SI for Cherns et al "Correlative tomography of exceptionally preserved Jurassic ammonite implies hyponome-propelled swimming"

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About
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This repository is associated with:

"Correlative tomography of exceptionally preserved Jurassic ammonite implies hyponome-propelled swimming"

Authored by:

Lesley Cherns (1), Alan R. T. Spencer (2,3), Imran A. Rahman (3,4), Russell J. Garwood (3,5), Chris Reedman (1,6), Genoveva Burca (7), Martin J. Turner (8), Neville T. J. Hollingworth (9), and Jason Hilton (10)

1 School of Earth and Environmental Sciences, Cardiff University, Cardiff, UK
2 Department of Earth Science and Engineering, Imperial College London, London, UK
3 Earth Sciences Department, Natural History Museum, London, UK
4 Oxford University Museum of Natural History, University of Oxford, Oxford, UK
5 Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
6 Jurassic Coast Trust HQ, Bridport, Dorset, UK
7 Science and Technology Facilities Council, Rutherford Appleton Laboratory, ISIS Facility, Harwell, UK
8 Department of Computer Science, University of Manchester, Manchester, UK
9 Science and Technology Facilities Council, Swindon, UK
10 School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK

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Contents
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This archive contains the following file(s):

- ct_dataset.zip
- dragonfly_sigaloceras_enodatum.zip
- neutron_dataset.zip
- neutron_dataset_cropped_cleaned.zip
- photogrammetry_block_model.ply
- photogrammetry_dataset.zip
- stl_model_meshes.zip
- video.mkv
- video_blender.zip

+ metadata.txt (this file)

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Note on .zip archives:
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All .zip archive where created using 7-zip (https://www.7-zip.org/), using the
default .zip settings.

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File Descriptions and Metadata:
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ct_dataset.zip
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X-ray CT data. A Nikon Metrology XTek XT H 225 at the University of Manchester
was used. The scan used a 0.5mm Copper filter, 145 kV, uA 85, capturing 6000 
projections on a 3192 x 2296 detector. The projection data was reconstructed 
using Nikon Metrology NV’s XT 5.1.4.3 software.

Dataset is consists of a .vol and .vgi (metadata) file. The .vol contains the
raw data for the individual slices. Each image has the following properties:

Images format: 32-bit float (raw)
Image x/y: 3189 x 3191 px 
Number of images: 1150
Caculated voxel size: 19.6419 µm

Uncompressed total size: 45 GB

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dragonfly_sigaloceras_enodatum.zip
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Contains: sigaloceras_enodatum_final.ORSSession | 8.8 GB (uncompressed)

The sigaloceras_enodatum_final.ORSSession file is a save DragonFly session.
The session conatains the full setup (aligned Nutron and CT datasets, ROIs, 
segments, and meshes) used to produce and interpret the ammonite. 

DragonFly version: 2021.1.0.977
See: https://www.theobjects.com/dragonfly/index.html

DragonFly was used under the terms of its Non-Commercial Use License.
Non-commercial licenses are granted free-of-charge to qualified researchers, 
academics, and non-commercial developers for non-profit research or development 
purposes. Non-commercial licenses are valid for a one-year period and can be renewed 
annually at no charge.

See: https://www.theobjects.com/dragonfly/get-non-commercial-licensing-program.html

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neutron_dataset.zip
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Neutron tomography was performed at the IMAT beamline of ISIS Neutron and Muon 
Source, UK. Imaging was undertaken using an optical camera box with a 
field-of-view of 120 x 120 mm2. A total of 1801 projections were acquired 
over 360° rotation, with an exposure time of 30 s per projection, giving a total 
duration of ~15 hours. Projections were reconstructed as two-dimensional 
slices using Octopus Imaging Software. These slices have an uncompressed total 
size of 15.4 GB. Each slice in the stack has the following properties:

Images format: 16-bit .tiff
Image x/y: 2048 x 2048 px 
Number of images: 2048
Caculated voxel size: 58 µm
Image size (uncompressed): 8192 MB each.

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neutron_dataset_cropped_cleaned.zip
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Neutron tomographic slices that have been cropped and cleaned (ie. had background 
noise removed) based on images in neutron_dataset.zip. Images in .tiff format.
1715 images in stack.

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photogrammetry_block_model.ply
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Model in .ply format (with coloured vertex) showing the limestone block and 
counter-part of the ammonite. 257136 vertices and 513513 faces.

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photogrammetry_dataset.zip
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Photographs, with backgrounds removed, used to generate the 3D block model via
photogrammetry. The .zip archive contains 142 photographs.

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stl_model_meshes.zip
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.zip archive containing the 49 .stl meshes used in the creation of the 3D
reconstructions. These meshes have been smoothed within DragonFly prior to 
exportation.

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video.mkv
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Video showing annimation starting with the limestone block and ammonite in
place, ammonite is then shown on its own, before the combinded neutron and x-ray
tomography results are presented.

Length: 00:43 min
Size: 20.6 MB
Format: .mkv

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video_blender.zip
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This .zip contains the Blender file used in the creation of the video.