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Segment vessel systems from radiographic images
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README.md
binomial_blur.ml
graphGL.ml
graphdisplay.ml
imageSet.ml
imageSet_t.ml
make.sh
mu.ml
muMap.ml
muSet.ml
mu_t.ml
pls2pg.ml
pngs2pls.ml
point.ml
pointGraph.ml
pointGraph_t.ml
skeletonize.ml
tree_dataset_t.ml
vesselTree.ml
vis.ml

README.md

angicart

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

Usage

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.

Example

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.

Citing angicart

For citing angicart in academic work, please cite the paper that introduced it,

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

Authors and community

Angicart was written by Mitchell Newberry mitchell@silverninja.net and is (c) Mitchell Newberry 2011-2015. Bug reports, comments, and feature requests are welcome.

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