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Computed tomography (CT) scans of extant and fossil chondrichthyans, of teeth organized into functional dentitions. These scans were taken on a Nikon Metrology HMX ST 225, in the Image and Analysis Centre, Natural History Museum, London.
The map shows the localities of significant fossil samples, either collected by BGS Staff, or donated by individuals and institutions. The BGS fossil collections contain over 2 million specimens, including a sizeable quantity of type, figured and cited material. Since a small number of fossil locations are confidential, you are unable to view this dataset at large scales. However, if you send a data enquiry, such information may be made available. Enquiries are normally free, but a charge may be levied depending upon the time taken; users will be notified in advance. Material is available for inspection on application by e-mail. Specimens are sometimes available for loan to bona fide academics.
The data are from X-ray tomographic analyses of tubular fossils. All scans were carried out using Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) except for specimen SMNH X 5324 which was also analysed using Ptychographic X-ray Computed Tomography (PXCT). The methods are described in the paper. The data consist of a stacked series of .tif files that represent maps of X-ray attenuation. The individual slices can be viewed with standard graphics software. The datasets can be studied in 3D using tomographic reconstruction software such as Avizo (www.vsg3d.com/), Spiers (www.spiers-software.org/), VG Studio Max (www.volumegraphics.com) etc. The voxel size, which is needed for scale calculations, varies between datasets and is given below. Some datasets consist of two 'blocks' of data, with slices named [specimen name]_B1 and [specimen name]_B2. These are placed in the same folder and follow on directly from one another. They can be opened together as a single dataset. The files relate to the following publication: Cunningham, J. A., Vargas, K., Liu, P., Belivanova, V., Marone, F., Martinez-Perez, C., Guizar-Sicairos, M., Holler, M., Bengtson, S. & Donoghue, P. C. J. 2015. Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota. Proceedings of the Royal Society Series B: Biological Sciences.
Reflectance Transformation Imaging files for the type specimen GSM105875 [IGSN:UKBGSGSM105875] and two paratypes GSM106040 [IGSN:UKBGSGSM106040] , GSM106112 [IGSN:UKBGSGSM106112] of Hylaecullulus fordi, a new species of rangeomorph from the Bradgate Formation (Ediacaran) of Charnwood Forest, UK. Supporting information for Kenchington, Dunn and Wilby - Modularity and overcompensatory growth in rangeomorphs (late Ediacaran, approx. 580-541 Ma): adaptations for coping with environmental pressures. Current Biology.
Table S1.xlsx is Table S1, which contains 2D measurements of cell clusters used in Fig. 5 (this is also available from the publisher's website). The folders SMNH X 4447, SMNH X 5331 and SMNH X 5357 contain data from X-ray tomographic analyses of fossils figured in the paper: For SMNH X 5331 (the conical fossil that is the focus of the paper) there are two zip archives: 1. Slice data and Avizo files, containing: - Slice data: the raw scan data (.tif image stack) - Label files for cell clusters and individual cells: Avizo projects (.hx) containing the labels and the files required to open the project file. The cluster labels are based on a downsampled version of the data which is included here as slice data (.tif image stack). Voxel sizes for this file are 0.325 x 1.3 x 0.325 micrometers. 2. Working files, containing: - Surface models: .ply files for clusters and individual cells. - Segmented stacks: the label files as .tif stacks (voxel sizes as per slice data: 0.325 x 0.325 x 0.325 micrometres (cell labels); 0.325 x 1.3 x 0.325 micrometers (cluster labels)). SMNH X 4447 and SMNH X 5357 (two specimens figured for comparison) there is: - Slice data: zip archives of the raw scan data (.tif image stack). The individual slices (.tif images) can be viewed with standard graphics software, and the datasets can be studied in 3D using tomographic reconstruction software such as Avizo (www.vsg3d.com/), Spiers (www.spiers-software.org/), VG Studio Max (www.volumegraphics.com) etc. The Avizo project and label files (.hx and .am files) require Avizo software (www.vsg3d.com/) to be opened. The 3D models (.ply files) are widely compatible with 3D freeware packages such as MeshLab (http://meshlab.sourceforge.net/) or Blender (https://www.blender.org/), or with proprietary software, e.g. Avizo (www.vsg3d.com/), Geomagic (http://www.geomagic.com/en/), Mimics (http://biomedical.materialise.com/mimics). The files relate to the following publication: Cunningham, J. A., Vargas, K., Marone, F., Bengtson, S. & Donoghue, P. C. J. 2016. A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China). Evolution & Development
Laser scans of Ediacaran Fossil Surfaces. Data collected 2016-2018 in Newfoundland Canada using a laser-line probe. Data is in the form of .wrp files so can only be opened in Geomagic. The scan files are in files of the bedding plane. All scan numbers with the same base were scanned with the tripod in the same position, so no alignment is needed. Manuel alignment is needed between bases.
