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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>
Figure 18 in A new genus of monstrilloid copepods (Crustacea) with anteriorly pointing ovigerous spines and related adaptations for subthoracic brooding
Figure 18. Antennules of two species of Maemonstrilla gen. nov., setules omitted, setal designations after Grygier & Ohtsuka (1995: fig. 6). A, Maemonstrilla okame sp. nov., female holotype (KMNH IvR 700 218), Sesoko Island, 22.v.1996, right antennule, ventral view. B, same, more fully armed tip of left antennule, ventral view (b5-seta seen to be bifid in another specimen). C, Maemonstrilla simplex sp. nov., female holotype (KMNH IvR 700 222), south coast of Ishigaki Island, 30.iv.1994, left antennule, dorsal view. D, same, more fully armed tip of right antennule, dorsal view. Scale bars = 0.1 mm.
Figure 21 in A new genus of monstrilloid copepods (Crustacea) with anteriorly pointing ovigerous spines and related adaptations for subthoracic brooding
Figure 21. Eggs and nauplius of Maemonstrilla gen. nov., SEM. A, eggs of female paratype of Maemonstrilla spinicoxa sp. nov. adhering to ovigerous spines (same specimen as Fig. 14A, q.v.). B–F, first nauplius hatched from egg mass of paratype female (LBM Reg. no. 1430000930) of Maemonstrilla okame sp. nov., Sesoko Island, 13.v.1996. B, habitus, ventral view. C, labral bulge and parts of right appendages. D, distal parts of antennule and antennal endopod and exopod. E, distal parts of mandible and of antennal endopod. F, mandible, apical view, showing insertion of seta on base of claw, thus confirming that the claw represents the endopod. Abbreviations: an, antennule; at, antenna; ba, basis; cx, coxal endite; en, endopod; ex, exopod; md, mandible. Scale bars = 20 Mm in A; 10 Mm in B; 2 Mm in C, D; 1 Mm in E, F.
Figure 24 in A new genus of monstrilloid copepods (Crustacea) with anteriorly pointing ovigerous spines and related adaptations for subthoracic brooding
Figure 24. Maemonstrilla turgida (A. Scott, 1909) comb. nov., female (KMNH IvR 700 225), Sesoko Island, 31.viii.1989. A, habitus, ventral view, only representative seta and setules shown (cf. Fig. 1B for dorsal view of same specimen). B, left antennule, ventral view, setules omitted, setal designations after Grygier & Ohtsuka (1995: fig. 6). C, urosome, ventral view, ovigerous spines and most setae cut short, some representative setules shown on furcal setae, copulatory pore arrowed. Scale bars = 0.5 mm in A, 0.1 mm in B, C.
Figure 12 in A new genus of monstrilloid copepods (Crustacea) with anteriorly pointing ovigerous spines and related adaptations for subthoracic brooding
Figure 12. Maemonstrilla polka sp. nov., female paratype (SO lab), south coast of Ishigaki Island, 30.iv.1994, details of swimming legs, SEM. A, basis and first exopodal segment of leg 1, outer view, proximal at top and anterior to right, showing one seta on each segment, anterior pore near basis seta (arrow), and spinule patches on exopod. B, third segments of endopod (right) and exopod (left) of leg 2, anterior view showing distal pore on each segment (arrows). C, proximal endopodal segment of leg 2, anterior view, showing vestigial button-like seta (arrow). D, detail of outer apical exopodal seta. Scale bars = 20 Mm in A–C; 10 Mm in D.
Figure 16 in A new genus of monstrilloid copepods (Crustacea) with anteriorly pointing ovigerous spines and related adaptations for subthoracic brooding
Figure 16. Maemonstrilla spinicoxa sp. nov., female holotype (KMNH IvR 700 217), Sesoko Island, 13.viii.1989, left legs 1–4, setules omitted and most setae cut short, showing invaginations or vestigial buttons in place of proximal inner endopodal seta of each leg (arrows). A, leg 1, anterior. B, leg 2, posterior. C, leg 3, anterior. D, leg 4, posterior. Scale 0.1 mm.
Figure 12 in New organic-walled Foraminifera (Protista) from the ocean's deepest point, the Challenger Deep (western Pacific Ocean)
Figure 12. Resigella bilocularis sp. nov. Scanning electron micrographs. A, general view; note collapsed initial chamber. B, detail of same specimen showing agglutinated coating of organic wall; note that the grains become more prominent towards proximal part of chamber. C–H, damaged specimen; the initial chamber has been lost. C, general view; areas within boxes are shown in more detail in E–H. D, surface of proximal part of chamber showing agglutinated grains. E, surface towards posterior end of chamber showing agglutinated grains and smoother, intervening areas; box indicates area shown in detail in F. F, detail of organic wall with mesh-like structures and a few flat areas. G, H, surface towards distal part of chamber showing smooth, flake-like features separated by areas with a fine, mesh-like structure. The flake-like features in F–H are probably clay particles.
Figure 13 in New organic-walled Foraminifera (Protista) from the ocean's deepest point, the Challenger Deep (western Pacific Ocean)
Figure 13. Resigella bilocularis sp. nov. Scanning electron micrographs. A, aperture of specimen shown in Figure 12C. B, general view of specimen with intact intial chamber and broken second chamber. C, D, broken cross-section of test wall showing organic layer overlain by agglutinated grains. E, F, general view of test and detail of organic surface with flake-like features (probably clay particles) separated by mesh-like structures.
