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64 results for “Lamella”
Synchrotron-based visualization and segmentation of elastic lamellae in the mouse carotid artery during quasi-static pressure inflation: dataset
<p>This dataset contains images that were obtained during quasi-static pressure inflation of mouse carotid arteries. Images were taken with phase propagation imaging at the X02DA TOMCAT beamline of the Swiss Light Source synchrotron at the Paul Scherrer Institute in Villigen, Switzerland. Scans of n=12 left carotid arteries (n-6 Apoe-deficient mice, n=6 wild-type mice, all on a C57Bl6J background) were taken at pressure levels of 0, 10, 20, 30, 40, 50, 70, 90 and 120 mmHg. For analysis we selected 75 images from the center of each stack (starting at the center of the stack, and skipping 2 of every three images in both cranial and caudal axial directions) for each sample and for each pressure level, resulting in a total of 75 x 12 x 9 = 8100 analyzed images from 108 different scans. Segmentation, 3D visualization and geometric analysis is presented in the corresponding manuscript. Files are uploaded in 16bit .tif format and are named: mouseid_pressurelevel_stacknumber, with mouseid consisting of either Apoe (Apoe-deficient) or Bl (wild-type) and the mouse number, pressurelevel varies from P0 to P120 and stacknumber indicates which image from the stack has been uploaded.</p>
Synchrotron-based visualization and segmentation of elastic lamellae in the mouse carotid artery during quasi-static pressure inflation: 2D segmentations
<p>This dataset contains 2D segmentations of images that were obtained during quasi-static pressure inflation of mouse carotid arteries. Images were taken with phase propagation imaging at the X02DA TOMCAT beamline of the Swiss Light Source synchrotron at the Paul Scherrer Institute in Villigen, Switzerland. Scans of n=12 left carotid arteries (n-6 Apoe-deficient mice, n=6 wild-type mice, all on a C57Bl6J background) were taken at pressure levels of 0, 10, 20, 30, 40, 50, 70, 90 and 120 mmHg. For analysis we selected 75 images from the center of each stack (starting at the center of the stack, and skipping 2 of every three images in both cranial and caudal axial directions) for each sample and for each pressure level, resulting in a total of 75 x 12 x 9 = 8100 analyzed images from 108 different scans. Segmentation algorithm, 3D visualization and geometric analysis are presented in the corresponding manuscript. Files are uploaded in .jpg format and are named: lamella_slicenumber, with slicenumber varying from 1 to 8100. There is also a Matlab file, UndulationData_Zenodo.mat, in which all the relevant variables post analysis are stored. This file contains a variable called "myFiles", which contains the link between the slicenumbers used here and the original dataset that is published in Zenodo (.tif synchrotron images).</p>
MicroED datasets from two proteinase K lamellae using a 20 micrometre C2 condenser aperture
<p>These four diffraction data sets were used to determine the proteinase K structure from two crystalline lamellae by electron diffraction, as deposited in the PDB with id <a href="http://doi.org/10.2210/pdb6ZEV/pdb">6ZEV</a> and published in <a href="https://doi.org/10.3389/fmolb.2020.00179">https://doi.org/10.3389/fmolb.2020.00179</a></p> <p>A script is provided that allows indexing of the diffraction spots using DIALS 3.1. This is adapted from the commands used to process the data for the publication, which used DIALS 1.10.</p>
Fig. 5. Ventral lamella between tarsal claws. A in The Supraspecific Structure Of The Subtribe Blaptina Leach, 1815 (Coleoptera, Tenebrionidae: Blaptinae)
Fig. 5. Ventral lamella between tarsal claws. A = Lithoblaps gigas (Linnaeus, 1767), comb. n.; B = Blaps (Blaps) mortisaga (Linnaeus, 1758); C = Blaps (Ablapsis) allardiana allardiana Reitter, 1889; D = Blaps (Dineria) halophila Fischer von Waldheim, 1820; E = Blaps (Arenoblaps) hiemalis Semenov et Bogatchev, 1940; F = Dilablaps paradoxa Bogatchev, 1976; G = Medvedevoblaps kashkarovi (G. S. Medvedev, 1998); H = Coelocnemodes tibialis Ren in Ren, Ba, Liu, Niu, Zhu, Li et Shi, 2016; I = Thaumatoblaps marikovskiji Kaszab et G. S. Medvedev, 1984
