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469 results for “Image analysis”
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
Background: Functional magnetic resonance imaging (fMRI) is an advanced and frequently used technique for studying brain functions in humans and increasingly so in animals. A key element of analyzing fMRI data is group analysis, for which valid spatial normalization is a prerequisite. In the current study we applied normalization and group analysis to a dataset from an auditory functional MRI experiment in anesthetized beagles. The stimulation paradigm used in the experiment was composed of simple Gaussian noise and regular interval sounds (RIS), which included a periodicity pitch as an additional sound feature. The results from the performed group analysis were compared with those from single animal analysis. In addition to this, the data were examined for brain regions showing an increased activation associated with the perception of pitch. Results: With the group analysis, significant activations matching the position of the right superior olivary nucleus, lateral lemniscus and internal capsule were identified, which could not be detected in the single animal analysis. In addition, a large cluster of activated voxels in the auditory cortex was found. The contrast of the RIS condition (including pitch) with Gaussian noise (no pitch) showed a significant effect in a region matching the location of the left medial geniculate nucleus. Conclusion: By using group analysis additional activated areas along the canine auditory pathways could be identified in comparison to single animal analysis. It was possible to demonstrate a pitch-specific effect, indicating that group analysis is a suitable method for improving the results of auditory fMRI studies in dogs and extending our knowledge of canine neuroanatomy.
Data from: An integrated iterative annotation technique for easing neural network training in medical image analysis
Neural networks promise to bring robust, quantitative analysis to medical fields. However, their adoption is limited by the technicalities of training these networks and the required volume and quality of human-generated annotations. To address this gap in the field of pathology, we have created an intuitive interface for data annotation and the display of neural network predictions within a commonly used digital pathology whole-slide viewer. This strategy used a 'human-in-the-loop' to reduce the annotation burden. We demonstrate that segmentation of human and mouse renal micro compartments is repeatedly improved when humans interact with automatically generated annotations throughout the training process. Finally, to show the adaptability of this technique to other medical imaging fields, we demonstrate its ability to iteratively segment human prostate glands from radiology imaging data.
Data from: Quantification and statistical analysis methods for vessel wall components from stained images with Masson's trichrome
Purpose: To develop a digital image processing method to quantify structural components (smooth muscle fibers and extracellular matrix) in the vessel wall stained with Masson's trichrome, and a statistical method suitable for small sample sizes to analyze the results previously obtained. Methods: The quantification method comprises two stages. The pre-processing stage improves tissue image appearance and the vessel wall area is delimited. In the feature extraction stage, the vessel wall components are segmented by grouping pixels with a similar color. The area of each component is calculated by normalizing the number of pixels of each group by the vessel wall area. Statistical analyses are implemented by permutation tests, based on resampling without replacement from the set of the observed data to obtain a sampling distribution of an estimator. The implementation can be parallelized on a multicore machine to reduce execution time. Results: The methods have been tested on 48 vessel wall samples of the internal saphenous vein stained with Masson's trichrome. The results show that the segmented areas are consistent with the perception of a team of doctors and demonstrate good correlation between the expert judgments and the measured parameters for evaluating vessel wall changes. Conclusion: The proposed methodology offers a powerful tool to quantify some components of the vessel wall. It is more objective, sensitive and accurate than the biochemical and qualitative methods traditionally used. The permutation tests are suitable statistical techniques to analyze the numerical measurements obtained when the underlying assumptions of the other statistical techniques are not met.
Data from: Geographic Object-Based Image Analysis Framework for Mapping Vegetation Physiognomic Types at Fine Scales in Neotropical Savannas
<p>Spatially-explicit information featuring a wide range of detailed vegetation structural types are necessary to support conservation and ecological analyses. A systematic approach that accurately maps such detailed categories at regional scales is currently lacking for neotropical savannas. We developed a systematic Geographic Object-Based Image Analysis (GEOBIA) framework that accounts for spectral and spatial properties to map Cerrado vegetation structural types at 5-m resolution. This framework counts with a two-step mapping approach: (1) image segmentation and a Random Forest land cover classification based on spectral information (Level 1 classification), followed by (2) a GEOBIA knowledge-based classification that follows contextual and topological spatial rules developed in a systematic manner for mapping Cerrado ecological classes (Level 2 classification).</p><p>The framework was tested for two large study sites covering most major Cerrado physiognomic types: a control site in central Brazil (Taquara watershed site, located in Brasilia, Federal District, and embraces the IBGE Ecological Reserve) and another larger site that is located in an agricultural landscape in the western portion of Bahia State (encompasses parts of the municipalities of: Sao Desiderio, Luis Eduardo Magalhaes, Barreiras, and Riachao das Neves), which brings additional mapping challenges related to intra-class spectral similarity. </p><p>Results demonstrate that our GEOBIA approach is effective for mapping 13 land cover classes with 87.6% overall accuracy, of which all 11 major vegetation classes were identified. For additional details, please check the associated publication with these datasets (Ribeiro et al. 2020).</p><p>The datasets developed in this study are available in shapefile format with attributed metadata following ISO 19115 standards: </p><ul><li><strong>wba_lcmap_geobiaL2_2011lucmask:</strong> final land cover map (Level 2 -- physiognomic types) for a section of the western bahia region in the Cerrado. This product uses a land use mask of 2011 derived from ancillary data</li><li><strong>wba_lcmap_geobiaL2_2013lucmask:</strong> final land cover map (Level 2 -- physiognomic types) for a section of the western bahia region in the Cerrado. This product accounts for the land use mask of 2011 as well as an updated land use mask of 2013 derived from ancillary data</li><li><strong>ibge_taquara_luc_L1_L2_2013_original:</strong> land cover maps (Levels 1 and 2) developed for the Taquara/IBGE site</li><li><strong>ibge_taquara_detailed_luc_2013:</strong> final land cover map (Level 2 -- physiognomic types) developed for the Taquara/IBGE site with additional detailed land use categories</li></ul><p> </p><p><strong>Data</strong></p><p>Mapped land cover classes: 1) cerrado woodland, 2) savanna, 3) open savanna, 4) shrubby grassland, 5) grassland (only present in the Taquara site), 6) cerrado scrub (only present in the western bahia site), 7) marsh, 8) shrub swamp, 9) palm swamp, 10) riparian forest, 11) semi-deciduous forest, 12) seasonally dry tropical forest (only present in the western bahia site), 13) invasive forbes (only present in the Taquara site), 14) non-natural/barren, 15) water, 16) shade, 17) clouds</p><p>The land-use mask incorporated into our maps feature the following classes: main roads, farming/crops, silviculture, and urban areas. </p><p> </p><p><strong>Coordinate Reference System</strong></p><p>Datasets were projected to <strong>South America Albers Equal Area</strong> <strong>Conic</strong>, with all areal calculations based on this projection.</p><p> </p><p><strong>Data Usage</strong> </p><p>The datasets are publicly available and should be cited appropriately (main publication: Ribeiro et al. 2020).</p><p> </p><p><strong>Additional information</strong></p><p>For any other data requests or questions, please contact Fernanda Ribeiro (fernanda.ffr@gmail.com).</p>
Dipper Throated Optimization with Deep Convolutional Neural Network-based Crop Classification on Remote Sensing Image Analysis
Open the record for dataset details and reuse information.
Odeuropa Image Analysis Demonstrator Data
This is the data required to run the Odeuropa Image Analysis Demonstrator Notebook
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.
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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.