Chris Armit

![microCT
seabed](http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-18.04.20-188x300.png){.alignright
.wp-image-2782 loading="lazy" decoding="async" width="248" height="396"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-18.04.20-188x300.png 188w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-18.04.20.png 434w"
sizes="(max-width: 248px) 100vw, 248px"}Just [out in full
text](https://doi.org/10.1093/gigascience/giy156) is a our first paper
showcasing our latest complete integration with the Sketchfab 3D viewer.
In this a 3D fossil seabed from the lower Devonian geologic period has
been digitally reconstructed using micro X-ray computed tomography
(microCT) imaging. A section of the fossil bed, measuring 2 x 1 metres
wide with an average thickness of 4cm, shattered into 55 fragments
during excavation in the region of Karbonaatjies farm, Western Cape,
South Africa. Researchers at University of Cape Town and Stellenbosch
University CT scanned 24 of these rock fragments, and then digitally
re-assembled them to generate a 3D reconstruction of the fossilised
remains. The re-assembled 'jigsaw puzzle' offers intriguing detail of a
panoply of prehistoric marine organisms including stylophorans and
brittle stars. The same group  [previously
published](https://doi.org/10.1186/s13742-015-0093-2) microCT of extant
(and still pregnant) brittle star species with us (that were featured in
[Echinoblog](http://echinoblog.blogspot.com/2015/11/),
[GigaBlog](http://gigasciencejournal.com/blog/brooding-brittle-star-babies-qa-jannes-landschoff/)
and [in the
Atlantic](https://www.theatlantic.com/science/archive/2016/02/brittle-stars-dissection-microct/462579/))
but this this takes the study of this species back to our prehistoric
past. Bringing lost worlds to life in colour and 3-dimensions.

::: {#attachment_2640 .wp-caption .alignleft style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2018/12/echinoderm_render_50MB-300x173.jpg){.size-medium
.wp-image-2640 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2640" width="300" height="173"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2018/12/echinoderm_render_50MB-300x173.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2018/12/echinoderm_render_50MB-768x444.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2018/12/echinoderm_render_50MB-1024x592.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2018/12/echinoderm_render_50MB.jpg 1303w"
sizes="(max-width: 300px) 100vw, 300px"}

3D reconstruction of fossil bed showing prehistoric marine organisms
including stylophorans and brittle stars.
:::

Brittle stars and stylophorans are both types of
[echinoderm](https://en.wikipedia.org/wiki/Echinoderm), the phylum in
the animal kingdom that includes starfish, sea cucumbers and sea
urchins. Most extant species of echinoderm, including brittle stars,
show pentameric symmetry in their body plan. Stylophorans are an extinct
species of echinoderm that are unusual in that they lack a pentameric
body plan and are instead markedly asymmetric. The use of microCT
enables striking detail to be observed in the fossilised remains,
enabling the morphology to be explored in fossilised echinoderm
specimens as small as 20mm in diameter. In addition, the sheer number of
specimens is outstanding, with the 3D reconstruction showing over 1,000
brittle star specimens and hundreds of stylophorans.

According to the authors, the stylophorans and brittle stars were
rapidly buried by sediments during a prehistoric storm 400 million years
ago. This type of rapid smothering of seafloor-dwelling communities is
known as an obrution event. The presence of fossilised stylophorans and
brittle stars within the same obrution bed highlights that these
communities were to be found in a similar geographic location at the
same time in the very remote past. We are unclear of the exact
ecological role of these ancient echinoderms, but it is of great
interest that researchers of extant species have [uncovered a critical
role](https://ocean.si.edu/ocean-life/invertebrates/brittle-star-may-be-corals-best-friend)
of brittle stars and sea stars in preserving coral reefs. In extant
species, this is thought to be due to the echinoderm's ability to brush
away sediment from the coral, which greatly improves its health.

