Scott Edmunds

**New research and data published in *GigaScience* and *PLOS ONE*
provides complete open access to detailed 3D images of earthworms**  
[![Screen shot 2014-05-18 at 4.25.14
PM](http://gigasciencejournal.com/blog/wp-content/uploads/2014/05/Screen-shot-2014-05-18-at-4.25.14-PM-300x225.png){.alignleft
.size-medium .wp-image-1110 fetchpriority="high" decoding="async"
width="300" height="225"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/05/Screen-shot-2014-05-18-at-4.25.14-PM-300x225.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/05/Screen-shot-2014-05-18-at-4.25.14-PM-768x576.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/05/Screen-shot-2014-05-18-at-4.25.14-PM.png 785w"
sizes="(max-width: 300px) 100vw, 300px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/05/Screen-shot-2014-05-18-at-4.25.14-PM.png)To
quote the American cartoonist Gary Larson: all things play a role in
nature, even the lowly worm---but perhaps never in such a visually
stunning way as that presented in two papers published last week in
[*GigaScience*](http://www.gigasciencejournal.com/content/3/1/6 "GigaScience worms paper"){target="_blank"
rel="noopener"} and [*PLOS
ONE*](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096617 "PLOS worm paper"){target="_blank"
rel="noopener"}. The work and data presented here provide the first-ever
comparative study of earthworm morphology and anatomy using a 3D
non-invasive imaging technique called micro-computed tomography (or
microCT), which digitizes worm structures. This opens the possibility of
scanning millions of specimens from museum collections, including
extinct species, all of which is important given that the earthworm is
both a benefit and a bane to ecosystems. Being open access, the stunning
high-resolution images, videos and interactive models also can be used
as teaching aids and make fantastic resources for understanding worm
anatomy (see the screenshot from the [PLOS supporting
data](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096617#s6 "PLOS worm paper supporting data section"){target="_blank"
rel="noopener"}).

From digging in the garden to fishing to playing with worm farms at
school, everyone has become aware of the importance of earthworms in
maintaining ecosystems and soil quality, but few realize that many
earthworm species are [invasive and can be a serious
threat](http://en.wikipedia.org/wiki/Invasive_earthworms_of_North_America "Worms as Invasive Species (wikipedia)"){target="_blank"
rel="noopener"} to their new environment. More difficult yet is
distinguishing one worm from another, and with thousands of known
species around the globe, differentiating them and resolving their
taxonomy is an enormous task. The difficulties in dissecting small,
soft-bodied organisms, as well as having access to valuable and rare
museum specimens, can make doing so nearly insurmountable. However, the
research published by Dr. Rosa Fernández and her colleagues from Harvard
University as well as Dr. Alexander Ziegler from Ziegler Biosolutions
provides the much-needed tools to carry out such analyses in a
non-destructive way and at a significantly quicker pace. Their work
combines two- and three-dimensional imaging techniques and shows that
commonly used morphological features for defining earthworm taxonomy can
now be assessed without the need for dissection. The researchers were
able to view the sediment inside the animal in 3D, as well as the
internal organs in context with each other. They also compared fresh
samples with preserved museum specimens, going as far back as 1945, and
revealed that this digital imaging technique is suitable for the
analysis of rare museum specimens.

On top of releasing beautiful high-resolution videos allowing
non-destructive 3D real-time dissection of earthworms, the authors made
supporting raw and derived data [available in our GigaDB
repository](http://dx.doi.org/10.5524/100092 "GigaDB worm DOI"){target="_blank"
rel="noopener"}, enabling future data mining by researchers, the
development of new tools, as well as provision of increased transparency
and confidence in the research. Lead and corresponding authors on the
papers, Dr. Rosa Fernández and Dr. Alexander Ziegler say that they would
be delighted if their study "will serve as a catalyst for future
high-throughput studies of zoological specimens and will also boost
enforced data deposition practices in biodiversity research", opening
new possibilities for computer-based interactive exploration and study
of museum specimens around the world.

