A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens

GigaScience

Alexander Ziegler¹  Gonzalo Giribet²  Rosa Fernández²  Sebastian Kvist²  Jennifer Lenihan² 

[1]Ziegler Biosolutions, Fahrgasse 5, 79761 Waldshut-Tiengen, Germany

[2]Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA

关键词: Imaging;    Repository;    μCT;    Aporrectodea;    Lumbricidae;    Taxonomy;    Anatomy;    Morphology;    MicroCT;   

Others  :  861329
DOI  :  10.1186/2047-217X-3-6

 received in 2014-04-18, accepted in 2014-05-01,  发布年份 2014

【 摘 要 】

Background

Although molecular tools are increasingly employed to decipher invertebrate systematics, earthworm (Annelida: Clitellata: ‘Oligochaeta’) taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if micro-computed tomography (μCT) in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, μCT scans of freshly fixed and museum specimens were gathered.

Findings

Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The μCT projection and reconstruction images have been deposited in the online data repository GigaDB and are publicly available for download.

Conclusions

The dataset presented here shows that earthworms constitute suitable candidates for μCT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but due to their digital nature the data also permit computer-based interactive exploration of earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable material. Finally, a number of aspects related to the deposition of digital morphological data are briefly discussed.

【 授权许可】

   
2014 Lenihan et al.; licensee BioMed Central Ltd.

【 参考文献 】

• [1]Metscher BD: MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC Physiol 2009, 9:11. doi:10.1186/1472-6793-9-11 BioMed Central Full Text
• [2]Fernández R, Kvist S, Lenihan J, Giribet G, Ziegler A: Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography. PLoS ONE 2014, 9(5):e96617. doi:10.1371/journal.pone.0096617
• [3]Metscher BD: X-ray microtomographic imaging of intact vertebrate embryos. Cold Spring Harb Protoc 2011, 12:1462-1471. doi:10.1101/pdb.prot067033
• [4]Lenihan J, Kvist S, Fernández R, Giribet G, Ziegler A: MicroCT scans of freshly fixed and museum earthworm specimens. GigaSci Database 2014. http://dx.doi.org/10.5524/100092 webcite
• [5]Xiao S, Bresler Y, Munson DC Jr: Proceedings of the 2003 International Conference on Image Processing (ICP 2003): 14–18 September 2003; Barcelona, Spain. IEEE; 2003:819-822. doi:10.1109/ICIP.2003.1246806
• [6]Elicieri KW, Berthold MR, Goldberg IG, Ibánez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam BR, Stuurman N, Swedlow JR, Tamancak P, Carpenter AE: Biological imaging software tools. Nature Meth 2012, 9:697-710. doi:10.1038/nmeth.2084
• [7]Rowe T, Frank LR: The disappearing third dimension. Science 2011, 331:712-714. doi:10.1126/science.1202828
• [8]Ziegler A, Ogurreck M, Steinke T, Beckmann F, Prohaska S, Ziegler A: Opportunities and challenges for digital morphology. Biol Direct 2010, 5:45. doi:10.1186/1745-6150-5-45 BioMed Central Full Text