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opencc-zeroApr 2024View details →

SeMRA Anatomy Mappings Database

Supports the analysis of the landscape of anatomy nomenclature resources. See instructions for reproduction and usage in the attached README.md.

opencc-by-4.0Nov 2023View details →

Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D

Abstract:Ultrasound Localization Microscopy (ULM) enables imaging microvessels in the brain with a resolution of a few tens of micrometers in vivo. The planar architecture of arterioles and venules was revealed with a 2D ultrasound scanner in the cortex of the rat brain. However, deeper in the brain, where the vascularization becomes tri-dimensional, 2D imaging remains limited by the elevation projection. In this study, volumetric ultrasound imaging was performed in the craniotomized rat brain to yield 3D ULM in vivo within 7.5 min of acquisition with a commercial system. For instance, it highlighted the thalamus or the circle of Willis with small vessels down to 21 µm. Microbubbles tracking also gave access to the 3D velocity vector of blood flow allowing to distinguish flow directions. Volumetric ULM resolved deep complex tri-dimensional vascular structures and was compared to 2D ULM. It is a safe, simple and repeatable system to image wide field of view in the brain.Data Description:Microbubbles have been detected, localized, and tracking with 3D ultrasound imaging in vivo in a rat brain with skull removal.Individual microbubble trajectories are described in 4 columns vectores: [z, x, y, time] for each position of the path. Space positions are given in [mm], and times are given in [ms]. Trajectories data are stored in .mat files (tracks_0xx.mat and zipped inside tracks.zip) as cell arrays.Tracks can be binned inside a volumetric grid with the sample code (ULM_rendering.m).Reference to be cited: Chavignon, Heiles, Hingot, Orset, Vivien and Couture.Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D.

opencc-by-4.0Jun 2022View details →

Data from: Cranial anatomy of the giant anteater from north-western Venezuela (Myrmecophaga tridactyla artata, Pilosa: Myrmecophagidae)

Annotated R codes and datasets used in: Carrillo et al. 2022. Cranial anatomy of the giant anteater from north-western Venezuela (Myrmecophaga tridactyla artata, Pilosa: Myrmecophagidae). Anartia

opencc-by-4.0Aug 2023View details →

Human Inner Ear Anatomy: Labeled Volume CT Data of Inner Ear Fluid Space and Anatomical Landmarks

The provided dataset comprises 43 instances of temporal bone volume CT scans. The scans were performed on human cadaveric specimen with a resulting isotropic voxel size of \(99 \times 99 \times 99 \, \, \mathrm{\mu m}^3\). Voxel-wise image labels of the fluid space of the bony labyrinth, subdivided in the three semantic classes cochlear volume, vestibular volume and semicircular canal volume are provided. In addition, each dataset contains JSON-like descriptor data defining the voxel coordinates of the anatomical landmarks: (1) apex of the cochlea, (2) oval window and (3) round window. The dataset can be used to train and evaluate algorithmic machine learning models for automated innear ear analysis in the context of the supervised learning paradigm.   Usage Notes The datasets are formatted in the HDF5 format developed by the <a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5 Group</a>. We utilized and thus recommend the usage of Python bindings <a href="https://www.h5py.org/">pyHDF</a> to handle the datasets. The flat-panel volume CT raw data, labels and landmarks are saved in the HDF5-internal file structure using the respective group and datasets: <pre><code>raw/raw-0 label/label-0 landmark/landmark-0 landmark/landmark-1 landmark/landmark-2</code></pre> Array raw and label data can be read from the file by indexing into an opened h5py file handle, for example as numpy.ndarray. Further metadata is contained in the attribute dictionaries of the raw and label datasets. Landmark coordinate data is available as an attribute dict and contains the coordinate system (LPS or RAS), IJK voxel coordinates and label information. The helicotrema or cochlea top is globally saved in landmark 0, the oval window in landmark 1 and the round window in landmark 2. Read as a Python dictionary, exemplary landmark information for a dataset may reads as follows: <pre><code class="language-python">{'coordsys': 'LPS', 'id': 1, 'ijk_position': array([181, 188, 100]), 'label': 'CochleaTop', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 44.21109689, -139.38058589, -183.48249736])}</code></pre>   <pre><code class="language-python">{'coordsys': 'LPS', 'id': 2, 'ijk_position': array([222, 182, 145]), 'label': 'OvalWindow', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 48.27890112, -139.95991131, -179.04103763])}</code></pre>   <pre><code class="language-python">{'coordsys': 'LPS', 'id': 3, 'ijk_position': array([223, 209, 147]), 'label': 'RoundWindow', 'orientation': array([-1., -0., -0., -0., -1., -0., 0., 0., 1.]), 'xyz_position': array([ 48.33120126, -137.27135678, -178.8665465 ])}</code></pre>

