1,721,018 research outputs found
A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
No full textEdgecombe, Gregory D., Vahtera, Varpu, Stock, Stuart R., Kallonen, Aki, Xiao, Xianghui, Rack, Alexander, Giribet, Gonzalo (2012): A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set. Zoological Journal of the Linnean Society 166 (4): 768-786, DOI: 10.1111/j.1096-3642.2012.00860.x, URL: https://academic.oup.com/zoolinnean/article-lookup/doi/10.1111/j.1096-3642.2012.00860.
Figure 6 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
No full textFigure 6. Single shortest cladogram for six genes and morphology in combination (14 570 steps) under parameter set 3221. Numbers above branches are jackknife frequencies> 50%. Navajo rugs (as explained in Fig. 5) for the six parameter sets shown below branches.Published as part of Edgecombe, Gregory D., Vahtera, Varpu, Stock, Stuart R., Kallonen, Aki, Xiao, Xianghui, Rack, Alexander & Giribet, Gonzalo, 2012, A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set, pp. 768-786 in Zoological Journal of the Linnean Society 166 (4) on page 781, DOI: 10.1111/j.1096-3642.2012.00860.x, http://zenodo.org/record/540903
Phase-contrast tomography of neuronal tissues: from laboratory- to high resolution synchrotron CT
No full textAssessing the three-dimensional architecture of neuronal tissues with sub-cellular resolution presents a significant analytical challenge. Overcoming the limitations associated with serial slicing, phase-contrast x-ray tomography has the potential to contribute to this goal. Even compact laboratory CT at an optimized liquid-metal jet micro- focus source combined with suitable phase-retrieval algorithms and preparation protocols can yield renderings with single cell sensitivity in millimeter sized brain areas of mouse. Here, we show the capabilities of the setup by imaging a Golgi-Cox impregnated mouse brain. Towards higher resolution we extend these studies at our recently upgraded waveguide-based cone-beam holo-tomography instrument GINIX at DESY. This setup allows high resolution recordings with adjustable field of view and resolution, down to the voxel sizes in the range of a few ten nanometers. The recent results make us confident that important issues of neuronal connectivity can be addressed by these methods, and that 3D (virtual) histology with nanoscale resolution will become an attractive modality for neuroscience research
X-ray phase contrast tomography from whole organ down to single cells
Full text linkWe use propagation based hard x-ray phase contrast tomography to explore the three dimensional structure of neuronal tissues from the organ down to sub-cellular level, based on combinations of synchrotron radiation and laboratory sources. To this end a laboratory based microfocus tomography setup has been built in which the geometry was optimized for phase contrast imaging and tomography. By utilizing phase retrieval algorithms, quantitative reconstructions can be obtained that enable automatic renderings without edge artifacts. A high brightness liquid metal microfocus x-ray source in combination with a high resolution detector yielding a resolution down to 1.5 μm. To extend the method to nanoscale resolution we use a divergent x-ray waveguide beam geometry at the synchrotron. Thus, the magnification can be easily tuned by placing the sample at different defocus distances. Due to the small Fresnel numbers in this geometry the measured images are of holographic nature which poses a challenge in phase retrieval
P05 imaging beamline at PETRA III: first results
No full textThe imaging beamline (IBL/P05) operated by Helmholtz Zentrum Geesthacht (HZG) at the DESY PETRA III storage ring consists of two experimental stations: A micro tomography and a nano tomography end station. Here an overview of the experimental setups and the data acquisition will be given. In addition some first results out of the wide range of applications using the micro tomography station at P05 will be shown. Furthermore, we present first results of the nano tomography end station. These were obtained with an x–ray microscopy setup, which currently operates at energies of 17.4 and 30 keV using polymer compound refractive lenses (CRLs) and rolled prism lenses. Taken together these results clearly show the high potential of the newly built imaging beamline IBL
High density resolution synchrotron radiation based X-ray microtomography (SR mu CT) for quantitative 3D-morphometrics in zoological sciences
No full textpeer reviewedZoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based X-ray microtomography (SR mu CT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR mu CT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SR mu CT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR mu CT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR mu CT further increase of density resolution in absorption contrast methods is desirable
A comparison of three different micro-tomography systems for accurate determination of microvascular parameters
No full textThe investigation of micro-vessel dimensions in 3D is currently problematic due to their complex structures and fine scale. Quantification of vascular parameters is important in several fields of biomedicine; including embryogenesis, wound healing, diseases characterized by uncontrolled angiogenesis (e.g. tumor growth and metastasis) and the development of implantable bio-materials where a functional vascular supply is critical to their successful integration into host tissue. However, techniques that can resolve the micron-scaled features of these capillary beds, such as scanning electron and confocal microscopy, do not allow for total image reconstitution in 3D in thick tissue samples [1]. The present study describes the use of an in vivo corrosion casting technique that provides a stable replica of the microvascular network and the subsequent evaluation of three different μCT systems in order to accurately quantify vessel dimensions. Stable replicas of micro-vascular networks in neonatal mouse eyes were first created using in vivo vascular corrosion casting and then imaged using a unique, laboratory scale, μCT unit. This system combines a LaB6 cathode with high-performance electron optics to obtain a high resolution x-ray source. Novel image analysis was then applied to the reconstructions to quantify the morphological parameters of the hyaloid vascular plexi in the developing eyes of post-natal day 2 (P2) wild-type mice. These results are compared to synchrotron scans, establishing vascular casting and x-ray μCT as a valid laboratory scale experimental method for accurate 3D quantification of the microvasculature, with potential applications to a wide variety of fields in biological and medical research.</p
Figure 2 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
No full textFigure 2. Scolopocryptops simojovelensis sp. nov. Holotype AMNH Ch-SH7. A, nearly dorsal view of tergites 17–22; arrows on TT17 and 18 indicate complete paramedian sutures. B, dorsolateral view of tergites 17–20; inset shows anastomizing ridges parallel to posterior margin on tergite 19. C, dorsal view of segment 23, showing tergite (T23), coxopleural process (cp), dorsomedial spinose process (ds) and ventral spinose process (vs) of prefemur. D, dorsolateral view of leg pairs 21–23. Scale bars: A, B, D = 1 mm; C = 0.5 mm.Published as part of Edgecombe, Gregory D., Vahtera, Varpu, Stock, Stuart R., Kallonen, Aki, Xiao, Xianghui, Rack, Alexander & Giribet, Gonzalo, 2012, A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set, pp. 768-786 in Zoological Journal of the Linnean Society 166 (4) on page 775, DOI: 10.1111/j.1096-3642.2012.00860.x, http://zenodo.org/record/540903
Figure 1 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
No full textFigure 1. Scolopocryptops simojovelensis sp. nov. Holotype AMNH Ch-SH7. A, dorsolateral view of complete specimen. B, distal part of right leg 20, showing tibial spur (ti) and tarsal spur (ta). C, dorsolateral view of cephalic plate and right antenna. D, distal part of tarsus and pretarsus of right leg 20, showing accessory spurs (ac). Scale bars: A = 5 mm; B = 0.5 mm; C = 1 mm; D = 0.1 mm.Published as part of Edgecombe, Gregory D., Vahtera, Varpu, Stock, Stuart R., Kallonen, Aki, Xiao, Xianghui, Rack, Alexander & Giribet, Gonzalo, 2012, A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set, pp. 768-786 in Zoological Journal of the Linnean Society 166 (4) on page 774, DOI: 10.1111/j.1096-3642.2012.00860.x, http://zenodo.org/record/540903
- …
