Combining Lobster Shell Bouligand Spiral with Basal Granule STL files to display a combined structure using an R script.

Published: 05-01-2017| Version 1 | DOI: 10.17632/vdrptbszv7.1
Contributor:
Joseph G Kunkel

Description

microCT was used to obtain density voxels of American lobster Ha2 cuticle structures with 0.5 um voxel edges. The software Analyze Pro was used to create STL files of select structures in the cuticle sample. Each STL file can be imported into an R workspace using the Rvcg library and ploted in a 3D space using the rgl library. Two STL files are provided which outline the structure of a Bouligand Spiral and a Basal Granule, two structures newly described for the endocuticle and membranous layer of the American lobster carapace (Kunkel et al. 2017). These files are read by an R-script which is included and results in producing movie frames that can be combined into an included movie using ImageJ. To create the movie, download the two STL files and the R-script to a directory that has a subdirectory ./frames. Make sure that your R installation is upgraded with the required libraries listed in the R-script and run the script. Modifying the R-script illustrates how two STL files can be loaded separately and plotted with their own distinctive color. JG Kunkel, M Rosa, AN Bahadur. (2017). 3D-Xray-tomography of American lobster shell structure: An overview. Fisheries Research 186: Part 1: 372–382.

Files

Steps to reproduce

1. Download the STL files to a convenient directory. 2. Download the R script to the same directory. 3. Create a sub-directory called 'frames'. 4. Open a R-environment and make the convenient directory the working directory . 5. Make sure the rgl and Rvcg libraries are installed. 6. Run the R-script. 7. Use ImageJ to Import the image sequence saved in the frames sub-directory. 8. Crop the images to remove excess white space surrounding the structures. 9. Save the images as an AVI movie file.