opencc-by-4.0Jul 2022View details →

Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments [software and dataset]

Simulation software and results for "Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments"

opencc-by-4.0Nov 2019View details →

Fig. 4 in Kidney anatomy, histology and histometric traits associated to renosomatic index in Gymnotus inaequilabiatus (Gymnotiformes: Gymnotidae)

Fig. 4. Histological cross-sections of the head and exocrine kidney demonstrating different granulomatous structures in Gymnotus inaequilabiatus. a. severe aggregation of MMCs outer to granuloma in the exocrine kidney; PAS, bar scale = 20 µm. b. a clump of melanogenic macrophages (dark pigmented cells) adjacent to granuloma in the head kidney. The hematopoietic tissue is edematous and atypical. Some rodlet cells (black arrow) are observed. Granuloma presents a compact and thick layer of collagen with internal necrotic content surrounded by epithelioid cells (white arrows); H&E, bar scale = 10 µm. c. two well-defined granulomas with substantial internal necrotic content involved by fibrous tissue. A slight layer of MMCs aggregates close to the external wall of granuloma. TM, bar scale = 10 µm. d. MMCs aggregates both internally and externally to granuloma in the exocrine kidney. HE, bar scale = 10 µm.

opencc-by-4.0Nov 2019View details →

Fig. 2 in Kidney anatomy, histology and histometric traits associated to renosomatic index in Gymnotus inaequilabiatus (Gymnotiformes: Gymnotidae)

Fig. 2. Cross-section of the head and exocrine kidney in Gymnotus inaequilabiatus. a. a transitional area between head (HE) and exocrine kidney (EX) drained by postcardinal vein (PCV). Lymphohematopoietic tissue is abundant in the head portion. MMCs are diffusely distributed in both portions. A thick fibrous capsule covers the organ (white arrow); HE, bar scale = 500 µm. b. the general aspect of the head kidney. Vascular sinusoids (white arrows) surrounding the lymphohematopoietic tissue enclosing the MMCs (black arrow); HE, bar scale = 200 µm. c. interstitial lymphohematopoietic tissue with MMCs deposits characterizes the exocrine kidney, in addition, the contoured tubules; renal corpuscle (white arrow); HE, bar scale = 200 µm. d. the exocrine kidney with a proximal convoluted tubule showing hyaline degeneration of the tubular epithelium often found in this species; HE, bar scale = 100 µm. e. exocrine kidney showing the corpuscle of Stannius (*). This structure is not lobulated, and is delimited by a fibrous capsule, and situated at the junction between head and exocrine portions; HE, bar scale = 500 µm. f. detail of junction between lymphohematopoietic tissue and corpuscle of Stannius in the head kidney. Fiber bundles subdivide both structures. Rodlet cells (white arrow), macrophages (M) and eosinophilic granulocytic cells (black arrow); granulocytic (G) and secretory cells (SC) internally fill the corpuscle; HE, bar scale = 50 µm.

opencc-zeroAug 2019View details →

FIG. 7 in Anatomy, affinities, and evolutionary implications of new silicified stems of Sphenophyllum Brongniart, 1828 from the early Carboniferous (Mississippian) of France and Germany

FIG. 7. — Reconstruction of MN911 at the level of branching based on a series of transverse sections. Because only the base of the leaves is well known, their tips are represented in dashed lines. Sections 1-6 correspond to polished surfaces MN911-B1i, MN911-B1s, MN911-B2i, MN911-B2s, MN911-B3i, and MN911- B3s; sections 7 and 8 correspond to slides MN911-A1 and MN911-A2. Artwork by Bernard Terreaux.

