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438 results for “3D imaging”
Data from: Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
<p>We have developed an open-source software called BIRDS (bi-channel image registration and deep-learning segmentation) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain. The BIRDS pipeline includes image pre-processing, bi-channel registration, automatic annotation, creation of a 3D digital frame, high-resolution visualization, and expandable quantitative analysis. This new bi-channel registration algorithm is adaptive to various types of whole-brain data from different microscopy platforms and shows dramatically improved registration accuracy. Additionally, as this platform combines registration with neural networks, its improved function relative to other platforms lies in the fact that the registration procedure can readily provide training data for network construction, while the trained neural network can efficiently segment incomplete/defective brain data that is otherwise difficult to register. Our software is thus optimized to enable either minute-timescale registration-based segmentation of cross-modality, whole-brain datasets or real-time inference-based image segmentation of various brain regions of interest. Jobs can be easily submitted and implemented via a Fiji plugin that can be adapted to most computing environments.</p>
Data from: Validation of perfusion quantification with 3D gradient echo dynamic contrast-enhanced magnetic resonance imaging using a blood pool contrast agent in skeletal swine muscle
The purpose of our study was to validate perfusion quantification in a low-perfused tissue by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) with shared k-space sampling using a blood pool contrast agent. Perfusion measurements were performed in a total of seven female pigs. An ultrasonic Doppler probe was attached to the right femoral artery to determine total flow in the hind leg musculature. The femoral artery was catheterized for continuous local administration of adenosine to increase blood flow up to four times the baseline level. Three different stable perfusion levels were induced. The MR protocol included a 3D gradient-echo sequence with a temporal resolution of approximately 1.5 seconds. Before each dynamic sequence, static MR images were acquired with flip angles of 5°, 10°, 20°, and 30°. Both static and dynamic images were used to generate relaxation rate and baseline magnetization maps with a flip angle method. 0.1 mL/kg body weight of blood pool contrast medium was injected via a central venous catheter at a flow rate of 5 mL/s. The right hind leg was segmented in 3D into medial, cranial, lateral, and pelvic thigh muscles, lower leg, bones, skin, and fat. The arterial input function (AIF) was measured in the aorta. Perfusion of the different anatomic regions was calculated using a one- and a two-compartment model with delay- and dispersion-corrected AIFs. The F-test for model comparison was used to decide whether to use the results of the one- or two-compartment model fit. Total flow was calculated by integrating volume-weighted perfusion values over the whole measured region. The resulting values of delay, dispersion, blood volume, mean transit time, and flow were all in physiologically and physically reasonable ranges. In 107 of 160 ROIs, the blood signal was separated, using a two-compartment model, into a capillary and an arteriolar signal contribution, decided by the F-test. Overall flow in hind leg muscles, as measured by the ultrasound probe, highly correlated with total flow determined by MRI, R = 0.89 and P = 10−7. Linear regression yielded a slope of 1.2 and a y-axis intercept of 259 mL/min. The mean total volume of the investigated muscle tissue corresponds to an offset perfusion of 4.7mL/(min ⋅ 100cm3). The DCE-MRI technique presented here uses a blood pool contrast medium in combination with a two-compartment tracer kinetic model and allows absolute quantification of low-perfused non-cerebral organs such as muscles.
TINKER_WP3_TU49 2D and 3D image dataset_071123
<p>Contains images taken during and after the pick-and-place assembly of the RADAR use case for project TINKER. </p><p>Machine assembly, before curing: 1) empty cavity snapshot, 2) Epoxy bright exposure, 3) Epoxy dark exposure, 4) Die placement </p><p>After curing: 5) Die after curing, 6) 3D topology data after curing</p>
3D drift correction for super-resolution imaging with a single laser light
<p>Original single-molecule image data and analysis results of Figures 4 and 5 in the paper</p>
Effects of 3D ultrasonography and 3D printed images on maternal-fetal attachment and its correlation with overall smoking within pregnancy: A pilot study.
Open the record for dataset details and reuse information.
Figures 31-33 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 31-33 Quasicalathus, light microscopic images of the holotypes of Q. agonicollis sp. nov. (31.) and Q. conservans sp. nov. (32, 33.). 31. Ventral side of head showing chaetotaxy of mentum; 32. General view of the amber piece with fossil in dorsal view; 32. Left lateral view. Abbreviations: ce – compound eye; el – elytron; ems – external seta of submentum; gu – gula; ims – internal seta of submentum; msf – mesofemur; mt – mentum; mtf – metafemur; prf – profemur; pt – pronotum.