These data represent a massive synchrotron based programme to study ancient life. Not all of these data have been processed yet, nor have we published all of the results that we intend to. These data are still very much a work in progress. NERC grant abstract: Building on our previous successes with identifying and mapping the chemical residues of eumelanin and beta keratin, herein we propose an analytical and experimental plan to enhance our ability to detect and image key components of soft tissue. First of all we will perform a series of experiments with extant soft tissue so that we can monitor and determine the breakdown reactions of organic compounds as a function of host lithology, moisture content, and trace metal inventory. Secondly, we will complete an analytical programme, including SRS-XRF imaging, which will include these experimental run products as well as a series of time-stepped fossil samples of varying ages and host lithology so that we may build up a database which allows us to refine our general understanding of reaction paths during fossil degradation. Because the techniques we have developed are non-destructive we now have opened up the possibility for detailed analysis of extremely rare specimens which hold important information but cannot be destructively sampled. Finally, these experimental and analytical results from fossils and comparable extant species will be combined in order to answer several critically important questions in palaeontology, biology, and geochemistry. Project partners: University of Nancy, CNRS, Prof. R. Michels Feather degradation experiments SLAC Linear Accelerator Center, Linac Coherent Light Source, Dr. U. Bergmann SRS-XRF scans of large objects and x-ray spectroscopy SLAC Linear Accelerator Center, Stanford Synchrotron Radiation Lightsource, Prof. C. Kao SRS-XRF scans of large objects DIAMOND Lightsource, Prof. Fred Mosselmans XAS spectroscopy.
The folders GMPKU2311, GMPKU3089, ELISN108-343 and ELISN31-5 contain data from X-ray tomographic analyses of fossil embryos and post-embryonic stages as described: There is one data folder provided for each specimen, each containing the following: - Raw data: zip archive containing the raw scan data (.tif image stack). - Working files: zip archive containing the segmented slices (.tif image stack exported from Avizo labels). - Avizo project: the Avizo .hx project file. - Avizo labels: the Avizo .am labels file, containing the segmentation information. - 3D model: the 3D surface computed from the segmented labels data (.stl file). In the case of GMPKU2311 only the raw data and 3D model file are provided, as the surface was computed directly from an isosurface of the specimen in Avizo. The individual slices (.tif images) can be viewed with standard graphics software, and the datasets can be studied in 3D using tomographic reconstruction software such as Avizo (www.vsg3d.com/), Spiers (www.spiers-software.org/), VG Studio Max (www.volumegraphics.com) etc. The Avizo project and label files (.hx and .am files) require Avizo software (www.vsg3d.com/) to be opened. The 3D models (.stl files) are widely compatible with 3D freeware packages such as MeshLab (http://meshlab.sourceforge.net/) or Blender (https://www.blender.org/), or with proprietary software, e.g. Avizo (www.vsg3d.com/), Geomagic (http://www.geomagic.com/en/), Mimics (http://biomedical.materialise.com/mimics). The files relate to the following publication: Dong, X.; Vargas, K.; Cunningham, J. A.; Zhang, H.; Liu, T.; Chen, F.; Liu, J.; Bengtson, S. & Donoghue, P. C. J. 2015. Developmental biology of the early Cambrian cnidarian Olivooides. Journal of Paleontology.
This layer of the GeoIndex shows the localities for which details of identified fossil specimens in the BGS Biostratigraphy Museum are databased. Only Ordovician and Silurian specimens listed currently. Samples and taxonomic identifications will be listed and will in future be able to be queried using the query-by-attribute tool to the right of the map. See also Fossil Localities. Material is available for inspection on application by e-mail; it is free for academic research but is charged for commercial work. Specimens are sometimes available for loan to bona fide academics.
Phylogenetic data matrices used to assess the differences between hard and soft morphological characters For more details see: Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees Robert S. Sansom & Matthew A. Wills Scientific Reports 3, Article number: 2545 (2013) doi:10.1038/srep02545