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Data from: Automated CT perfusion imaging for acute ischemic stroke: pearls and pitfalls for real world use
Recent positive trials have thrust acute cerebral perfusion imaging into the routine evaluation of acute ischemic stroke. Updated guidelines state that in patients with anterior circulation large vessel occlusions presenting beyond 6 hours from time last known well, advanced imaging selection including perfusion based selection is necessary. Centers that receive acute stroke patients must now have the capability to perform and interpret CT or MR perfusion imaging, or provide rapid transfer to centers with the capability of selecting patients for a highly impactful endovascular therapy, particularly in delayed time windows. Many stroke centers are quickly incorporating the use of automated perfusion processing software to interpret perfusion raw data. As CT perfusion is being assimilated in real world clinical practice, it is essential to understand the basics of perfusion acquisition, quantification and interpretation. It is equally important to recognize the common technical and clinical diagnostic challenges of automated CTP including ischemic core and penumbral misclassifications that could result in underestimation or overestimation of the core and penumbra volumes. This review highlights the pitfalls of automated CT perfusion along with practical pearls to address the common challenges. This is particularly tailored to aid the acute stroke clinician who must interpret automated perfusion studies, in an emergency setting to make time-dependent treatment decisions for acute ischemic stroke patients.
RWTHmediTEC/VSDFullBodyBoneModels: 3D surface models of the pelvis and femur created from CT datasets of the open source VSDFullBody database
<p>Was used in: Fischer <em>et al.</em> A robust method for automatic identification of femoral landmarks, axes, planes and bone coordinate systems using surface models. <em>Scientific Reports</em> <strong>10</strong>, 20859; <a href="https://doi.org/10.1038/s41598-020-77479-z">10.1038/s41598-020-77479-z</a> (2020).</p>
Figure 3 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 3 Male genitalia and associated metasomal sternum of paratype of Ceratina (Ceratinula) fioreseana sp. nov., deposited at the Entomological Collection of the Natural History Museum of the Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil A genital capsule in dorsal view B genital capsule in ventral view C genital capsule in lateral view D seventh sternum in dorsal view (E7) E sixth sternum in dorsal view (E6) F fifth sternum in dorsal view (E5) G seventh tergum in dorso-lateral view.
Figure 4 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 4 Female syntype of Ceratina (Ceratinula) manni Cockerell, 1912 deposited at the Entomological Collection of the American Museum of Natural History (AMNH, New York, United States of America) A head in frontal view (Photograph: I_HHG3587) B body in dorsal view (Photograph: I_HHG3585) C body in lateral view (Photograph: I_HHG3586) D labels (Photograph: I_HHG3588). Ownership rights to these images and their copyright belong to AMNH and Hadel Go. Photographs by Copyright Hadel Go 2011-2016 downloaded from the Discover Life Website.
Figure 1 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 1 Female holotype of Ceratina (Ceratinula) fioreseana sp. nov., deposited at the Entomological Collection of the Natural History Museum of the Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil A head in frontal view B body in lateral view C head in lateral view D mesosoma in lateral view E labrum in frontal view.
Figure 9 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 9 Head of Ceratina (Ceratinula) Moure, 1941 species in frontal view, showing the supraclypeal area and median paraocular area A, B female holotype of Ceratina (Ceratinula) fioreseana sp. nov., specimen deposited at the Entomological Collection of the Natural History Museum of the Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil C, D female specimen of Ceratina (Ceratinula) manni Cockerell, 1912 from Amélia Rodrigues, Bahia, deposited at the Reference Collection of the Laboratório de Bionomia, Biogeografia e Sistemática de Insetos (BIOSIS), Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil. Details: pls = puncture line delimiting the supraclypeal plain raised area above; ues = upper part of the epistomal suture.
Figure 6 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 6 Male of Ceratina (Ceratinula) manni Cockerell, 1912, specimen from Crato, Ceará, deposited at the Entomological Collection of the Federal University of Integração Latino-Americana (CE-UNILA), in Foz do Iguaçu, Paraná, Brazil A head in frontal view B body in lateral view C labrum in frontal view D head and mesosoma in lateral view.
Figure 2 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 2 Male paratypes of Ceratina (Ceratinula) fioreseana sp. nov., deposited at the Entomological Collection of the Natural History Museum of the Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil: Paratype A head in frontal view B body in lateral view C head in lateral view D mesosoma in lateral view. Paratype E labrum in frontal view F head in frontal view.