opencc-zeroAug 2019View details →

FIG. 2 in Anatomy, affinities, and evolutionary implications of new silicified stems of Sphenophyllum Brongniart, 1828 from the early Carboniferous (Mississippian) of France and Germany

FIG. 2. — General aspect of the specimens in transverse section at the same scale. The primary xylem is in dark grey, the secondary xylem – when present – is in black. A, MN201(slide MN201-E2); B, same specimen as A at a level of branching (slide MN201-F1); C, largest axis resulting from the branching of MN911 with two leaf bases (slide MN911-A1); D, same axis as in C at another level with one leaf base and the production of two traces from one arm of the stele (slide MN911-A2); E, smallest axis resulting from the branching of MN911 (slide MN911-A2); F, MN864 showing secondary xylem all around the stele (slide MN864-C1); G, KLC3 showing a small amount of secondary xylem (slide KLC3-C); H, KLC4 showing a small amount of secondary xylem like KLC3 but a much smaller cortex (slide KLC4-B2). Scale bar: 2 mm.

opencc-zeroAug 2019View details →

FIG. 1 in Anatomy, affinities, and evolutionary implications of new silicified stems of Sphenophyllum Brongniart, 1828 from the early Carboniferous (Mississippian) of France and Germany

FIG. 1. — Maps showing the location of the localities in Southern France (A) and Thuringia, Germany (B). Detailed maps modified from Galtier et al. 1988 and Meyer-Berthaud & Rowe 1997.

FIG. 50 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 50. — Lateral view of the right pelvic bones of some extant mysticetes. A, Balaenoptera musculus; B, Balaenoptera musculus; C, Megaptera novaeangliae; D, E, Balaena mysticetus. The iliac, pubic and ischial portions are, respectively, in blue, yellow and green. Modified from Struthers (1893).

FIG. 49 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 49. — Lateral view of innominate of some extinct cetaceans. A, Georgiacetus vogtlensis (GSM 350); B, Basilosaurus isis (CGM 42176, cast); C, Basilosaurus cetoides (USNM 12261); D, Chrysocetus healyorum (SCSM 87-195, cast, right innominate, reversed); E, Mystacodon selenensis (MUSM 1917). Not to scale.

FIG. 48 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 48. — Mystacodon selenensis (MUSM 1917, holotype). Left innominate: A, lateral view; B, dorsal view; C, medial view; D, ventral view. Scale bar: 5 cm.

FIG. 39 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 39. — Ribs transverse sections of Mystacodon, basilosaurids, and chaeomysticetes. A, Mystacodon selenensis (MUSM 1917, holotype): section of an anterior-median (right?) rib of the thoracic cage in the median region of the diaphysis; B, Dorudon atrox (UM 101222): section of a left R4 at mid-diaphysis (reversed); C, Basilosaurus isis (WH 074): section of a left R4 at mid-diaphysis. B and C are reproduced from Houssaye et al. (2015). D, Piscobalaena nana (MNHN.F. SAS1618). E, Balaenoptera acutorostrata (IRSNB uncatalogued). Abbreviations: ant, anterior; med, medial. Scale bar: 1 cm.

FIG. 42 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 42. — Mystacodon selenensis (MUSM 1917, holotype). Right humerus: A, lateral view; B, medial view; C, anterior view; D, posterior view. Scale bar: 5 cm.

FIG. 6 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 6. — Lateral view of the skull of Mystacodon selenensis (MUSM 1917, holotype). Oblique lines and grey-shaded regions indicate respectively broken and reconstructed parts. Scale bar: 20 cm.

FIG. 1 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 1. — Views of the extraction of the postcranial skeleton of Mystacodon selenensis (MUSM 1917 holotype) at Playa Media Luna (Ica Department, Peru).

FIG. 27 in Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

FIG. 27. — Mystacodon selenensis (MUSM 1917, holotype). A-C, right i2 or i3 (tooth I); D-F, left i3 or c (tooth II); G-I, right?p1 (tooth III); A, labial view; B, lingual view; C, occlusal view; D, labial view; E, lingual view; F, occlusal view; G, labial view, H, lingual view; I, occlusal view. Scale bar: 3 cm.