Painting my way to a 3D limpet

I’ve been in Munich for the last 3 months, three months to turn histological limpet sections into a 3D anatomical masterpiece (and enjoy living in charming Bavaria).  I’ve been so busy enjoying my work, the people, and my general surroundings that this is the first chance I’ve had to try to summarize what it is I came to Munich to accomplish.

View of Munich from the top of Alte Peter Tower

Alright, so last summer I was in Japan reconstructing a limpet in 2D with the oh so modern tool, a box of crayons. This spring I graduated to using a program (AMIRA) that is quite reminiscent of the computer program “Paint” to make a 3D anatomical model of one of the tiny snails I study.

Basically this is how it works:

1. Put your specimen in a block of plastic

2. Slice that block of plastic very thinly and put the slices on a glass slide

3. Stain those slices so you can see the bits inside (these were ready for me beforehand, by about 10 years)

4. Take photos of every other slice or so keeping the magnification constant

5. Align those photos to make a stack, kind of like an MRI

Two overlapping slices in contrasting colors so you can check to make sure they are all lined up right

6. Now you can scroll through the image stack and identify organs and follow them through the specimen

7. Paint over each organ using different colors, you can skip a bunch of slices and the computer fills in the gaps for you to make nice smooth links

each organ is labelled with a different color following it all the way through the animal

8. Once all the organs are labelled through all the slices, you can isolate each one and make it look smooth and pretty and then put them back together again to show all the parts together or as separate organ systems.

looking at the reproductive system from the right side of the animal

9. Voila! Now you have a 3D model of your tiny animal that once had very difficult anatomy to visualize and the use of so many cool tools to measure volume, surface area, shape, and generally just have a better understanding of it’s morphology and ways to actually quantify that morphology.

ta da!

Although this was quite a time-consuming process, tools like AMIRA and other 3D reconstruction software allow us to quantify and compare morphology more precisely . More and more, evolutionary biologists are relying on molecular tools (which are great too!), frequently alone, to infer evolutionary patterns. However, it is morphology that will tell me how a snail’s digestive tract has changed and whether that might have something to do with the substrate it’s living on, whether it’s teeth are acting like saws or are so reduced that they are essentially non-functional, or any number of other morphological characters that are directly relevant to how the animal interacts with it’s environment and other organisms in it’s vicinity be they predators, competitors, symbionts, or parasites. Of course, molecular tools are needed to further elucidate many of these relationships, but how will you know there is something to elucidate unless you are first able to observe it? Some things you would never even recognize without actually “seeing” them!


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