Figure 8 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 8 Head of Ceratina (Ceratinula) Moure, 1941 species in frontal view A (female holotype) B (male paratype) Specimens of Ceratina (Ceratinula) fioreseana sp. nov., deposited at the Entomological Collection of the Natural History Museum of the Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil C, DCeratina (Ceratinula) manni Cockerell, 1912: C female specimen from Amélia Rodrigues, Bahia, deposited at the Reference Collection of the Laboratório de Bionomia, Biogeografia e Sistemática de Insetos (BIOSIS), Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil D male specimen from Crato, Ceará, deposited at the Entomological Collection of the Federal University of Integração Latino-Americana (CE-UNILA), in Foz do Iguaçu, Paraná, Brazil. Drawings by Luisa de Lima Ruschioni.
Figure 10 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 10 Geographic distribution map of Ceratina (Ceratinula) fioreseana sp. nov. and Ceratina (Ceratinula) manni Cockerell, 1912 in and Brazil: (1) Goiás, Água Fria de Goiás, Fazenda Nossa Senhora Aparecida, Bayer Forward Farming (fioreseana Type locality); (2) Bahia, Maracás; (3) Bahia, Milagres; (4) Bahia, Amélia Rodrigues; (5) Piauí, Caracol; (6) Ceará, Crato; (7) Rio Grande do Norte, Serra Negra do Norte, Estação Ecológica do Seridó; (8) Paraíba, Cacimba de Dentro, Fazenda Cachoeira da Capivara; (9) Paraíba, Mamanguape; (10) Paraiba, João Pessoa, Periurban Area – Sítio ponta de Gramame; (11) Paraíba, Conde, Granja Pitumirim; (12) Paraíba, Alhandra, Assentamento Tapuiu – Sítio Olho D'água; (13) Paraíba, Guarabira (manni Type locality).
Figure 5 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 5 Female of Ceratina (Ceratinula) manni Cockerell, 1912 A head in frontal view B body in lateral view C head and mesosoma in lateral view D labrum in frontal view E median paraocular area and clypeus in detail F head in frontal view A, E specimen from Amélia Rodrigues, Bahia, deposited at the Reference Collection of the Laboratório de Bionomia, Biogeografia e Sistemática de Insetos (BIOSIS), Federal University of Bahia (MHNBA-MZUFBA), in Salvador, Bahia, Brazil; Specimens B,C, F from Caracol, Piauí, and D Milagres, Bahia, deposited at the Entomological Collection of the Federal University of Integração Latino-Americana (CE-UNILA), in Foz do Iguaçu, Paraná, Brazil.
Figure 7 from: de Oliveira FF, de Sousa Silva LR, Zanella FCV, Garcia CT, Pereira HL, Quaglierini C, Pigozzo CM (2020) A new species of Ceratina (Ceratinula) Moure, 1941, with notes on the taxonomy and distribution of Ceratina (Ceratinula) manni Cockerell, 1912, and an identification key for species of this subgenus known from Brazil (Hymenoptera, Apidae, Ceratinini). ZooKeys 1006: 137-165. https://doi.org/10.3897/zookeys.1006.57599
Figure 7 Male genitalia and associated metasomal sternum of Ceratina (Ceratinula) manni Cockerell, 1912, specimen from Serra Negra do Norte, Rio Grande do Norte, Brazil, deposited at the Entomological Collection of the Federal University of Integração Latino-Americana (CE-UNILA), in Foz do Iguaçu, Paraná, Brazil A genital capsule in dorsal view (red arrow shows the bidentate apex) B genital capsule in ventral view C genital capsule in lateral view D seventh sternum in dorsal view (E7) E sixth sternum in dorsal view (E6) F fifth sternum in dorsal view (E5).
Data from: Beauty is more than skin deep: a non-invasive protocol for in vivo anatomical study using micro-CT
Microcomputed tomography (μCT) is a widely used tool in biomedical research, employed to investigate tissues and bone structures of small mammals in vivo. The application of in vivo μCT scanning in non-medical studies greatly lags behind the rapid advancements made in the biomedical field wherein the methodology has evolved to allow for longitudinal studies and eliminate the need to sacrifice the animal. Ecological and evolutionary studies often involve morphological measurements of a large sample of live animals; however, the potential of in vivo μCT imaging as a method for data acquisition has yet to be delineated. Here, we describe a protocol for in vivo μCT imaging of the internal anatomy of reptiles and amphibians, commonly used study organisms in ecological and evolutionary research. We consider the skeletal and extraskeletal (i.e. osteoderms) bones of a lizard as a case study to elucidate the potential of in vivo μCT imaging. First, we explore the effects of various parameter settings on radiation dose, scan time and image quality. Secondly, we develop a protocol to immobilize and restrain study organisms during scanning without need for the administration of anaesthetics and compare the results of the in vivo protocol to images obtained post-mortem. To immobilize animals, we replace the use of anaesthetics by cooling, thereby allowing the use of previously unsuitable rotating gantry μCT scanners that are readily available in scientific institutions. The resultant image quality of in vivo μCT scans is similar to that of post-mortem μCT scans, especially in the abdominal region. We discuss the effect of tube voltage, distance to X-ray source and metal filtration on radiation dose, and how these parameters could be altered to reduce the cumulative radiation dose while maintaining optimal image quality. The proposed in vivo μCT protocol offers a new approach to acquire anatomical information for non-biomedical studies. We offer specific suggestions as to how the protocol can be employed to suit a variety of model organisms.
