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Data released on October 06, 2014

MRI scans of whole sea urchin specimens.

Faber, C; Mueller, S; Nagelmann, N; Schroder, L; Ziegler, A; Ziegler, A (2014): MRI scans of whole sea urchin specimens. GigaScience Database. http://dx.doi.org/10.5524/100124 RIS BibTeX Text

Magnetic resonance imaging (MRI) is routinely used in human diagnostics, but can also be applied to study the internal anatomy of zoological specimens. Here, we present 141 MRI scans from 98 representative extant sea urchin species. The scanned specimens were whole sub-adult or adult individuals ranging in size from 5 to 43 mm. The specimens were almost entirely obtained from museum collections. Some of the samples were collected and fixed more than 135 years ago, while others were collected a few months prior to scanning. The detailed MRI acquisition and reconstruction parameters can be found in the metadata files deposited together with the raw image data. In addition, image stacks in tagged image file format (TIFF, .tif) were generated for each scan. Potential uses of the dataset include morphometric and volumetric analyses or comparative studies of internal organs.


For convenience users can choose to down load all 141 datasets in a single TAR archive file called 141_MRI_scans.tgz (39GB) from the FTP server.


***Message from GigaDB team***
Please note that due to the conditional formatting of the "Samples" table currently used in GigaDB, the authors wish to point out that the NCBI taxonomy information (columns 2-5) is inappropriate for this study. Instead, the authors strongly recommend the use of the Species names and Aphia IDs provided in the "Sample attributes" section of the "Samples" table, and in the Sea_urchin_samples Excel file .

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Read the peer-reviewed publication(s):

Ziegler, A., Faber, C., Mueller, S., Nagelmann, N., & Schröder, L. (2014). A dataset comprising 141 magnetic resonance imaging scans of 98 extant sea urchin species. GigaScience, 3(1). doi:10.1186/2047-217x-3-21

Imaging

/images/uploads/image_upload/Images_157.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
BMNH 1890.6.27.5-8 (1)-1None assignedNone assignedNone assigned Aphia ID:213111
Exp-Scan method:RARE
Exp-Scan name:2D_Magnevist
...
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BMNH 1890.6.27.5-8 (2)-1None assignedNone assignedNone assigned Aphia ID:213111
Exp-Scan method:FLASH
Exp-Scan name:3D_79_um
...
+
BMNH 1914.8.12.126-127 (1)-1None assignedNone assignedNone assigned Aphia ID:174951
Cruise:British Antarctic Expedition Station 355
Exp-Scan method:RARE
...
+
BMNH 1914.8.12.126-127 (2)-1None assignedNone assignedNone assigned Aphia ID:174951
Cruise:British Antarctic Expedition Station 355
Exp-Scan method:FLASH
...
+
BMNH 1925.10.30.103-11372719  Cidaris cidaris Aphia ID:124257
Cruise:R/V Triton
Depth:439
...
+
BMNH 1932.4.28.227-34-1None assignedNone assignedNone assigned Aphia ID:513356
Cruise:Great Barrier Reef Expedition
Depth:15
...
+
BMNH 1952.3.26.31-367640 black urchinArbacia lixula Aphia ID:124249
Collection date:16527
Exp-Scan method:GEFI
...
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BMNH 1952.3.26.64-8337417Centrostephanus longispinus (Philippi, 1845) Centrostephanus longispinus Aphia ID:124331
Collection date:17167
Exp-Scan method:GEFI
...
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BMNH 1956.10.5.1-1None assignedNone assignedNone assigned Aphia ID:513636
Cruise:Challenger Expedition Station 150
Depth:274
...
+
BMNH 1966.9.27.35240836Loxechinus albus (Molina, 1782) Loxechinus albus Aphia ID:160809
Collection date:20058
Cruise:Royal Society Expedition Station 39
...
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Displaying 1-10 of 141 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
ZMB 5854 (1)VideoGIF25.82 MB2014-09-18
ZMB 5854 (2)VideoGIF28.18 MB2014-09-18
ZMB 5854 (2)Mixed archiveTAR483.34 MB2014-09-18
ZMB 5854 (1)Mixed archiveTAR423.9 MB2014-09-18
ZMB 6334VideoGIF30.09 MB2014-09-18
ZMB 6334Mixed archiveTAR114.61 MB2014-09-18
ZMH E7381VideoGIF19.09 MB2014-09-18
ZMH E7381Mixed archiveTAR407.48 MB2014-09-18
ZMB 1439VideoGIF8.19 MB2014-09-18
ZMB 1439Mixed archiveTAR399.07 MB2014-09-18
Displaying 1-10 of 283 File(s).

History:

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