Monday, October 31, 2011

Inkscape tutorial for taxonomists.

If my readers are anything like me, we are all often disappointed with the way our line drawings turn out. I spend hours with a microscope, freehand drawing with a gridded eye piece, trace and ink on vellum, scan to computer, clean up in GIMP, and hope that the finished product is passable. My illustrations tend to be pixellated and messy after rescaling. What was that again, a harpago or a seta?

The expensive alternative is making a basic line drawing (no inking, no clean up), scanning and importing the image into Adobe Illustrator, and tracing a vector image from the hand drawing. I say expensive because Illustrator will run you about $450 USD; roughly the same amount as a new Asus Eee PC netbook. At the moment I don't have that kind of money, which I expect is true for most taxahackers and pro-am entomologists. For those of you who can afford the CS software suite, Dr. Ralph Holzenthal has an excellent guide to the program for entomologists.

I recently found Inkscape to be an excellent, inexpensive alternative to Illustrator. The software is a free, open source vector image program which can operate on Windows, Mac OS, and Linux platforms, and it can do almost everything that Illustrator can do with a few exceptions. In addition, continuous updates mean the tools are constantly improving.

In the rest of this post I'll be presenting my basic methods for line drawing illustration in Inkscape. Before you use this, I'd suggest doing some of the tutorials on this page, or at least completing the kokeshi doll tutorial. Once you know these basics, the rest of this post will make sense.

Line Drawing Tutorial in Inkscape

1. Before you even open inkscape, you need your drawing or other image scanned and saved as some sort of image file. Jpeg, tiff, or bmp works best.

2. Open inkscape, go to File > Import, and select your image from file. The drawing will be imported directly into the open Inkscape window.

3. First, you probably want to resize the image to the area of the 8x11 provided. This will make it easier for when you make plates with other images for publication.

4. Open up the Layers and Fill and Stroke tooboxes (ctrl+shift+L and ctrl+shift+F, respectively). It's good to have these two open at all times, because you will be shifting back and forth between them repeatedly.

5. In Layers, right click Layer 1 and add a new layer, above the original layer. Make Layer one about 50% opacity with the slide bar below, so you can tell the difference between your original and the vectors you are laying on top. If you are not actively working on a particular layer, it's best to click the lock icon next to the layer name to keep any changes from being made. The eye icon makes the highlighted layer invisible, which is useful for checking how your vector image compares to the original as you progress.

6. If your image isn't bilaterally symetrical, you're ready to start with the outlines. If however it is symmetrical, there is a simple way you can preserve symmetry. In the original layer, draw a line through the center of the illustration using the bezier tool, and make sure it's vertical or horizontal by holding control. Now rotate the image using the general selection tool so that it runs through the center of the drawing symmetrically. Now your work is cut in half, because you only have to trace half the drawing! When one half is done (details and all), just duplicate (ctrl+d) and flip the duplicate, and line them up opposite, then group them using ctrl+g.

7. The first step in any image is tracing the outline and major inner lines with the bezier tool. This works best if you try to straddle curves portions with nodes, as this will make the curves smoother. Once you've finished a portion, select the nodes and click the "make selected nodes auto-smooth" button on the top toolbar. Now adjust the curves so they match the lines underneath using the edit paths tool. You can adjust the width of the lines in the fill and stroke toolbar, under the stroke style tab. I tend to use several sizes throughout the drawing, wider for outlines and heavily sclerotized regions, thinner for structures within the outline and membrane.

8. Once the lines are done, it's time to fill in the details. Since fill shadings can get expensive in publications, I tend to use stippling. The easiest way to do this is to make a small circle with the circle tool the size you want the stiples, trace object to path (ctrl+shift+c), drag it across the drawing and press spacebar where you want the dots. If you drag and press spacebar, you can 'stamp' any path on your illustration, which can be useful for repetative details. I recommend making different layers for outline, shading, inner structures, setae, and annuli, as well as any other major details, so you can't alter or interfere with what you've already done while working on the next part.

9. Inner structures (those that would be on the interior of the specimen but are shown as if the surface is transparent) can be traced using the stippling as above, or traced as a path with the bezier tool and in stroke style, change the line in the dashes drop down menu to a dotted or dashed line, according to your preference. In my experience, the line width should be comparable to the outline line width, or the dots won't show very well.

10. Setae, and their corresponding basal annuli, are by far the most difficult detail to work in Inkscape. Unlike Illustrator, Inkscape does not yet have a custom brushes ability, so all setae have to be crafted, resized and placed by hand. Despite this issue, I've developed a work around.
  • First, open a new Inkscape document.
  • Create a series of vertical triangles of several lengths using the bezier tool with the shape drop down menu (in the top toolbar on the left) set to 'triangle in'. These will probably look way too wide at this point; don't worry about that.
  • Select all the triangles and object to path (shift+ctrl+c)
  • Use the side arrows on the general selection tool to make the triangles thinner.
  • Make annuli by using different sizes and shapes of unfilled ovals using the circle tool, and make them paths
  • Save the document and keep it open. Now you have a general reference file of setae and annuli for any project. ctrl+c to copy and ctrl+v to paste them in your illustration
  • If you paste a few models near the side of the illustration, you can drag and stamp them using spacebar, just as the stippling. I suggest doing the setae first and annuli second.
  • Once the seta is in the illustration, you can alter the length and width and rotate it using the general selection tool. Don't worry about curves, the next step will take care of that.
  • Since we traced all our "brushes" to path, their shape can be altered with the edit paths tool. To curve a seta, pull one edge to the side so it bows out, then pull the other towards it to narrow it. You can add more nodes by double clicking so the seta has more than one major curve.
  • With the annuli, I try to position them so that the setal base is barely visible, the size varying with the width of the seta.
11. Arrows to various structures can be added using the regular bezier shape with the stroke and fill option 'start marker' set to the arrow shape of your choosing. You can also make arrows by combining a regular bezier line with an arrow in shape and grouping them; this can be stamped just as the rest of the paths.