◂Fig. 13 Crystallographic structure on the columellar lamellae of Dinaride Zospeum and Iberozospeum shells; (a) Zospeum spelaeum, (AJC 847), Betalov Spodmol jama, Slovenia (45.7922 14.1877), pattern of low, non-overlapping, wedges of crystallographic structure on the lamella; (b) Zospeum spelaeum, (MCBI CSR SASA 37049a), Velika Pasica, Slovenia (N45.9189 E14.4934), non-overlapping wedges of crystallographic structure on lamella in old shell; (c) Iberozospeum sp., (RMNH.MOL. 234,120), Cueva Refugio, Trucios, overview of dense, overlapping, scale-like wedges of localized, crystallographic structure on upper part of the lower lamella; (d) ibid., closeup view of c; (e) Iberozospeum sp., (RMNH.MOL. 234,104), Cueva del Comediante, Santander, upper part of the lamella of chemically treated shell showing dense, overlapping wedges of localized, crystallographic structure; (f) Iberozospeum sp., (RMNH. MOL. 234,141), Cueva a Sul, Oviedo, localized, overlapping wedges of crystallographic structure on lamella of chemically treated shell; (g) Iberozospeum vasconicum, (AJC 1849), Cueva Arrikrutz, overview of dense, localized, crystallographic structure on lower part of the lamella; h, ibid., closeup view of g. — Magnification varies for each perspective, see scale bars; Figs. a–b, g–h) imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main; Figs. c–f imaged by Dirk Vendermarel, Naturalis Biodiversity Center in Molecular investigation and description of Iberozospeum n. gen., including the description of one new species (Eupulmonata, Ellobioidea, Carychiidae)
◂Fig. 13 Crystallographic structure on the columellar lamellae of Dinaride Zospeum and Iberozospeum shells; (a) Zospeum spelaeum, (AJC 847), Betalov Spodmol jama, Slovenia (45.7922 14.1877), pattern of low, non-overlapping, wedges of crystallographic structure on the lamella; (b) Zospeum spelaeum, (MCBI CSR SASA 37049a), Velika Pasica, Slovenia (N45.9189 E14.4934), non-overlapping wedges of crystallographic structure on lamella in old shell; (c) Iberozospeum sp., (RMNH.MOL. 234,120), Cueva Refugio, Trucios, overview of dense, overlapping, scale-like wedges of localized, crystallographic structure on upper part of the lower lamella; (d) ibid., closeup view of c; (e) Iberozospeum sp., (RMNH.MOL. 234,104), Cueva del Comediante, Santander, upper part of the lamella of chemically treated shell showing dense, overlapping wedges of localized, crystallographic structure; (f) Iberozospeum sp., (RMNH. MOL. 234,141), Cueva a Sul, Oviedo, localized, overlapping wedges of crystallographic structure on lamella of chemically treated shell; (g) Iberozospeum vasconicum, (AJC 1849), Cueva Arrikrutz, overview of dense, localized, crystallographic structure on lower part of the lamella; h, ibid., closeup view of g. — Magnification varies for each perspective, see scale bars; Figs. a–b, g–h) imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main; Figs. c–f imaged by Dirk Vendermarel, Naturalis Biodiversity Center
Sytlegomydas daltoni Seguy, male genitalia: 65, ventral view; 66, dorsal view;.67, lateral view; a. l: anal lamellae; ae: aedeagus; bst: apical processes of basistylus: ce: cerci; ep: epandrium; hy + bst: fusion of hypandrium with basistyli. in The American Genera of Mydidae (Diptera), with the Description of three new Genera and two new Species
Sytlegomydas daltoni Seguy, male genitalia: 65, ventral view; 66, dorsal view;.67, lateral view; a. l: anal lamellae; ae: aedeagus; bst: apical processes of basistylus: ce: cerci; ep: epandrium; hy + bst: fusion of hypandrium with basistyli.
Fig. 9 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 9. Conceptual figure showing growth accompanied amplification of pyramidial shaped multi−foliated gills. A. Limulid type of gills with low−relief conical profile. B. Decapod type of gills with high relief.