Figures 47-51 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 47-51 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 47. Dorsal aspect; 48. Left lateral aspect; 49. Ventral aspect; 50. Pronotum (the arrows point to the insertions of the lateral setae); 51. Prosternum (for better view the prolegs are partly removed using the clipping plane function of Amira software. Abbreviations: cx – procoxa; psp – prosternal process; tr – protrochanter.
Figures 6-12 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 6-12 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "Groehn 7889" (6–8.) and "Groehn 7962" (9–12.). 6, 10. General view of the amber pieces (in Fig. 6, only the part of the large amber piece bearing the Quasicalathus fossil is shown); 7. Ventral side of body; 8. Left mesotarsi iv + v; 9. Pronotum and anterior part of elytra, left side of body; 11, 12. Medial part of left elytron (Fig. 12 shows the enlarged part of the elytron marked by the white frame in Fig. 11; the white arrow points to the insertion of the discal seta). Abbreviations: bs – insertion of the pronotal laterobasal seta; hm – humerus; I–VIII – elytral intervals 1–8.
Figures 34-38 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 34-38 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "Groehn 4879" (34–37.) and "Groehn 7814" (38.). 34. Dorsal aspect; 35. Right lateral aspect; 36. Ventral aspect; 37, 38. Prosternum and basal portions of prolegs. Abbreviations: cx – procoxa; fm – profemur; psp – prosternal process; tr – protrochanter.
Figures 81-89 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 81-89 Quasicalathus conservans sp. nov., volume rendering of the holotype. 81. Head, dorsal aspect (the arrows point to the insertions of the supraorbital setae); 82. Head, ventral aspect; 83. Left external part of metathorax, ventral view; 84. Submentum (the arrows point to the insertions of the four lateral setae); 85. Posterior part of prosternum and procoxae; 86. Posterior part of metasternum and metacoxae; 87–89. Preserved remains of the aedeagus (87. Right lateral aspect; 88. Dorsal aspect; 89. Left lateral aspect). Abbreviations: bb – basal bulb of aedeagal median lobe; ce – compound eye; cxp – metacoxal plate; eph – partly evaginated lobes of endophallus; gu – gula; mem – metepimeron; mes – metepisternum; mtt – mentum tooth; mv – metaventrite; pcx – procoxa; pmr –preserved distal part of right paramere of aedeagal median lobe; psp – prosternal process; sc – scutellum; sps – setae of sensory pit; tl – terminal lamella of aedeagal median lobe.
Figures 61-64 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 61-64 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "MAIG 76" (61–63.) and "GZG 16185" (64.); 61. Dorsal aspect; 62. Right lateral aspect; 63, 64. Pronotum (the pronotal outline on left side is highlighted by dotted line in Fig. 64).
Figures 39-46 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 39-46 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7814" using different grey scales of the Amira software. 39. Dorsal aspect; 40. Lateral aspect. The displaced aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software in Figures 39 and 40; 41. Head (the arrows point to the insertions of the supraorbital setae); 42. Pronotum (the arrows point to the insertions of the lateral setae); 43–46. Remains of the aedeagus in right lateral aspect (43.); Left lateral aspect (44.); Left lateral aspect (45.); Dorsal aspect (46.). The distal margins of the styloid apophysis of the right paramere in Fig. 43 and the lobate apophysis of the left paramere in Fig. 45 are highlighted by red dotted lines. Abbreviations: bb – basal bulb of aedeagal median lobe; os – distal ostium; pml – left paramere; pmr – right paramere; tl – terminal lamella of median lobe.
Figures 78-80 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 78-80 Quasicalathus conservans sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 78. Dorsal aspect; 79. Left lateral aspect (aed – aedeagus); 80. Ventral aspect; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software.
