Angicart analyses 3d radiographic images of blood vessels to determine the centerlines, topology, radius, length, and volume of blood vessel segments, as applied in Newberry MG, Ennis DB, Savage VM (2015) Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks. PLoS Comput Biol 11(8): e1004455. doi:10.1371/journal.pcbi.1004455
Angicart is composed of a series of command-line programs that each do a small
task. These programs are pngs2pls, pls2pg, skeletonize, vis, and
graphdisplay. To build a program, invoke make.sh as
./make.sh graphdisplay native
which will create an executable graphdisplay.native. Any program may be
invoked to display its options, eg:
$ ./skeletonize.native --help
Usage: skeletonize -o output [-f] lcc.pg
Skeletonize a connected pointgraph
-f pointgraph, created by output_value
-o Output file
-help Display this list of options
--help Display this list of options
The behavior of each program in the context of the analysis of Newberry et al. 2015 is described in the example. The invocations in the example can be adapted to combine the programs in unanticipated ways.
The example directory contains scripts and input data to reproduce the
analysis of the original paper. This shows how angicart works in practice, and
it can be adapted to a variety of situations. For details, see
example/README.md.
For citing angicart in academic work, please cite the paper that introduced it,
Angicart was written by Mitchell Newberry mitchell@silverninja.net and is (c) Mitchell Newberry 2011-2015. Bug reports, comments, and feature requests are welcome.