[Coral-List] coralCT: software tool for calcification and bioerosion analyses

tdecarlo at whoi.edu tdecarlo at whoi.edu
Thu Jul 14 14:35:14 EDT 2016

Dear Coral-List,

I am pleased to release our software program "coralCT" for analyzing  
calcification and bioerosion rates from CT scans of coral skeletons.  
coralCT is an easy-to-use platform for quantifying calcification and  
bioerosion rates from skeletal CT scans.

My goal with coralCT is to provide a tool to help standardize coral  
growth analyses across labs. Like many other groups, we initially used  
medical CT software such as Osirix; however these programs use only a  
very small percent of the 3-D data, make it difficult to extract the  
desired density and extension data, are often inaccurate for species  
with large calyces, and generally provide un-traceable analyses.

coralCT uses all of the available 3-D CT data to track the growth  
paths of corallites, map annual bands in 3-D along density maxima or  
minima, and provides accurate annual density, extension, and  
calcification measurements in an Excel spreadsheet. Perhaps most  
importantly, the 3-D banding maps are saved alongside the CT data so  
that the analysis is easily revised, and everything is traceable to  
the raw data. I hope this sparks a community-wide effort to archive  
our coral CT scans and traceable growth rate analyses. coralCT also  
serves as a platform that we can build upon to pull even more data  
from our scans - potentially including stress banding, budding rates,  
and seasonal density patterns.

Presently, coralCT is written in MATLAB and is calibrated for Porites,  
Favia, Diploastrea, Siderastrea, and Orbicella. A version in R is  
in-progress. It is also possible to add more coral genera, so please  
contact me if you have scans from other genera that you would like to  

You can download coralCT through Zenodo/GitHub. Please refer to the  
citation information provided on Zenodo and within the README file.  
The download also includes detailed instructions (no coding/MATLAB  
experience required), a tutorial, and some example output. Any future  
releases, features, or bug-fixes will be posted on GitHub. And please  
contact me with any questions or issues.

Zenodo link: https://zenodo.org/record/57855#
GitHub link: https://github.com/tdecarlo19/coralCT and  


Tom DeCarlo
(tdecarlo at whoi.edu)

Tom DeCarlo
PhD Student
MIT/WHOI Joint Program in Oceanography
Geology and Geophysics department

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