Non-tetrapod sarcopterygian fossil material (Holoptychius sp., Rhizodontida indet., Dipnoi indet.) from Iveragh Peninsula (Ireland) - CT-Data, 3D-Models

SND-ID: 2023-84-1. Version: 1. DOI: https://doi.org/10.57804/s0tg-cb09

Citation

Creator/Principal investigator(s)

Vincent Dupret - Uppsala University orcid

Research principal

Uppsala University - Department of Organismal Biology rorId

Description

The data set forms part of a study of fossil fish material from Southwest Ireland (Sarcopterygii: Dipnoi indet., Rhizodontida indet. och Holoptichius sp.; Givetian of the Iveragh Peninsula). The data consist of CTscan image stacks and subsequent working files (i.e. segmentation, visualisation files, STLs and 3D PDF files).

1. CT-scans datasets
At the Natural History Museum in London, the material was CT-scanned with a Nikon HMX ST 225 system, Nikon Metrology, Leuven, Belgium, with a tungsten reflection target. Detailed settings were adjusted for each specimen and are given in associated article (see "Material and Methods"). The specimen required stitching performed with an in-house NHM script written in Octave. In Oslo, at the Natural History Museum, University of Oslo, the scanning was carried out with a Nikon Metrology XT H 225 ST microfocus CT instrument at the Natural History Museum, University of Oslo, at 220 kV, 1245 µA, 4444 projections, 2 frames per projection,1 mm tin filter, Fast CT protocol (not minimising ring artefacts) and a voxel size of 23.9 µm. Detailed settings are given

... Show more..
The data set forms part of a study of fossil fish material from Southwest Ireland (Sarcopterygii: Dipnoi indet., Rhizodontida indet. och Holoptichius sp.; Givetian of the Iveragh Peninsula). The data consist of CTscan image stacks and subsequent working files (i.e. segmentation, visualisation files, STLs and 3D PDF files).

1. CT-scans datasets
At the Natural History Museum in London, the material was CT-scanned with a Nikon HMX ST 225 system, Nikon Metrology, Leuven, Belgium, with a tungsten reflection target. Detailed settings were adjusted for each specimen and are given in associated article (see "Material and Methods"). The specimen required stitching performed with an in-house NHM script written in Octave. In Oslo, at the Natural History Museum, University of Oslo, the scanning was carried out with a Nikon Metrology XT H 225 ST microfocus CT instrument at the Natural History Museum, University of Oslo, at 220 kV, 1245 µA, 4444 projections, 2 frames per projection,1 mm tin filter, Fast CT protocol (not minimising ring artefacts) and a voxel size of 23.9 µm. Detailed settings are given in in associated article.

2. Drishti and Mimics files (segmentation)

3. STL files

4. 3D pdfs
In Mimics, each individual structure corresponding to a mask was used to generate a high quality 3D object, itself transformed into an STL file. Each .stl file was then imported into Materialise 3-matic (v. 15.0) and Blender (v. 2.82). In 3matic, the following operations were applied to each .stl file to increase manageability while preserving accuracy: reduce number of triangles (geometrical error 0.1, preservation of surface contours) and smoothing (factor 0.1). A 3D pdf file was finally generated and can be open in Adobe Acrobat.

for the following specimens
a. NHMUK PV P 59686
Rhizodontida indet. (anterior coronoid with fang, one indet. facial bone), Dipnoi indet. (left lower jaw tooth plate), Bothriolepis dairbhrensis (indet anatomical element and Ml2, not analysed in the article). Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 10 mm.

b. NMING:F35232
Holoptychius sp. (dermal scale). Segmentation in Mimics, treatment of STLS and 3d PDF exportation in 3-matic. The scale of the reference cube edges is 1 mm.

**LINKS TO PREVIOUSLY MENTIONED SOLUTIONS**
MATERIALISE MIMICS and 3-MATIC (segmentation, 3D modelling):
https://www.materialise.com/en/healthcare/mimics-innovation-suite

DRISHTI (3D visualisation):
https://github.com/nci/drishti
Ajay Limaye; Drishti: a volume exploration and presentation tool. Proc. SPIE 8506, Developments in X-Ray Tomography VIII, 85060X (October 17, 2012) Show less..

Data contains personal data

No

Language

Data collection
Geographic coverage

Geographic spread

Geographic description: Valentia Slate Formation, Iveragh Peninsula, Ireland

Administrative information

Responsible department/unit

Department of Organismal Biology

Funding 1

  • Funding agency: Knut and Alice Wallenberg Foundation rorId

Funding 2

  • Funding agency: European Research Council (ERC) rorId
  • Funding agency's reference number: ERC-2020-ADG 101019613
Topic and keywords

Research area

Geology (Standard för svensk indelning av forskningsämnen 2011)

Zoology (Standard för svensk indelning av forskningsämnen 2011)

Other natural sciences not elsewhere specified (Standard för svensk indelning av forskningsämnen 2011)

Publications

Dupret, Byrne, Challands, Hammer, Higgs, Long, Niedźwiedzki, Qvarnström, Stössel & Ahlberg. 2023. Non-tetrapod sarcopterygians from the Valentia Slate Formation (Givetian, Devonian) of the Iveragh Peninsula, south-western Ireland: systematic reappraisal and palaeobiogeographic implications. Spanish Journal of Palaeontology 38 (1): 37-46, doi: https://doi.org/10.7203/sjp.26527
DOI: https://doi.org/10.7203/sjp.26527

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Published: 2023-05-31
Last updated: 2023-06-21