**New Integrations in *GigaScience*: Sketchfab and Thingyverse** 
3D visualisations are a powerful means of exploring fossil morphology
and a Sketchfab 3D viewer, embedded in the paper enables the
reconstructed fossiliferous obrution deposit to be explored using a web
browser. We previously have been embedding the Sketchfab images in the
associated dataset landing pages of our GigaDB database (see more on
this [in
GigaBlog](http://gigasciencejournal.com/blog/interact-with-the-crabs-in-your-computer-new-gigadb-imaging-widgets/)),
but this is the first example where Oxford University Press can now
embed these in the [online version of our
paper](https://academic.oup.com/gigascience/article/8/3/giy156/5232983#132776365). 
The original surface-rendered image file generated by the South African
research teams was very large (\>700MB) and so the *GigaScience* team
generated a version of this 3D reconstruction with smaller file size
(\<50MB) that is more suited to interactive exploration using a web
browser. The ability to build upon the original model in this way is due
to the Creative Commons CC0 1.0 Public Domain Dedication license
ascribed to these data. *GigaScience* is a firm advocate of [Open Data
and
CC-licenses](http://gigasciencejournal.com/blog/gigascience-goes-cc4-a-handy-cut-out-and-keep-guide-to-our-licenses/),
and the Creative Commons CC0 1.0 Public Domain Dedication waiver applies
to all published data in this journal.

*GigaScience* has published many microCT datasets, and interactive
visualisations of the 3D reconstructions are all made publicly available
via our Sketchfab portal (<https://sketchfab.com/GigaDB>). This
palaeontology example of fossilised echinoderms is the latest in a
growing collection of *GigaScience* 3D models that includes 3D
reconstructions of museum specimens. Using the Sketchfab viewer,
researchers and citizen scientists can use their computer or tablet to
explore the stunning morphology of weird and wonderful biological
specimens including [Jackson's three-horned
chameleon](https://sketchfab.com/3d-models/jacksons-chameleon-whole-chameleon-8bf1b1daf5fa478ca2c8028d5c59b5ec),
[snake
fangs](https://sketchfab.com/3d-models/amplorhinus-multimaculatus-c142f4dced1f42acbce273adf00d29e1)
from twenty different serpents, and crustacean morphology of seven
species of [hermit
crab](https://sketchfab.com/3d-models/paragiopagarus-atkinsonae-f-paratype-0b576006076748488be9bb137c6635df).

![](http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-12.07.20-300x193.png){.alignright
.wp-image-2780 loading="lazy" decoding="async" width="334" height="215"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-12.07.20-300x193.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-12.07.20-768x495.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-12.07.20-1024x660.png 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/04/Screen-Shot-2019-04-01-at-12.07.20.png 1964w"
sizes="(max-width: 334px) 100vw, 334px"}More recently, the *GigaScience*
team have made all 3D printable STL files publicly available on
Thingiverse, which is a widely-used resource dedicated to the sharing of
3D digital designs. The Thingiverse '*Universe of Things*' is a
repository for discovering, making and sharing 3D printable objects, and
these can include characters designed and created using digital media.
*GigaScience* is using the Thingiverse platform to share real-world
examples of 3D biological specimens to a wider community, including
educators, game developers, graphic designers, and digital artists
(<https://www.thingiverse.com/GigaScience/designs>). One of the best
things about the platform is its active community who share, discuss and
compare "makes" of their models.  It's [brilliant to
see](https://www.thingiverse.com/make:365299) what downstream users have
managed to do with our Jackson's three-horned chameleon data, even if it
didn't survive a summer of their son playing with it.

The scope of *GigaScience* covers both biological and biomedical data,
and these fossil echinoderms are our first example of palaeontological
data. We believe that this recent and wonderful addition will have
useful implications for understanding echinoderm biology and evolution,
and provides an invaluable perspective on the palaeoecology of marine
organisms in the deep past.

