Using ImageJ for Root Analysis

Today I spent some more time getting acquainted with ImageJ. I’m running version 1.46g. My primary task is to calculate root lengths in the scans I have collected.

When ImageJ opens it has a very simple interface. I have a dual monitor set-up, and I use the second monitor for ImageJ. The leaf background on my monitor occupies far more space than the program. At first it is just a compact menu.

The ImageJ interface.

When an image is opened it appears in another box, which can be sized as desired.

An image open for analysis.

ImageJ works by measuring pixels. If you want to convert the numbers it calculates into another measurement you need to set the scale by defining the measurement of something in the image. In the scan above I have a scale bar to the right of the rhizotron that identifies one centimeter.

After calibration the next step is to trace the area to be measured. You can use all sorts of tools to do this, the best choice depends upon what measurement you are seeking to determine. The best method I found for determining root length is a freehand line. I found a plug-in that measures the line and labels it (appropriately called Measure and Label), leaving a thick light-colored line behind. This is helpful because it makes it evident which roots have been traced.

Tracing a root system.

In the picture above the roots I have traced are indicated by the lines. The data are in the box located in the upper left corner of the screen. The area measurement is worthless to me, since I am not trying to accurately trace the thickness of the roots.

All in all it’s a rather painless process. A bit time consuming–but not that bad. (It is yet to be determined if my opinion will change after analyzing all my images.)



Filed under General, Horticulture

3 responses to “Using ImageJ for Root Analysis

  1. Silvia

    Hello, I found your article interesting. I have obtained some pictures of roots for similar kind of analysis. Could you please post a link for that Measure and Label plugin?

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s