Computational protocol: X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov.

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Protocol publication

[…] The internal structures of the cones were first probed using XMT on a Nikon Metrology HMX-ST 225 scanner at the Natural History Museum London. The scan was performed with a tungsten reflection target at 180 µA and 130 kV, 0.25 s exposure time for 6284 projections. No filter was used. The 4 MP (2,000 × 2,000) Perkins Elmer detector panel provided a voxel size of 8.8 µm for specimen NHMUK V 68524 and 6.5 µm for the compressed cone (specimen NHMUK V 68525). The results from the XMT were sufficient to demonstrate the high quality of the internal preservation and the ovulate nature of the cone, however the compressed cone had poor attenuation contrast and a greatly distorted internal anatomy so was not investigated further. In order to achieve improved resolution and observe crucial cellular detail, additional scans of specimen NHMUK V 68524 were performed at the Diamond Light Source (DLS) synchrotron. The I12—JEEP (Joint Engineering, Environment and Processing)—beamline was selected for its high brilliance and ability to perform high resolution scans on macro-sized objects. Experiment Hutch (EH1) was used with a monochromatic beam set at 70 KeV with a cadmium tungstate crystal scintillator capturing attenuation contrast images on a PCO.4000 camera. The second scan used Module 2, with 0.5 s exposure time for 1,800 projections, providing a voxel size of 5.0 µm and a field of view of 20 × 13.2 mm. The third very high resolution scan used Module 3 through a quadrant of the cone base, with an increased exposure time of 2.5 s for 1,800 projections, generating a voxel size of 1.8 µm with a field of view 7.2 × 4.8 mm.Due to their higher resolution, the SRXMT datasets acquired at DLS were subsequently selected as the basis for three-dimensional models created with the SPIERS software suite (). Following the methods described by and , false colour models illustrating the locations, form and interrelationships between various anatomical features were produced. Raytraced images and videos of the three-dimensional models where composited and rendered using the open source three-dimensional animation package Blender™ (www.blender.org; ). The images used in figures/plates were edited and processed (cropped, rotated, edge enhanced and equalised) in GIMP 2, ImageJ () and Corel Paint Shop Pro Photo X2™ with figures constructed in Adobe Illustrator CS5™, Corel Creative Suite X5™ and Inkscape 0.48. The tomographic datasets are available upon request from the Natural History Museum (London).A literature survey was conducted to plot the palaeogeographic distribution of all published pollen- and seed-cones of the Cheirolepidiaceae. Palaeogeographic latitude and longitudes were calculated using PointTracker after determining modern geographical co-ordinates from topographic and geological maps in tandem with Google Earth™. These were plotted using Corel Creative Suite X5™ on to a series of Mesozoic palaeomaps showing individual time slices. The palaeomaps were based on global palaeo-reconstruction maps by Ron Blakey (). See . […]

Pipeline specifications

Software tools ImageJ, Adobe Illustrator, Inkscape
Applications Miscellaneous, Microscopic phenotype analysis
Organisms Dipturus trachyderma