Methods – how to measure injured leaf area in ImageJ

Text and picture by Valentina Zolotarjova

zolotarjova-for-blog

Recently I have encountered a challenge to measure injured (withered) leaf area (LA) for one experiment. I ordinarily use GIMP for LA measurements, but in this case there was not much use from it. I shared my problem with colleagues and Vivian suggested to try ImageJ (free software for scientific analysis based on images). With the help of available tutorial, I have prepared a manual for measuring damaged LA (total minus green color LA) in ImageJ:

ANALYZE -> Set scale -> pixel (Click to Remove Scale)

IMAGE -> Adjust –> Color Treshold (choose the color for defining area of interest, the color itself does not matter, eg red). Remove V from Dark background

RADISH:

total LA: Color space: LAB: L= 0 and 181; a=0 and 255, b=133 and 181 Filtered –> Select –>

ANALYZE -–> Measure –> Area (pixels)

green LA: Color space:  LAB: L=0 and 181; a=100 and 124; b=33 and 186 Filtered –> Select –>  ANALYZE -> Measure –> Area (pixels)

Color settings could vary for different plant species (and scan settings), eg:

ROCKET:

total LA: Color space: LAB: L= 0 and 181; a=0 and 255, b=133 and 181

green LA: Color space:  LAB: L=0 and 181; a=100 and 127; b=133 and 181

 

NB! If lots of data is to be processed, there exists a risk that you could miss clicking “select” prior to pixel calculation, therefore all pixels of the image will be measured. To check later, whether there is such a mistake in your data, you can calculate the total nr of pixels of your image (in my case 8936794 pixels with 300dpi scan) and check if there is a match (if there is – redo the calculation).

 

Advertisements
This entry was posted in Other news and tagged , , , , . Bookmark the permalink.

Leave a Reply

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

WordPress.com Logo

You are commenting using your WordPress.com 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