Fig. 8 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 8. Body−weight specific lamellar numbers and average single lamellar area in bi−logarithmic coefficients. A. Bi−logarithmic graph of total number of lamellae with respect to dry−body weight in Limulus polyphemus (close circle), Tachypleus rotundicauda (open circle), Callinectes sapidus (solid square) and Libinia dubia (open square). B. Results of allometric analysis shown in Fig. 5A. Sample size (N), correlation coefficient (r), reduced major axis of logW = αlogNL + logβ, and K = α – α / [(s)2 + (s)2]1/2 where s is the standard deviation of α. K is a statistic with the standard normal distribution used for 1 2 α1 α2 α discrimination of the differences of α significant or not. If K>1.96 or K <−1.96, the difference is significant. See also Fig. 7 for the abbreviations of W and NL. C. Bi−logarithmic graph of average area per lamella with respect to dry−body weight. Abbreviations as in Fig. 5A. D. Results of allometric analysis shown in Fig. 5C. Same abbreviations as in Fig. 5B. The data of two decapods are referred to Hughes (1983), which presented average, maximum and minimum specific dry−body weight and lamellar number among the examined samples as well as α and logβ of the allometric analysis with respect to their dry−body weight. Readers are referred to the results of T. rotundicauda as reference data, because too small numbers have been examined. This is to show the trend that the results of a species fall in a neighboring area to that of a taxonomically close species.
Fig. 7 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 7. Allometric relationships between respiratory surface and dry−body weight in Limulus polyphemus (dots and solid regression line) in bi−logarithmic coefficients. Abbreviations are: correlation coefficients (r); drybody weight (W); total area for respiratory surface (A); allometric scaling exponent (α). For comparisons, the results on the gills of decapod crustaceans Callinectes sapidus and Libinia dubia are shown in dashed lines, the data are referred to Hughes (1983).
Fig. 6 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 6. Phyllobranchiate gill of a decapod crustacean Atergatris sp. Top one−fourth is shown. SEM photo.
Fig. 5 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 5. The area of every gill lamella of selected first branchial appendages. A. Instar stage 4 of dry−body weight 0.01 g. B. Instar stage 10 of dry−body weight 0.43 g. C. Instar stage 14 of dry−body weight 6.7 g. D. Instar stage 18 of dry body weight 177.09 g. Grey shaded area corresponds to possible newly established lamellae in each instar stage. Darker shade ranges to minimum established number, while lighter maximum. Total respiratory area (T), respiratory area for newly established lamellae of minimum (Nmin) and maximum value (Nmax) are also noted. These ratios relative to the total area are shown in parentheses. The lamellae left to dashed lines lack an osmoregulatory area.
Fig. 4 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 4. Growth−related change in gill morphology of Limulus polyphemus shown in instar−stage series. A. Mean total respiratory (white bars) and osmoregulatory area for each instar stage (grey bars) and their increment rates (black and grey line graph denotes respiratory and osmoregulatory area, respectively). B. Average total lamellar number for each instar stage (bar graph) and its increment rates (line graph). C. Average area per single lamellae for each instar stage (bar graph) and its increment rates (line graph). The bar graphs should refer to left indexes shown in exponential form (A and C) or in actual numbers (B), and the line graphs right indexes. Error bars denote the maximum and the minimum lamellar numbers. Numbers shown above the columns represent the numbers of examined specimens.
Fig. 10 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 10. Lamellipedian exopod of the trilobite Olenoides serratus. A. Camera lucida drawing; traced from Whittington (1980: text−fig. 6). B. Estimated area of each exite shown in A.
Fig. 3 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 3. Posterior view of first instar stage of Limulus polyphemus Linnaeus, 1758. Only five gill lamellae (gl) are visible between the operculate division of first (ba1) and second branchial appendage (ba2). Other abbreviations: op, operculum; pr, prosoma. SEM photo.
Fig. 2 in Morphological requirements in limulid and decapod gills: A case study in deducing the function of lamellipedian exopod lamellae
Fig. 2. Book gill of Limulus polyphemus Linnaeus, 1758. A. Dorsal view of left first branchial appendage of instar stage 14. Endopod and exopod of the operculate division of branchial appendage as well as lamellae of book gill are shown. SEM photo. B. Dorsal view of left first branchial appendage of instar stage 4. SEM photo. C. Transparent microscopic photo of a gill lamella dyed with toluidine blue, showing osmoregulatory and respiratory area.