Making the data openly available is especially unique because, although
open access to supporting data is the norm in some areas of research,
for the morphology and taxonomy community this is much less common and,
in practice, more difficult. Such issues have led to community concerns
that data deposition policies adopted by journals such *GigaScience* and
*PLOS* may not be able to deal with large and complex datasets, such as
these large stacks of imaging files. Thus, the data release effort by
the authors and by *GigaScience* and *PLOS ONE* working together
constitutes a major step forward in data transparency, making use of the
online database
[MCZbase](http://mczbase.mcz.harvard.edu "MCZbase"){target="_blank"
rel="noopener"} and the big data capabilities of our
[GigaDB](http://gigadb.org/ "GigaDB homepage"){target="_blank"
rel="noopener"} repository. This follows up our recent release of
similar centipede microCT data in GigaDB last year (see ["the cyber
centipede"](http://blogs.biomedcentral.com/gigablog/2013/10/28/the-cyber-centipede-giving-online-species-descriptions-a-leg-up/ "Cyber Centipede blog"){target="_blank"
rel="noopener"}), demonstrating the utility of the platform for large
scale imaging datasets that otherwise would not have a home. Despite
some of the folders being close to 10 GB in size, the data reviewers
were able to retrieve each of those in as little as half an hour using
our high-speed Aspera internet connection (for more on that see [our
previous
post](http://blogs.biomedcentral.com/gigablog/2013/06/07/faster-dataset-kill-kill/ "Aspera blog post"){target="_blank"
rel="noopener"}).

As with all our research, peer-review was carried out transparently and
is viewable from the [pre-publication
history](http://www.gigasciencejournal.com/content/3/1/6/prepub "Earthworm prepublication history"){target="_blank"
rel="noopener"} of the article. Dr. Sarah Faulwetter of the Hellenic
Centre for Marine Research, who served as a reviewer, felt that the
level of data availability brings taxonomy into a new age, saying,
"Instead of having to go through the lengthy process of obtaining the
physical specimen from a museum, I can now download a fairly accurate
representation from the web." With the goal to maximise future reuse of
the data, Dr. Faulwetter further comments: "The authors have also made
the raw data (the CT projection images) available -- this gives me as a
researcher the additional possibility to reconstruct the 3D dataset
again with different parameters, allowing me to focus exactly on the
features I need."

As the British natural scientist Charles Darwin said of the humble
earthworm in the late 1800s, "It may be doubted whether there are many
other animals which have played so important a part in the history of
the world, as have these lowly organized creatures", but, today, how
they are organized has never been seen so clearly or been so easily
viewed.

### **References**

1\. Lenihan, J; Kvist, S; Fernández, R; Giribet, G; Ziegler, A (2014) A
dataset comprising four micro-computed tomography scans of freshly fixed
and museum earthworm specimens. *GigaScience*, **3**:6
[http://dx.doi.org/10.1186/2047-217X-3-6](http://www.gigasciencejournal.com/content/3/1/6 "GigaScience worms paper"){target="_blank"
rel="noopener"}

2\. Lenihan, J; Kvist, S; Fernández, R; Giribet, G; Ziegler, A (2014):
MicroCT scans of freshly fixed and museum earthworm specimens.
GigaScience Database.
[http://dx.doi.org/10.5524/100092](http://dx.doi.org/10.5524/100092 "GigaDB worm DOI"){target="_blank"
rel="noopener"}

3\. Fernández, R; Kvist, S; Lenihan J, Giribet G, Ziegler A (2014) Sine
systemate chaos? A versatile tool for earthworm taxonomy:
non-destructive imaging of freshly fixed and museum specimens using
micro-computed tomography *PLOS ONE* **9** (5) e96617
doi:[10.1371/journal.pone.0096617](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096617 "PLOS worm paper"){target="_blank"
rel="noopener"}

The post [The Early Earthworm Catches on to Full Data
Release](http://gigasciencejournal.com/blog/the-early-earthworm-catches-on-to-full-data-release/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


New research and data published in
 
 GigaScience
 
 and
 
 PLOS ONE
 
 provides complete open access to detailed 3D images of earthworms

To quote the American cartoonist Gary Larson: all things play a role in nature, even the lowly worm—but perhaps never in such a visually stunning way as that presented in two papers published last week in

 GigaScience

and

 PLOS ONE

. The work and data presented here

Messages de Rogue Scholar

The Early Earthworm Catches on to Full Data Release