Five days ago, I released a program for drawing comparative figures of vertebral columns, such as this one from our neural-spine bifurcation paper. With my idiot computer-scientist hat on, I gave that program the startlingly unmemorable name vcd2svg — the reasoning being that it takes Vertebral Column Descriptions and translates them into Scalable Vector Graphics.

In a comment on that post, Vertebrat rightly noted:

The name is a bit opaque. It sounds like a tool for people who have VCD files and want to convert them to SVG. Maybe this means extracting frames from Video CD files as SVG (a rather inappropriate format)? :)

Your target users don’t have VCD files, don’t want to convert anything, and have little or no preference for SVG. They want to make diagrams of vertebrae.

A fair point. Accordingly, I have renamed the program VertFigure — a name chosen in part because Google doesn’t know of anything else with the same name. The canonical GitHub page is now but the old address still works, and git checkouts made from the old name will also continue to work. The command-line program that does the conversion is now also named VertFigure.



I think it’s fair to say that this “bifurcation heat-map”, from Wedel and Taylor (2013a: figure 9), has been one of the best-received illustrations that we’ve prepared:

Wedel and Taylor 2013 bifurcation Figure 9 - bifurcatogram

(See comments from Jaime and from Mark Robinson.)

Back when the paper came out, Matt rashly said “Stand by for a post by Mike explaining how it came it be” — a post which has not materialised. Until now!

This illustration was (apart from some minor tweaking) produced by a program that I wrote for that purpose, snappily named “vcd2svg“. That name is because it converts a vertebral column description (VCD) into a scalable vector graphics (SVG) file, which you can look at with a web-browser or load into an image editor for further processing.

The vertebral column description is in a format designed for this purpose, and I think it’s fairly intuitive. Here, for example, is the fragment describing the first three lines of the figure above:

Taxon: Apatosaurus louisae
Specimen: CM 3018
Data: —–YVVVVVVVVV|VVVuuunnn-

Taxon: Apatosaurus parvus
Specimen: UWGM 155556/CM 563
Data: –nnn-VVV—V-V|VVVu——

Taxon: Apatosaurus ajax
Specimen: NMST-PV 20375

Basically, you draw little ASCII pictures of the vertebral column. Other directives in the file explain how to draw the various glyphs represented by (in this case) “Y”, “V”, “u”, and “n”.

It’s pretty flexible. We used the same program to generate the right-hand side (though not the phylogenetic tree) of Wedel and Taylor (2013b: figure 2):

Wedel and Taylor (2013b: Figure 2).

Wedel and Taylor (2013b: Figure 2).

The reason I mention this is because I released the software today under the GNU General Public Licence v3.0, which is kind of like CC By-SA. It’s free for anyone to download, use, modify and redistribute either verbatim or in modified form, subject only to attribution and the requirement that the same licence be used for modified versions.

vcd2svg is written in Perl, and implemented in part by the SVG::VCD module, which is included in the package. It’s available as a CPAN module and on GitHub. There’s documentation of the command-line vcd2svg program, and of the VCD file format. Also included in the distribution are two documented examples: the bifurcation heat-map and the caudal pneumaticity diagram.

Folks, please use it! And feel free to contribute, too: as the change-log notes, there’s work still to be done, and I’ll be happy to take pull requests from those of you who are programmers. And whether you’re a programmer or not, if you find a bug, or want a new feature, feel free to file an issue.

A final thought: in academia, you don’t really get credit for writing software. So to convert the work that went into this release into some kind of coin, I’ll probably have to write a short paper describing it, and let that stand as a proxy for the actual program. Hopefully people will cite that paper when they generate a figure using the software, the way we all reflexively cite Swofford every time we use PAUP*.

Update (12 April 2014)

On Vertebrat’s suggestion, I have renamed the program VertFigure.


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Illustration talk slide 66

The rest of the series is here. As promised, here are the files for the talk, in PPT and PDF formats.

Wedel 2014 Photography and illustration lecture (PPT, ~53 Mb)

Wedel 2014 Photography and illustration lecture (PDF, ~21 Mb)


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The rest of the series.