Рис. 1–3. ЭнΔофаΛΛус Valgus hemipterus (Linnaeus, 1758). 1 – энΔофаΛΛус в ΛатераΛьной проекции (Турция, провинция Амасья, СарайΔжик); 2 – спираΛевиΔный и ΛанцетовиΔный скΛериты; 3 – копуΛятивная пΛастинка. Figs 1–3. Endophallus of Valgus hemipterus (Linnaeus, 1758). 1 – endophallus, laterally (Turkey, Amasya Province, Saraycık); 2 – lamella spiraliformis and lamella lanceolata; 3 – lamella copulatrix. in Morphology of the endophallus of Valgus hemipterus (Linnaeus, 1758) (Coleoptera: Scarabaeidae)
Рис. 1–3. ЭнΔофаΛΛус Valgus hemipterus (Linnaeus, 1758). 1 – энΔофаΛΛус в ΛатераΛьной проекции (Турция, провинция Амасья, СарайΔжик); 2 – спираΛевиΔный и ΛанцетовиΔный скΛериты; 3 – копуΛятивная пΛастинка. Figs 1–3. Endophallus of Valgus hemipterus (Linnaeus, 1758). 1 – endophallus, laterally (Turkey, Amasya Province, Saraycık); 2 – lamella spiraliformis and lamella lanceolata; 3 – lamella copulatrix.
Text-fig. 9. Tachyglossus aculeatus. Transverse section through the orbital region of the head of a juvenile specimen. ms: sphenobturatory membrane; plb: palatine bone; psw: primary endocranial sidewall; sll: secondary lateral lamella of Kuhn (1971); this endocranial process (blue) is here interpreted as a derivative of the cartilago teniformis. (From Kuhn and Zeller 1987.) in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 9. Tachyglossus aculeatus. Transverse section through the orbital region of the head of a juvenile specimen. ms: sphenobturatory membrane; plb: palatine bone; psw: primary endocranial sidewall; sll: secondary lateral lamella of Kuhn (1971); this endocranial process (blue) is here interpreted as a derivative of the cartilago teniformis. (From Kuhn and Zeller 1987.)
Figure 13. Lamellae antevaginales, ventral views. A in The phylogenetic relationships of Morgan's Sphinx, Xanthopan morganii (Walker), the tribe Acherontiini, and allied long-tongued hawkmoths (Lepidoptera: Sphingidae, Sphinginae)
Figure 13. Lamellae antevaginales, ventral views. A, Manduca rustica, BMNH sphingid preparation #1076. B, Xanthopan morganii, BMNH sphingid preparation #1013. C, Meganoton rubescens, BMNH sphingid preparation #990. D, Megacorma obliqua, BMNH sphingid preparation #1027.
MicroED datasets from 3 proteinase K wedge-shaped lamellae
<p>Plunge-frozen grids containing crystals of proteinase K with approximate dimensions of 12 x 10 x 10 µm were coated with a layer of organoplatinum using the in situ gas injection system of the Scios DualBeam cryoFIB instrument (Thermo Fisher Scientific). A series of initial milling steps produced lamellae of approximately 0.5 µm thickness. Wedged lamellae were then generated by tilting the stage through a defined angle away from the initial milling position before further milling from the underside only. The defined angle was calculated to produce a lamella where the leading edge measured approximately 200 nm and the back edge of the crystal within the lamella measured approximately 400 nm.</p> <p>Electron diffraction data were collected using a Thermo Fisher Scientific Talos Arctica transmission electron microscope equipped with a Ceta-D camera. The microscope was operated at an accelerating voltage of 200 kV using gun lens 8, a spot size of 11 and a 50 µm C2 aperture. These conditions gave a beamsize of 1.3 µm and an approximate electron dose of 0.04 e/Å<sup>2</sup>/s at the sample position.</p> <p>Diffraction images can be read in DIALS using the <a href="https://github.com/dials/dxtbx_ED_formats/blob/master/FormatMRC.py">FormatMRC</a> plug-in, after renaming the files to conform to a standard serial number template.</p>
SPACEtomo training dataset for Yeast lamella map segmentation using nnU-Netv2
<p><strong>Training data used to train a nnU-Net 2D segmentation model for TEM montages of cryoFIB-milled lamellae from Yeast.</strong></p> <p>Medium magnification map pieces (2.283 nm/pixel) from starved <em>S. cerevisiae</em> were manually segmented into 17 categories (see publication) and used to train a 2D nnU-Net. </p> <p>This training dataset contains 50 images and segmentations of starved Yeast cells (kindly provided by Anna Bieber and Cristina Capitanio) and 10 additional images of Baker's Yeast under exponential growth conditions.</p>
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International Brain Laboratory public data
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OpenNeuro
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