PhD week 17: A tutorial on shading curves in Inkscape

As part of my research, I will need to illustrate anatomical structures that are useful for the identification of the weevils that I will be working with. I intend to use a combination of photographs and line drawings, using the different formats in different situations. Photos will be used in some instances (i.e. habitus images) to give a realistic idea of what the creatures look like. In some cases though, photographs give too much information, and line drawings are the way to go. To create my line drawings, I will be using the free and open-source vector graphics program Inkscape.

As the structures I will be working with are 3-dimensional, I want to convey that (to a degree) in my illustrations. Traditional line drawings would depict this by using the method of stippling. If this is replicated in Inkscape, the resulting file becomes massive and unwieldly, due to the huge number of dots that it has to handle. The digital way of doing this it to use gradients. Unfortunately, curved gradients are not supported in the SVG specifications, which means we have to fake it. A method for doing this is presented below.

Invertebrate Macro Photography

Earlier this year, I met up with up-and-coming New Zealand nature photography Bryce McQuillan, who specialises in macro photography of invertebrates, particularly spiders. He puts the majority of his photos on Flickr and are well worth checking out.

Nature photographers are uniquely able to capture and portray the beauty and wonder of the natural world, and communicate it to the public in a way that can be broadly appreciated. The photos of the chalcidoid wasp above and the entomobryoid springtail below demonstrate this. These invertebrates are minute and incredibly beautiful. They are common and widespread, but their small size means that most people are not aware of them. The adage of one picture being worth 1000 words is particularly relevant in this situation.

Bryce's favorite group are spiders, which are particularly needy in the PR department. His photographs are able to capture their beauty and personality in such a way that even those who have no natural fondness for spiders are able to see beyond their "creepy-crawly" facade.

And this is why nature photographers are so important. Photos are an acccessable medium that people are easily able to understand and relate to. They are vital in the communication of the importance of biodiversity to the general public.

Simplifying polygon shapefiles in R

Recently I downloaded the Crosby Code shapefile from Landcare Research's LRIS server for use in some publications I'm preparing. This shapefile is incredibly detailed, far more so than what I require. This detail means that it takes a while for the map to be plotted each time. As detail is less important for me than speed of plotting, I decided to try and simplify the map.

Image-stacking software for Linux

Back in the day, when I was still Windows-based, I was able to get some pretty decent focus-stacked ("automontage") photos of insects using the brilliant freeware programs DeepFocus and PrepareStack written by Stuart Ball. Unfortunately, I can't find the download anywhere, though his detailed manual is still available. While commercial applications are available, I have not yet found an open-source version that will suffice. Internet searches indicate that ImageMagick's "combine" might be suitable, when given a suitable stack of photos. Preparing that stack is a little trickier. There are suggestions that GIMP might be suitable, however as far as I can see, there are no published scripts or tutorials that make it easier beyond tedious manual adjustments. I will continue to look around and see if I can work out some sorta fix.

Biomolecular Graphics

A recently published article in PLoS Computational Biology is one by Cameron Mura and colleagues that discusses the great potential held by biomolecular graphics. It discusses the terminology, tools and how to go about teaching yourself the basics. While it is very biochemistry-focussed, the highlight of the paper "Box 2: Nine Simple Rules for Biomolecular Graphics" present some very useful hints to guide any scientific illustrator.

Reference:

Mura C, McCrimmon CM, Vertrees J, Sawaya MR. (2010). An Introduction to Biomolecular Graphics. PLoS Computational Biology 6(8): e1000918. doi:10.1371/journal.pcbi.1000918

Inkscape tutorials

A little while ago in a previous post about vector graphics, I complained that there weren't any good online tutorials on biological illustrating with Inkscape (or other vector graphics packages for that matter).

I still haven't found any with an explicit biological focus (except maybe how to draw a gherkin), however there are a few which may be useful:

How to trace and colour photos, creating a "hackergotchi";

The Inkscape tutorial blog;

and finally, some general tips and tricks.

Biological graphics and illustration

Illustration is a key part of biological communication, and is particularly important in taxonomic descriptions where subtle differences in shape can be the best definition of a species. Body elongate, gradually and almost uninterruptedly narrowed towards the front anyone?

For this reason, I've recently been playing around with graphics a bit and have been learning about the different formats and their strengths and weaknesses. In particular, I'm starting to get rather excited about using vector graphics for the line illustrations that are so useful for species descriptions. The biggest obstacle that I can see is drawing from the specimen in question into the computer program. I'm not sure how the best way of going about this is. Unfortunately, there does not appear to be widespread awareness of the benefits of vector graphics, and there are no tutorials that I've found on biological illustration using vector graphics.

There is however this very good introduction to modifying photographs for publication in the brilliant Zootaxa.

If you're wondering, I use GIMP for modifying bitmaps, and Inkscape for vector graphics.