MRI scans of whole sea urchin specimens.
Dataset type: Imaging
Data released on October 06, 2014
Ziegler A; Ziegler A; Faber C; Mueller S; Nagelmann N; Schroder L (2014): MRI scans of whole sea urchin specimens. GigaScience Database. http://dx.doi.org/10.5524/100124
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 .
Additional details
Read the peer-reviewed publication(s):
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
BMNH 1890.6.27.5-8 (1) | -1 | None assigned | None assigned | None assigned | Aphia ID:213111 Exp-Scan method:RARE Exp-Scan name:2D_Magnevist ... + |
BMNH 1890.6.27.5-8 (2) | -1 | None assigned | None assigned | None assigned | Aphia ID:213111 Exp-Scan method:FLASH Exp-Scan name:3D_79_um ... + |
BMNH 1914.8.12.126-127 (1) | -1 | None assigned | None assigned | None assigned | Aphia ID:174951 Cruise:British Antarctic Expedition Station 355 Exp-Scan method:RARE ... + |
BMNH 1914.8.12.126-127 (2) | -1 | None assigned | None assigned | None assigned | Aphia ID:174951 Cruise:British Antarctic Expedition Station 355 Exp-Scan method:FLASH ... + |
BMNH 1925.10.30.103-113 | 72719 | Cidaris cidaris | Aphia ID:124257 Cruise:R/V Triton Depth:439 ... + | ||
BMNH 1932.4.28.227-34 | -1 | None assigned | None assigned | None assigned | Aphia ID:513356 Cruise:Great Barrier Reef Expedition Depth:15 ... + |
BMNH 1952.3.26.31-36 | 7640 | black urchin | Arbacia lixula | Aphia ID:124249 Collection date:1951-Jan Exp-Scan method:GEFI ... + | |
BMNH 1952.3.26.64-8 | 337417 | Centrostephanus longispinus (Philippi, 1845) | Centrostephanus longispinus | Aphia ID:124331 Collection date:1957-Jan Exp-Scan method:GEFI ... + | |
BMNH 1956.10.5.1 | -1 | None assigned | None assigned | None assigned | Aphia ID:513636 Cruise:Challenger Expedition Station 150 Depth:274 ... + |
BMNH 1966.9.27.35 | 240836 | Loxechinus albus (Molina, 1782) | Loxechinus albus | Aphia ID:160809 Collection date:1958-Dec Cruise:Royal Society Expedition Station 39 ... + |