**Links: 
**Interact with the 3D fossil seabed on Sketchfab:

<https://sketchfab.com/models/adad7e91e68049e9bc46f5250a33fd56>

Interact with the 3D printable version of the fossil on Thingyverse

<https://www.thingiverse.com/thing:3233744>

** Further Reading 
**1. Landschoff J, Du Plessis A, Griffiths CL. 2015. A dataset
describing brooding in three species of South African brittle stars,
comprising seven high-resolution, X-ray micro tomography scans.
GigaScience 2015: 4:52.
doi:[10.1186/s13742-015-0093-2.](https://doi.org/10.1186/s13742-015-0093-2)** 
**

2\. Reid M, Bordy EM, Taylor WL, le Roux SG, du Plessis A. A micro X-ray
computed tomography dataset of fossil echinoderms in an ancient obrution
bed: a robust method for taphonomic and palaeoecologic analyses.
Gigascience. 2019 Mar 1;8(3). pii: giy156. doi:
[10.1093/gigascience/giy156.](https://doi.org/10.1093/gigascience/giy156)

3\. Reid ML; Bordy EM; Taylor WL; le Roux SG; Du Plessis A (2018):
Supporting data for "A micro X-ray computed tomography dataset of fossil
echinoderms in an ancient obrution bed: a robust method for taphonomic
and palaeoecologic analyses" GigaScience Database.
<http://dx.doi.org/10.5524/100539>** **

The post [Lost worlds: via Sketchfab a 3D fossil offers a glimpse of
prehistoric marine
life](http://gigasciencejournal.com/blog/sketchfab-3d-fossil-seabed/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

Just out in full text is a our first paper showcasing our latest complete integration with the Sketchfab 3D viewer. In this a 3D fossil seabed from the lower Devonian geologic period has been digitally reconstructed using micro X-ray computed tomography (microCT) imaging.

Lost worlds: via Sketchfab a 3D fossil offers a glimpse of prehistoric marine life

University of Glasgow

Roderic Page

Really just a shameless attempt to get one over [David
Shorthouse](http://ispiders.blogspot.com), but there has been
[some](http://blogs.nature.com/news/thegreatbeyond/2007/10/52m_year_old_spider_xray.html)
[buzz](http://news.bbc.co.uk/1/hi/sci/tech/7068160.stm) about Very High
Resolution X-Ray Computed Tomography (VHR-CT) of a fossil of
*Cenotextricella simon*.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPnjAhbjH7ZR0jxRyFBJ3BIeu5aReCHPad4kSFomdGhJ2tax49nBYZz9IfDJ_N9K_8UqH8GIKm8gj0jCGAg3m4H28PWSEaJ_6baP3sUM-55Qiqt_m4y2_IaLNvQw2aOGhKETzf/s320/spider.jpg){#BLOGGER_PHOTO_ID_5127405251510902594
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPnjAhbjH7ZR0jxRyFBJ3BIeu5aReCHPad4kSFomdGhJ2tax49nBYZz9IfDJ_N9K_8UqH8GIKm8gj0jCGAg3m4H28PWSEaJ_6baP3sUM-55Qiqt_m4y2_IaLNvQw2aOGhKETzf/s1600-h/spider.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The paper describing the work is in *Zootaxa* (link
[here](http://www.mapress.com/zootaxa/2007f/z01623p053f.pdf)). *Zootaxa*
is doing great things for taxonomic publishing, but they really need to
get some sort of stable identifier set up. Linking to *ZooTaxa* articles
is not straightforward. If they had DOIs (or even OpenURL access) they
wuld make it much easier for people to convert lists of papers that
include *ZooTaxa* publications to lists of resolvable links.


Really just a shameless attempt to get one over David Shorthouse, but there has been some buzz about Very High Resolution X-Ray Computed Tomography (VHR-CT) of a fossil of

 Cenotextricella simon

.The paper describing the work is in

 Zootaxa

(link here).

 Zootaxa

is doing great things for taxonomic publishing, but they really need to get some sort of stable identifier set up. Linking to

 ZooTaxa

articles is not

Publicaciones de Rogue Scholar

Lost worlds: via Sketchfab a 3D fossil offers a glimpse of prehistoric marine life

Amber spider