The Echinoid Directory

3D visualization of sea urchin anatomy

created by Alexander Ziegler, Institut für Biologie, Freie Universität Berlin, Germany
In cooperation with:
Cornelius Faber, Experimentelle Physik V, Universität Würzburg, Germany
Susanne Mueller, Berlin NeuroImaging Center, Charité-Universitätsmedizin, Germany

This project systematically visualizes the internal (and external) anatomy of selected sea urchin specimens representing 13 of the 14 currently recognized sea urchin orders. The only specimens that successfully resisted scanning were members of the order Echinothuroida (or leather urchins). Their flexible endoskeleton and powerful longitudinal muscles result in a pancake shape after fixation.
Image pages
Click here to go to an index of image pages.
How to view the 3D images
In order to use the full 3D capability of the models found on our species pages, please download and install the latest Adobe Acrobat Reader (link below). Once the Reader is installed, open the file and click onto the image to initiate the 3D viewer. Please refer to the Reader Help section for all information regarding handling and manipulation of the 3D models.
How the images were created
The technique that was predominantly used in this study is called magnetic resonance imaging (MRI) - for an explanation of the principle behind MRI and further applications please refer to the MRI section of Wikipedia. The freshly fixed and museum sea urchin specimens were put into plastic or glass tubes filled with distilled water or formalin that were then placed inside the coil of the MRI machine. The instruments used in this study are all high-field MRI instruments with 7 T and 17.6 T magnets. For an in-depth explanation regarding all technical parameters of this study please refer to the article by Ziegler et al. (2008).

After the process of image acquisition, the virtual sections were transformed into 3D models using a process called segmentation. Click here for a demonstration of how a model is generated by segmenting each slice. In most cases, interpolation of structures (e.g. gonads) across several slices allowed for a faster segmentation - however, in some cases each organ had to be manually segmented slice by slice.
References and links
Ziegler, A., Faber, C., Mueller, S. & Bartolomaeus, T. 2008. Systematic comparison and reconstruction of sea urchin (Echinoidea) internal anatomy: a novel appraoch using magnetic resonance imaging. BMC Biology 6:33.

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