How we study lateral root growth

Most of my studies of root behavior in the past have followed single roots as they respond to physical cues like gravity and light. We placed a petri dish in front of a camera and zoomed in on a single root. The camera was attached to a computer, and a program on the computer would snap a photo, analyze the shape of the root, and calculate the growth of the root.

When we decided we wanted to start looking at lateral roots, we would set the camera up just like before, but sometimes that root wasn’t growing very much, making for a boring experiment. Other times, the root we had chosen would grow at one angle, but other roots nearby were growing at different angles, making it difficult to compare one experiment to another. By focusing on one root at a time, we were getting lots of details, but were afraid we were missing the forest for the trees. We needed to zoom out, to see the bigger picture — literally!

For our lateral root studies, we switched to using regular digital cameras instead of our custom cameras. This let us take photos of entire root systems at once instead of one root at a time, so we could track all of the lateral roots on the Petri dish at once. This gives us a better idea of how the whole root system is behaving. Some digital cameras have a setting that lets you take a photo every so often, usually called ‘intervalometer’ or ‘time-lapse’ mode, but these tend to be the fancier models that cost a lot. Cameras with interval shooting mode have become harder and harder to find, too — to see what I mean, search on dpreview for this feature. We found a way to add this feature to relatively cheap Canon cameras using the Canon Hardware (or Hack) Developer Kit, CHDK for short. This amazing software opens up all kinds of possibilities by temporarily inserting extra code into the camera’s memory as it starts up. We added a script for taking time-lapse photos at specified intervals that we modified slightly to set the focal distance each time it takes a photo, and it works perfectly.

We can program the camera, then, to take our photos every 20 minutes for 24 hours, and when we come back we have a full record of how every root on the plate grew over that period. That’s the easy part — the much harder part is looking at each root at each time point over the 24 hours and measuring its angle. To do this, we used free software called ImageJ and the students spent a lot of time in front of the computer measuring root angles — thousands and thousands of root angles. Eventually what began to emerge was a picture of how the entire root system controls its position, but I’ll pick up there next time.

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