[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
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
(tdecarlo at whoi.edu)
MIT/WHOI Joint Program in Oceanography
Geology and Geophysics department
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