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Linked collectors and determiners for: Colección de Tejidos del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-CT).
Natural history specimen data linked to collectors and determiners held within, "Colección de Tejidos del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-CT)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9c2d26f1-0ce0-4cde-9f8d-de8284404fff">https://bionomia.net/dataset/9c2d26f1-0ce0-4cde-9f8d-de8284404fff</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9c2d26f1-0ce0-4cde-9f8d-de8284404fff">https://gbif.org/dataset/9c2d26f1-0ce0-4cde-9f8d-de8284404fff</a>. Formatted as a Frictionless Data package.
Radiographic, CT and anatomical dorsal hoof wall measurements
Open the record for dataset details and reuse information.
Foot CT measurements data
<p>Dorsal, medial and lateral hoof wall and solar thickness measurements in 110 feet</p>
Data from: Can perfusion CT unmask postictal stroke mimics? A case-control study of 133 patients
OBJECTIVE: To study the diagnostic value of volume perfusion CT (VPCT) in patients with transient focal neurological deficits following and during epileptic seizures, that mimic symptoms of stroke. METHODS: a retrospective case-control study was performed on 159 patients that presented with a seizure and received an emergency VPCT within the first 3.5 hours of admission, after being misjudged to have an acute stroke. The reference test was a clinical-based, EEG-supported diagnostic algorithm for seizure. RESULTS: We included 133 patients: 94 stroke-mimicking cases with postictal focal neurological deficits ("Todd's phenomenon", n=67) or ongoing seizure on hospital admission ("ictal patients", n=27), and 39 postictal controls without focal neurological deficits. Patients with Todd's phenomenon showed normal (64%), hypo (21%)- and hyperperfusion (14%) on early VPCT. Ictal patients displayed more hyperperfusion compared to postictal patients (p=0.015). Test sensitivity of hyperperfusion for ictal patients is 38% CI [20.7-57.7], specificity 86% CI [77.3-91.7], positive predictive value (ppv) is 42% CI [27.5-58.7], the negative predictive value (npv) 83% CI [78.6-86.9]. A cortical distribution was seen in all hyperperfusion scans, compared to a cortico-subcortical pattern in hypoperfusion (p<0.001). A history of complex focal seizure and age were associated with hyperperfusion (p= 0.046 and 0.038, respectively). CLASSIFICATION OF EVIDENCE: This study provides Class IV evidence that VPCT accurately differentiates ictal stroke mimics from acute ischemic stroke. CONCLUSION: VPCT can differentiate ictal stroke mimics with hyperperfusion from acute ischemic stroke, but not postictal patients who display perfusion patterns overlapping with ischemic stroke.
In situ μ-CT measurements during freeze-drying offers detailed information
<p>In situ μ-CT measurements during freeze-drying offers detailed information</p>
Figure 1 from: Samyn Y, Sonet G, d'Acoz C (2021) Exploring the use of micro-computed tomography (micro-CT) in the taxonomy of sea cucumbers: a case-study on the gravel sea cucumber Neopentadactyla mixta (Östergren, 1898) (Echinodermata, Holothuroidea, Phyllophoridae). ZooKeys 1054: 173-184. https://doi.org/10.3897/zookeys.1054.67088
Figure 1 Neopentadactyla mixta (Östergren, 1898) A focus-stacked view of the dorsal-lateral view of dissected specimen B focus-stacked view of the ventral–lateral view of dissected specimen C focus-stacked view of the dorsal–lateral view of a non-dissected specimen D focus-stacked view of the ventral–lateral view of a non-dissected specimen ESEM view of the rosettes from the shaft of a tentacle FSEM view of the 2-pillared tables from the introvert GSEM view of the rods and rosettes from a tentacle tip HSEM view of the 4-pillared tables from the dorsal body wall ISEM view of the 4-pillared tables from the ventral body wall JSEM view of the plates from the dorsal tube feet KSEM view of the plates from the ventral tube feet LSEM view of half of an end-plate from a ventral tube foot. Scale bars: 1 cm (A–D); 50 μm (E–L).
