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Basic Guide

Angicart depends on OCaml and other open-source UNIX utilities, and is known to work on most Linux distributions and on OS X. OCaml is not currently supported on Windows. Lines beginning with
$
are meant to be typed at the command-line (i.e., a terminal) without the
$
. Lines beginning with
#
are meant to be typed at a root shell. If you need help, please contact the author as described in the README. Each program can be built using the accompanying script
make.sh
. For example, the program graphdisplay can be built using
$ ./make.sh grapshdisplay native
while the other four programs can be built by replacing
graphdisplay
with the desired program name.

Program descriptions:



FAQ

(Compiled from the various README.md files)

What information can Angicart extract about networks?

Angicart analyses 3D radiographic images of blood vessels to determine the centerlines, topology, radius, length, and volume of blood vessel segments. A complete list of output data is listed on the reproducing the analysis page, with an example given on the data page.

What types of inputs does Angicart accept?

Angicart expects sequentially-numbered PNG images.

Where can I download the latest version of Angicart?

The source code for Angicart is available via GitHub at https://github.com/mnewberry/angicart.

How do I use Angicart?

Angicart requires an OCaml compiler. See the installation page for instructions on getting Angicart setup.

How can I quickly retrieve a list of options in the command line?

Use the standard option
--help
(or
-help
). For example:
	$ ./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

I recently updated to the latest OS X, how do I get Angicart working again?

Ensure that you have accepted any new terms and conditions for Xcode, and that Homebrew and OPAM are up-to-date using
    $ sudo xcodebuild -license
        [ ... ]
    $ brew update
        [ ... ]
    $ brew upgrade
        [ ... ]
    $ opam update
        [ ... ]
    $ opam upgrade
        [ ... ]
and responding to the promts given during each process.

Why OCaml?

See the OCaml description from ocaml.org for a list of benifits to the language.

How do I cite Angicart?

Please cite the introductory paper: 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