Data from: Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice
Manual phenotyping of rice tillers is time consuming and labor intensive and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive phenotyping of rice tiller traits at a high spatial resolution and high-throughput for large-scale assessment of rice accessions is urgently needed. In this study, we developed a high-throughput micro-CT-RGB (HCR) imaging system to non-destructively extract 730 traits from 234 rice accessions at 9 time points. We could explain 30% of the grain yield variance from 2 tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by GWAS, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at nine time points, which contained a major gene TAC1. Significant variants associated with tiller angle were enriched in the 3'-UTR of TAC1. Three haplotypes for the gene were found and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci contained associations with both vigor-related HCR traits and yield. The superior alleles would be beneficial for breeding of high yield and dense planting.
Carmustine wafers in vitro on MRI and CT
<p>We investigated detailed serial imaging changes of carmustine wafers in vitro using phantoms simulating a surgical resection cavity to estimate the underlying mechanisms of reported imaging changes associated with carmustine wafers in the clinical setting.</p>
FIGURE 4 in Automated segmentation of insect anatomy from micro-CT images using deep learning
FIGURE 4 Data augmentation. (a) Initial 2D image of a full head scan of an Atta texana ant specimen (original 1000 × 1000 px). Preprocessing is performed in two steps: (b) The image is cropped (original 520 × 520 px) around the brain area, keeping some of the muscles, nerves, and fibers that are close (or even attached) to the brain. The manual segmentation of the brain is indicated in blue. (c) Histogram equalization is used for additional augmentation, which enhances the contrast and projects the inner parts of the brain more clearly.
Micro-CT video files of melt embayments
<p>Videos of 3D volumes of olivine hosted melt embayments from the 2018 eruption at Mount Veniaminof. </p> <p>This work was performed at GeoSoilEnviroCARS (The University of Chicago, Sector 13), Advanced Photon Source (APS), Argonne National Laboratory. GeoSoilEnviroCARS was supported by the National Science Foundation – Earth Sciences (EAR – 1634415). Tomography capability developments were supported by DOE BES Geosciences (DE‐SC0020112). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.</p> <p> </p> <p>Segmenting was completed using<a href="https://www.slicer.org"> 3D Slicer. </a></p> <p>Segmentation colors are as follows:</p> <ul> <li>Brown: External silicate melt</li> <li>Green: Olivine host</li> <li>Black: Melt Embayments</li> <li>Lilac: Melt Inclusions</li> <li>Blue: Bubbles/Vesicles</li> <li>White: Oxides</li> </ul>
Figure 8 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 8. – CT scan image of skull and anterior portion of vertebral column and dorsal fin of Mastiglanis durantoni, MZUSP 118118, paratype. A: Dorsal view; B: Right lateral view; C: Ventral view. Anterior to top. A more detailed view of the Weberian complex is provided in Fig. 13. Abbreviations: af, anterior fontanel; bo, basioccipital; epi, epioccipital; ex, exoccipital; fr, frontal; le, lateral ethmoid; me, mesethmoid; np1-2, nuchal plates 1 and 2; ns, neural spine; orb, orbitosphenoid; pa, parasphenoid; par, parapophysis; pf, posterior fontanel; plr, pleurar rib; pro, prootic; pt, pterotic; ptr, pterosphenoid; pts, posttemporo-supracleithrum; sn, supraneural; soc, supraoccipital; socs, supraoccipital spine; sph, sphenotic; vc5-9, vertebral centra 5 to 9; vo, vomer; wc, Weberian complex.
Figure 11 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 11. – CT scan image of mesethmoid and premaxilla of Mastiglanis durantoni, MZUSP 118118, paratype, dorsal view. Anterior to top. Abbreviations: me, mesethmoid; pm, premaxilla.
Figure 4 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 4. – CT scan image of supraoccipital of Mastiglanis durantoni, MZUSP 118118, paratype. A: Dorsal view; B: Ventral view. Anterior to top.
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.