was used as the outgroup. Ŋe position of Orchomenella rinamontiae is shown in yellow.
Figure 11 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 11. Orchomenella rinamontiae. Holotype, ♀, 24.4 mm. Less uropods (U1, U2, and U3) and telson (T) in dorsal view. Scale bars: 0.5 mm.
Figure 12 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 12. Unrooted non-redundant maximum likelihood tree of the Lysianassoidea COI. Leaves represent individual specimens, coloured by genus where this information was available in the NCBI database. Our samples of Orchomenella rinamontiae, from both RNA sequencing and DNA sequencing, are coloured in red. Ŋe area of the tree illustrated in Figure 13 is enclosed by a grey doưed line. A complete list of sequences in each genus group can be found in the Supporting Information (Table S1).
Figure 9. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 9. Synchrotron radiation X-ray phase-contrast micro-tomography (A, B) and scanning electron microscopy (C–F) of gnathopods of Orchomenella rinamontiae. Paratypes, ♂♂, 11.3 mm (A, B) and 11.3 and 15.4 mm (C–F). A, lateral view of right gnathopod 2. B, medial view of right gnathopod 2. C, lateral view of less gnathopod 1. D, medial view of right gnathopod 1. E, lateral view of less gnathopod 2. F, medial view of right gnathopod 2. Abbreviations: a, gnathopod 1 lateral spine; b, gnathopod 1 medial spine; c, gnathopod 2 tip of dactyl. Scale bars: 200 µm.
Figure 10 in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 10. Orchomenella rinamontiae. Holotype, ♀, 24.4 mm. Medial view of less gnathopod 2 (Gn2). Scale bars: 1 mm.
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.