Figure 2 from: Samyn Y, Sonet G, d'Acoz C (2021) Exploring the use of micro-computed tomography (micro-CT) in the taxonomy of sea cucumbers: a case-study on the gravel sea cucumber Neopentadactyla mixta (Östergren, 1898) (Echinodermata, Holothuroidea, Phyllophoridae). ZooKeys 1054: 173-184. https://doi.org/10.3897/zookeys.1054.67088
Figure 2 Neopentadactyla mixta (Östergren, 1898) A micro-CT scan visualizing the position of the calcareous ring B lateral view with micro-CT imaging of the anterior part of the calcareous ring (AR: most anterior radial piece; AIR: most anterior interradial pieces; SAR: subsequent anterior radial pieces; SAIR: subsequent interradial anterior pieces; Mesh: meshwork of radial and interradial median to distal pieces) C oblique view with micro-CT imaging showing a guttered internal side of the calcareous ring D focus-stacked view of the calcareous ring and associated structures (T: tentacles; LM: longitudinal muscle with bifurcation point (BfP); PV: Polian vesicle: SC: stone canal). Scale bars: 1 cm (A–D).
RibSeg Dataset and Strong Point Cloud Baselines for Rib Segmentation from CT Scans
<p>Manual rib inspections in computed tomography (CT) scans are clinically critical but labor-intensive, as 24 ribs are typically elongated and oblique in 3D volumes. Automatic rib segmentation methods can speed up the process through rib measurement and visualization. However, prior arts mostly use in-house labeled datasets that are publicly unavailable and work on dense 3D volumes that are computationally inefficient. To address these issues, we develop a labeled rib segmentation benchmark, named RibSeg, including 490 CT scans (11,719 individual ribs) from a public dataset. For ground truth generation, we used existing morphology-based algorithms and manually refined its results. Then, considering the sparsity of ribs in 3D volumes, we thresholded and sampled sparse voxels from the input and designed a point cloud-based baseline method for rib segmentation. The proposed method achieves state-of-the-art segmentation performance (Dice<span class="math-tex">\(\approx95\%\)</span>) with significant efficiency (<span class="math-tex">\(10\sim40\times\)</span> faster than prior arts). The RibSeg dataset, code, and model in PyTorch are available at <a href="https://github.com/M3DV/RibSeg">https://github.com/M3DV/RibSeg</a>.</p> <p> </p> <p><strong>Note:</strong> This repository provides rib segmentation ("RibFrac31-rib-seg.nii.gz") and centerline ("RibFrac31-rib-cl.nii.gz") <em>annotations</em> for 490 cases in RibFrac dataset. Please download the corresponding CT <em>images </em>("RibFrac31-image.nii.gz") at <a href="https://ribfrac.grand-challenge.org/">https://ribfrac.grand-challenge.org/</a> (1-click registration is needed via <em>"Join"</em>).</p>
Fig. 24 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning
Fig. 24. Close-up of lateral basicranial foramina in Tribodus limae (UERJ-PMB-40). Scale bar is 1 cm.
Fig. 7 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning
Fig. 7. Transverse CT scan slices through the Tribodus limae braincase. Orbital region. A, slice 187, at the level of the optic nerve; B, slice 209, at the level of the oculomotor nerve; C, slice 216, at the level of the oculomotor nerve showing the anterior semicircular canal originating anterior to the postorbital process; D, E, slices 222 and 226, respectively, at the level of the efferent pseudobranchial foramen and the foramen for the superficial ophthalmic complex and profundus nerve; F, slice 239, at the level of the utricular recess and abducens foramen; G, H, slices 241 and 242, respectively, showing the course of the superficial ophthalmic complex and abducens nerve within the cartilage of the orbit. No scale.
Figure 8 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 8 - NanoCT−SEM Plate 2. A–F Zospeum isselianum, neotype (CSR SASA 37013), Turjeva jama G–H Zospeum isselianum (SMNH 2216), Jama na Zgornjih Brsnikih I–L Zospeum sp. (CSR SASA 37698a), Konečka zijalka.
