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Data released on May 02, 2014

MicroCT scans of freshly fixed and museum earthworm specimens.

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 RIS BibTeX Text


Micro-computed tomography (µCT), a digital X-ray-based imaging technique, has developed into an important tool for the study of animal morphology. 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 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 collected.
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 projection as well as the reconstruction images are archived here and are publicly available for download.
The dataset presented 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 they also permit interactively exploring 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 museum material.

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Related manuscripts:

doi:10.1371/journal.pone.0096617
doi:10.1186/2047-217X-3-6

Accessions (data not in GigaDB):

http://mczbase.mcz.harvard.edu/guid/MCZ:IZ:24804
http://mczbase.mcz.harvard.edu/guid/MCZ:IZ:24805
http://mczbase.mcz.harvard.edu/guid/MCZ:IZ:95557
http://mczbase.mcz.harvard.edu/guid/MCZ:IZ:95901

Imaging

http://gigadb.org/images/uploads/image_upload/Images_139.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
MCZ_24804408844segmented wormsAporrectodea trapezoidesAporrectodea trapezoides Collected by:Rosa Fernández Garcia
Collection date:39815
Geographic location (country and/or sea,region):Sp...
...
+
MCZ_24805302032segmented wormsAporrectodea caliginosaAporrectodea caliginosa Collected by:Rosa Fernández Garcia
Collection date:40088
Geographic location (country and/or sea,region):Un...
...
+
MCZ_95557302032segmented wormsAporrectodea caliginosaAporrectodea caliginosa Collected by:Juan Arturo Rivero
Collection date:23346
Geographic location (country and/or sea,region):Ve...
...
+
MCZ_95901408844segmented wormsAporrectodea trapezoidesAporrectodea trapezoides Collected by:not available
Collection date:15323
Geographic location (country and/or sea,region):no...
...
+
Displaying 1-4 of 4 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
MCZ_24805MicroCTTAR8.03 GB2014-05-02
MCZ_24805MicroCTTAR367.47 MB2014-05-02
MCZ_95557MicroCTTAR7.67 GB2014-05-02
MCZ_95557MicroCTTAR211.45 MB2014-05-02
MCZ_24804MicroCTTAR7.19 GB2014-05-02
MCZ_24804MicroCTTAR658.36 MB2014-05-02
MCZ_95901MicroCTTAR8.37 GB2014-05-02
MCZ_95901MicroCTTAR596.91 MB2014-05-02
MD5sumTEXT0.31 KB2014-05-02
ReadmeTEXT0.61 KB2014-05-02
Displaying 1-10 of 10 File(s).

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