The files contained here 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. 



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 scan settings for each specimen are provided below: 

Specimen GMPKU2311
Post-embryonic stage 
Specimen was scanned using synchrotron radiation X-ray tomographic microscopy (SRXTM). SRXTM analyses were carried out at the X04SA Materials Science and X02DA TOMCAT beamlines of the Swiss Light Source, Paul Scherrer
Institute, Villigen, Switzerland. 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.
voxel size: 1.85 x 1.85 x 1.85  micrometres
field dimensions: 1024 x 1024
energy: 17.5 keV
projections: 1001
exposure: 0.5 
objective: 4x
scintillator: 50x

Specimen GMPKU3089 
Embryo stage
Data originally published in Dong X-P, Cunningham JA, Bengtson S, Thomas C-W, Liu J, Stampanoni M, Donoghue PCJ. 2013 Embryos, polyps and medusae of the Early Cambrian scyphozoan Olivooides. Proc R Soc B 280: 20130071.http://dx.doi.org/10.1098/rspb.2013.0071
Specimen was scanned using synchrotron radiation X-ray tomographic microscopy (SRXTM). SRXTM analyses were carried out at the X04SA Materials Science and X02DA TOMCAT beamlines of the Swiss Light Source, Paul Scherrer
Institute, Villigen, Switzerland. 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.
voxel size: 0.650 x 0.650 x 0.650  micrometres
field dimensions: 1641 x 1065
energy: 17.5 keV
projections: 1501
exposure: 340 ms
objective: 10x
scintillator: 20x

Specimen ELISN108-343 
Embryo stage
Data originally published in Han J, Kubota S, Li G, Yao X, Yang X, Shu D, et al. (2013) Early Cambrian Pentamerous Cubozoan Embryos from South China. PLoS ONE 8(8): e70741. doi:10.1371/journal.pone.0070741
Specimen was scanned using computed microtomography (Micro-CT). The data was provided to us by the authors and it has been reoriented from previous originally acquired micro-CT data. 
Voxel size: 0.504 x 0.504 x 0.504 micrometres
The following information was supplied by the authors:
trimming form; rect
trimming size; -553, 541, -546, 586, -447, 435
trimming magnification; 1.000000
trimming rotate matrix; 0.989729, -0.130668, 0.057991, 0.000000, 0.119779, 0.979400, 0.162569, 0.000000, -0.078039, -0.153953, 0.984992, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000
scale; 0.000504, 0.000504, 0.000504, mm
color control point 1; 0, 0
color control point 2; 65535, 65535

Specimen ELISN31-5
Embryo stage
Data originally published in Han J, Kubota S, Li G, Yao X, Yang X, Shu D, et al. (2013) Early Cambrian Pentamerous Cubozoan Embryos from South China. PLoS ONE 8(8): e70741. doi:10.1371/journal.pone.0070741
Specimen was scanned using computed microtomography (Micro-CT). The data was provided to us by the authors and it has been reoriented from previous originally acquired micro-CT data. 
voxel size: 0.812 x 0.812 x 0.812 micrometres
The following information was supplied by the authors:
trimming form; rect
trimming size; -412, 412, -455, 455, -363, 363
trimming magnification; 1.000000
trimming rotate matrix; 1.000000, 0.000000, -0.000000, 0.000000, -0.000000, -1.000000, -0.000000, 0.000000, 0.000000, 0.000000, -1.000000, 0.000000, 0.000000, 0.000000, 0.000000, 1.000000
scale; 0.000812, 0.000812, 0.000812, mm
color control point 1; 0, 0
color control point 2; 65535, 65535