Figures 52-57 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 52-57 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 52. Head, ventral aspect (the arrows point to the insertions of the setae near base of mentum tooth and on submentum); 53. Abdomen, left lateral aspect (the arrows point to the insertions of the setae on ventrites IV, V, and VI); 54. Metacoxal area (the arrows point to the insertions of the coxal setae); 55. Apical gonocoxites, ventral aspect; 56. Apical gonocoxites, dorsal aspect; 57. Gonocoxites and remains of the bursa copulatrix (the latter was highlighted by red colour using the segmentation function of Amira software). Abbreviations: at – apical tooth of retinacle; kes – metathoracic katepisternum; cx – metacoxa; cxp – metacoxal plate; des – dorsal ensiform setae; ep – elytral epipleuron; fm – metafemur; gu – gula; mdl – left mandible; gx1 – basal gonocoxite; gx2 – apical gonocoxite; mdr – right mandible; mo – molar; mt – mentum; sp – sensory pit; tr – metatrochanter; ves – ventral ensiform setae; v3, v4, v5, v6 – ventritres III, IV, V, VI.
Figures 73-77 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 73-77 Quasicalathus agonicollis sp. nov., volume rendering of specimen "GZG 16188". 73. Dorsal aspect; 74. Basal portion of pronotum and anterior part of elytra (right side of body; the arrows point to the insertions of the pronotal basolateral seta and the parascutellar seta); 75. Prosternum with basal portion of prolegs; 76. Left apical gonocoxite, ventral aspect; 77. Gonocoxites, ventral aspect. Abbreviations: cx – procoxa; des – dorsal ensiform setae; fm – profemur; gx1 – basal gonocoxite; gx2 – apical gonocoxite; hm – humerus; pst – prosternum; sc – scutellum; sps – setae of sensory pit; tr – protrochanter; ves – ventral ensiform setae.
Figures 13-17 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 13-17 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "CCHH 952" (13–15.) and "OSAC 269" (16, 17.). 13. Dorsal view of body; 14. Pronotum and anterior part of elytra showing the markedly concave basal margin and projected humeri (the white arrows point the insertion pores of the parascutellary setae); 15, 17. General view of the amber pieces; 16. Posterior part of left elytron (the white arrow points to the insertion of the discal seta).
Figures 18-24 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 18-24 Quasicalathus, light microscopic images of Q. elpis Ortuño & Arillo, 2009 (18–20.) and Q. agonicollis sp. nov. (21–24.). 18. General view of the amber piece "MAIG 76" (only that part of the large amber piece bearing the Quasicalathus fossil is shown; the fossil is widely covered by milky coating); 19. General view of the two fragments of specimen "GZG 16185"; the left one bears only the negative imprint of the left elytra on the inclusion wall; 20. Right anterior part of body of specimen "GZG 16185" showing part of head, pronotum and humerus; 21, 22. General view of the amber piece "GZG 16188" (21. With fossil in dorsal view; 22. In ventral view); 23. Anterior part of specimen "GZG 16188"; 24. Head of specimen "GZG 16188". Abbreviations: a1–a6 – antennomeres 1–6; as – anterior supraorbital seta; bs – pronotal laterobasal seta; ms – pronotal lateral seta; ps – posterior supraorbital seta.
Figures 58-60 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 58-60 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of the dorsal aspects of specimens "Groehn 7962" (58.), "CCHH 952" (59.), and "OSAC 265" (60.).
Figures 65-72 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 65-72 Quasicalathus agonicollis sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 65. Dorsal aspect (the negative imprint of the fossil on the inclusion wall is shown); 66. Basal portion of pronotum and anterior part of elytra (positive of the fossilized beetle is shown; the arrows point to the insertions of the pronotal basolateral setae and the parascutellar setae); 67. Metacoxa (the arrows point to the insertions of the three coxal setae each side); 68–71. Aedeagus in dorsal aspect (68.), Right lateral aspect (69.), Ventral aspect (70.), Left lateral aspect (71.); The remains of the parameres are coloured (red: left paramere; green: right paramere); 72. left lateral aspect of beetle body; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software. Abbreviations: bb – basal bulb of aedeagal median lobe; hm – humerus; os – distal ostium of median lobe; sc – scutellum; tl – terminal lamella of median lobe.
Figures 1-5 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 1-5 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "Groehn 4879" (1–3.) and "Groehn 7814" (4, 5.). 1, 5. General view of the amber pieces; 2. Ventral side of head (the white arrow points to the mentum tooth; note that the mentum is somewhat detached from the head capsule); 3. Pronotum and anterior part of elytra showing the markedly concave basal margin and projected humeri; 4. Right lateral view of body.
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.