Figure 2 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 2 - Historical material: A Zospeum isselianum syntype (MZUT M3232): upper mountains of Natisone River valley B–F Zospeum isselianum topotype: Turjeva jama G–P Specimens labelled as "Zospeum alpestre" in the Bourguignat Collection (MHNG 7898/2) from "Cav[erne]. de Carniole".
Figure 17 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 17 - Light micrograph of a section of the reproductive tract of Zospeum sp. (Konečka zijalka) (CSR SASA 21675). A Gonad (g) with acinus of the ovotestis including the germinal epithelial ring (ger) surrounding the acinar lumina (al), sustentacular cells (Sertoli cells) (sc) and oogonia (og) B Digestive gland (dg), hermaphroditic duct (hd) lined with cilia (c), posterior loop of the intestine (pi), receptaculum seminis (rs) containing allospermatozoa with spermatozoa oriented towards and apical ends touching the epithelial cells, and long motile cilia (ce) of intestine (i).
Figure 16 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 16 - Light micrograph of the histological appearance of the digestive tract of Zospeum sp. (Konečka zijalka) (CSR SASA 21675). A−B Bilobed muscular gizzard (mg) with epithelium showing columnar cells (cc) with microvillous apical surfaces (mv), posterior loop of the intestine (pi) with ciliated epithelium (ce) B Elaborate muscular plates (mp), thick cuticle (cu), highly ciliated rectum (r), gastric pouch (gp), digestive gland (dg) and hermaphroditic duct.
Figure 14 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 14 - Images of the radula of Zospeum isselianum (Turjeva jama) (CSR SASA 37013 conspecific) and Zospeum sp. (Konečka zijalka) (CSR SASA 21675). A−D SEM of the radular ribbon of topotypic Zospeum isselianum A Radular ribbon showing adhesive layer of contact zone with odontophore B SEM overview showing rachidian teeth (r) and lateral teeth (l) C Rows of lateral teeth bearing fine medial groove D Marginal teeth E Light micrograph showing the histological appearance of the radular sheath of Zospeum sp. (Konečka zijalka) showing the inferior epithelium (ie) attached to the radular membrane (rm) mineralizing cells (mc) with degenerating nuclei and radular teeth (rt).
Figure 4 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 4 - Overview of morphological assignments, molecular species delimitation results and integrative taxonomic treatment of each of the four clusters, which are indicated by the longitudinal black bars for either the ABDG or the SP approach. Numbers indicate individual specimens; ABGD = Automatic Barcode Gap Discovery; SP = Statistical Parsimony.
Figure 13 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 13 - A Light micrograph showing the histological appearance of Zospeum sp. (Konečka zijalka) (CSR SASA 21675) with the mantel cavity (mc), mucus glands (mg), oesophagus (oe) bearing thick cuticular sheath (cs) and leading into the crop (c), the buccal ganglia (bg), and the cephalopodial portion of the reproductive system including penis (p) and vas deferens (vd) B Paired cerebral ganglia united by the cerebral commissure situated just dorsal to the origin of the oesophagus in the buccal mass.
Figure 12 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 12 - Light micrograph showing histological overview of the digestive system of Zospeum sp. (Konečka zijalka) (CSR SASA 21675). A Mouth and buccal apparatus. Mouth slit between oral lappets (m), crescent-shaped jaw (j), radula (r), pharynx (ph), digestive gland (dg), intestine (i), kidney (k), columellar muscle (cm), and pedal ganglia (peg) B Mantle gland (mag), sigmoid intestine (si), radular sac (rs), cerebral ganglion (cg), mucus glands (mg), kidney (k), heart showing auricle and ventricle (h), digestive gland (dg), columellar muscle (cm), oesophagus (oe) and salivary glands (sg).
Figure 7 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 7 - Kimura−2-parameter (K2P) genetic distance table in %. Delineated species are marked with boxes. For each individual specimen, its morphospecies designation and genetic distance data to all remaining specimens are given.
Figure 11 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
Figure 11 - Type and shell images Plate 5: A–E Zospeum kupitzense holotype: (SMF 256354) F–H Zospeum kupitzense (SMNH 3291), Ložekarjeva zijalka I–M Zospeum amoenum (RS59), Potočka zijalka.
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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.