Figure 6 from: van Ofwegen LP, Aurelle D, Sartoretto S (2014) A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). ZooKeys 462: 1-10. https://doi.org/10.3897/zookeys.462.8533
Figure 6 - Unrooted ML phylogenetic tree based on mitochondrial COI-IGR with RaxML. Blue dots refer to groups on the right with more than 90% bootstrap support (over 1 000 bootstraps). Blue branches indicate Alcyonium species and red branches indicate Complexum species. *Alcyonium valdiviae has been transferred to the genus Parasphaerasclera by McFadden and Ofwegen (2013b). **Because of pre-occupation Alcyonium roseum has been renamed Alcyonium varum by McFadden and Ofwegen (2013b).
Figure 3 from: van Ofwegen LP, Aurelle D, Sartoretto S (2014) A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). ZooKeys 462: 1-10. https://doi.org/10.3897/zookeys.462.8533
Figure 3 - Complexum pusillum sp. n., holotype (RMNH Coel. 41604). A point spindles; B collaret spindles C–D clubs of surface layer E spindles of interior.
Figure 2 from: van Ofwegen LP, Aurelle D, Sartoretto S (2014) A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). ZooKeys 462: 1-10. https://doi.org/10.3897/zookeys.462.8533
Figure 2 - A, B Complexum pusillum sp. n. A holotype (RMNH Coel. 41604) B paratype (RMNH Coel. 41605). Scale bar 10 mm.
Figure 5 from: van Ofwegen LP, Aurelle D, Sartoretto S (2014) A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). ZooKeys 462: 1-10. https://doi.org/10.3897/zookeys.462.8533
Figure 5 - Complexum pusillum sp. n., Banc du Conflit, depth 10 m. A General view of a small patch of colonies on rocky bottom B Magnified view of some colonies C small piece of rock colonized by the new species, sponges (green arrow) and small stony corals (Polycyathus cf. senegalensis – red arrow).
Data of Qyer Comments on Points of Interest in Switzerland until November 2017, including User Information
<p>The dataset contains a set of observations about comments on the Microblog "Qyer.com". For every comment, there is Information about time and place and about the user who uploaded the comment.</p>
Pre-calculated turning points of Stability-curve for stationary Shakura-Sunyaev accretion disc
<p>The pre-calculated turning points for surface density <span class="math-tex">\(\Sigma\)</span>, effective temperature <span class="math-tex">\(T_{\rm eff}\)</span> and accretion rate <span class="math-tex">\(\dot{M}\)</span> of S-shaped stability curve for stationary Shakura-Sunyaev viscous accretion disc. Calculations performed for 20 linearly scaled values of central source mass from <span class="math-tex">\(1\, M_{\odot}\)</span> to <span class="math-tex">\(20\, M_{\odot}\)</span>, 20 logarithmically scaled values of viscous parameter <span class="math-tex">\(\alpha\)</span> from <span class="math-tex">\(3\cdot10^{-4}\)</span> to 0.7, 20 logarithmically scaled values of radius from <span class="math-tex">\(7\cdot10^7\)</span> cm to <span class="math-tex">\(5\cdot10^{11}\)</span> cm.</p> <p><a href="https://github.com/AndreyTavleev/DiscVerSt">The new open-source Python3 code</a> is used to calculate the vertical structure of the disc with tabular opacity (solar chemical composition) and both convective and radiative energy transport taking into account. As a result, one can obtain S-shaped stability curve — a graphically depicted sequence of solutions of the vertical-structure equations, obtained at a single disc radius, in the coordinates of accretion rate or effective temperature versus the surface density. S-curve turn points allow to investigate the stability of disc with respect to temperature and surface density fluctuations. </p> <p>Reading of the data (Python3):</p> <pre><code class="language-python">import numpy as np data = np.genfromtxt('Turn_points_array.dat', names=True)</code></pre> <p> </p>
Viable counts of bacteria under various pH conditions at each time point
<p>Viable counts of pathogenic bacteria under various pH conditions at each time point</p>
Landscape structure affects metapopulation-scale tipping points
<p>Even when environments deteriorate gradually, ecosystems may shift abruptly from one state to another. Such catastrophic shifts are difficult to predict and sometimes to reverse (so-called hysteresis). While well studied in simplified contexts, we lack a general understanding of how catastrophic shifts spread in realistically spatially structured landscapes. For different types of landscape structures, including typical terrestrial modular and riverine dendritic networks, we here investigate landscape-scale stability in metapopulations whose patches can locally exhibit catastrophic shifts. We find that such metapopulations usually exhibit large-scale catastrophic shifts and hysteresis and that the properties of these shifts depend strongly on the metapopulation spatial structure and on the population dispersal rate: an intermediate dispersal rate, a low average degree or a riverine spatial structure can largely reduce hysteresis size. Our study suggests that large-scale restoration is easier with spatially clustered restoration efforts and in populations characterized by an intermediate dispersal rate.</p>
Data for the manuscript "Calculations of Excited Electronic States by Converging on Saddle Points Using Generalized Mode Following"
<p>Data of all energy curves presented.</p>
Augmented Street-Level Imagery with Points of Interest (Data and Resources Track)
<p>Augmented Street-Level Imagery with Points of Interest (Data and Resources Track)</p>
Supplementary material 2 from: Mas H, Santoiemma G, Lencina JL, Gallego D, Pérez-Laorga E, Ruzzier E, Rassati D (2023) Investigating beetle communities in and around entry points can improve surveillance at national and international scale. NeoBiota 85: 145-165. https://doi.org/10.3897/neobiota.85.103904
List of beetle species trapped from 2017 to 2021
Supplementary material 1 from: Gugele SM, Baer J, Spießl C, Yohannes E, Blumenshine S, Roberts BJ, Mota-Ferreira MR, Brinker A (2023) Stable isotope values and trophic analysis of invasive three-spined stickleback in Upper Lake Constance points to significant piscivory. NeoBiota 87: 73-102. https://doi.org/10.3897/neobiota.87.100355
Supplementary information
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.