12. Labels can be added with the text tool on the sidebar, and resized and rotated just as any other path. I suggest waiting to add these till all your illustrations are in plates so the labels and figure numbers are all the same size.

13. Once all the details are done, resize as necessary, set the original layer (the one with the hand drawing) to invisible, and save the illustration as an svg file.

14. Vector files are great as working illustrations, but to put them in a word processing document as a picture, they have to be converted into something more normal. Export the image as a bitmap using shift+ctrl+e. You can choose the width and height, as well as the density of pixels per inch (dpi). For now, I suggest something between 800 and 1000 dpi. Exporting will save the picture as a bitmap file with your specified settings. You can easily convert the bitmap to a jpeg or tiff by saving it as such in GIMP.


I guarantee your illustrations will look better than ever using this program. There are all kinds of ways you can tweek the image and details beyond the basic methods above, including ways I haven't discovered yet.

Monday, October 24, 2011

Book Review: Atlas of Ohio Aquatic Insects Volume I. Trichoptera.

Brian Armitage et al. recently published an atlas of the Trichoptera of Ohio (teaser here), and to be honest it was not what I was expecting. Armitage and his colleague Steve Hamilton have published a number of caddisfly atlases in the past covering the entire fauna of several North American families. Generally, these are guidebooks with genus keys and species pages with summaries, maps, and illustrations of male genitalia. And although trichopterologists have been waiting 15 years for the next volume to come out (if it ever will come out), these are great resources. I was expecting the Ohio book to be similar, with lots of illustrations of genitalia, a definitive diagnostic guidebook to the Trichoptera of Ohio. A 'new Ross 1944' if you will.

Although the book has many nice distributional maps, several checklists and many years of collection data, it is not what I would consider to be an atlas by the earlier works. The only genitalic illustrations are associated with the determination of a few new hydroptilid species, and no keys to genera or species of any kind. The publication is a very nice contribution to our knowledge of the distribution of species, and compiles a great deal of information, but what would be far more useful is an atlas of the diagnostic kind. For $25 dollars and with my small budget, the content doesn't match the price.

And I really am disappointed that it's unclear if the atlas series will ever be completed. I have distant plans to complete a very basic pictorial atlas of male genitalia with an accompanying genus key (similar to Hans Malicky's Atlas of European Trichoptera), but this is in very early development and I have far less resources than these authors. A good guidebook for the North American Trichoptera adults would be a major boon for professional entomologists and pro-ams/taxahackers alike.

Available through Ohio Biological Survey

Phryganeidae: The Giant Casemakers.

The Phryganeidae are a small family of caddisflies distributed throughout North America, Europe, and Asia. Wiggins (1996) lists the total as 15 genera and ~75 species; by my count from the World Trichoptera Checklist (Morse 2011) there are 80 extant and 37 fossil species. This family includes the largest known caddisflies. The larvae are case makers (as the common name suggests), and fashion tube cases of spiral or circular wrapped vegetation.
Oligostomis pardalis larva (© D.S. Chandler / Discover Life)

The genus name Phryganea has a long history of use, starting in the 10th edition of the Systema Naturae (Linnaeus 1758). Carl von Linne included 17 species of caddisflies in this work, all under the genus Phryganea (from the French word for caddisflies). Needless to say, most of these species have been removed to other families and genera. At the time, caddisflies, stoneflies, dragonflies and mayflies were all included under the order Neuroptera; it wasn't until 1813 that the Order Trichoptera was erected. Due to the original status of the genus, there are many nomenes dubius and synonyms that by far outnumber the species now in the entire family.

Banksiola dossuaria (© Trichoptera Barcode of Life)

In addition to large size (often greater than 25 mm), the adults are characterized by colorization ranging from the black and white checkers of Banksiola to the fall leaf orange of Ptilostomis to the yellow and dark purple of Eubasillissa. The largest species, Eubasillissa regina, is over 4 cm with an 7 to 8 cm wingspan. Dr. John Morse, who has spent much time collecting and studying aquatic insects in Southeast Asia, told me they look like a small bird with a strange flight pattern from afar.

Eubasilissa regina, the worlds largest caddisfly.

The larvae often have contrasting patterns of orange and black stripes on head and thorax, and are just as impressive as the adults in size. One of the most curious larval tendencies is the ease at which they leave their cases behind when disturbed. If one larva looses it's case and other of a similar size is occupied nearby, the two larvae will fight over the case (as illustrated in this video). Though they inhabit a wide variety of aquatic habitats, they are found most often around the roots and stems of aquatic vegetation, and in root balls of woody plants, with a diet of mostly aquatic invertebrates.

The definitive guide for the family is an eponymously named book by Glen Wiggins (1998), and despite being over ten years old is still in print and in demand. The book includes genus keys and diagnoses for all the species know at its publication, including all 28 North American species. Wiggins splits the family into the Yphriinae (which includes a single species of Yphria from Western North America), and the Phryganeinae, though the separation is drawn due to 'primitive characters' possessed by Yphria is to me not particularly convincing, and may be paraphyletic.


References

Morse, J.C. (ed.) 2011. Trichoptera World Checklist. http://entweb.clemson.edu/database/trichopt/index.htm [Accessed 24 October 2011.]

Wiggins GB. 1977. Larvae of the North American Caddisfly Genera. University of Toronto Press, Toronto, ON.

Wiggins, G.B. 1998. The Caddisfly Family Phryganeidae (Trichoptera). University of Toronto Press, Toronto, ON.