Problems calculating 'proportion green' from pictures

[sarah Al-beidh]

Hello all,

I am new to the list and to Image J and would be really grateful if one of you could offer some advice / assistance.
For a few months now, I have been trying to work out how to measure the vegetation cover from aerial photographs of 3m x3m plots (see attached photo for example). What I would like is a means of estimating the proportion of vegetation in each of my photographs wihtout having to draw lines around each green patch.
I have located a pdf on the Image J website describing how to determine the photosynthetic portion of a variegated leaf; however, this method (involving converting the image to greyscale and then binary) does not work for my photographs as the background here (bare soil) is not white and therefore this is not excluded when converting the image to black and white.
If anyone can give me a bit of help / direction regarding 1) whether this is possible with Image J and 2) how I could go about doing this with my photos, it would be greatly appreciated.

Many thanks in advance,
Sarah

[Michael Ellis]

Not an expert in this but here are a couple of ideas.

1. Use the colour threshold in imageJ to see if a green'ish portion of the image can be thresholded. ImageJ's partical analysis can then be used to calculate the portion of the image that was determined as being green.

2. If colour thresholding proves not suitable, split the image into red, green and blue, then integrate the intensity of each of the components and then calculate total green / (total red + total green + total blue) Tthis will give some crude measure to how overall green the image is.

Next apply the above to a selection of images and compare these results with the measurements you get by doing by hand. If there is a good correlation, then the quick and dirty measure of image greenness might be good enough for your needs.

Things to watch out for: does the soil (background) vary in hue significantly from sample to sample?

Just random Tuesday morning thoughst!


On 5 Oct 2010, at 11:40, sarah Al-beidh wrote:

> Hello all,
>
> I am new to the list and to Image J and would be really grateful if one of you could offer some advice / assistance.
> For a few months now, I have been trying to work out how to measure the vegetation cover from aerial photographs of 3m x3m plots (see attached photo for example). What I would like is a means of estimating the proportion of vegetation in each of my photographs wihtout having to draw lines around each green patch.
> I have located a pdf on the Image J website describing how to determine the photosynthetic portion of a variegated leaf; however, this method (involving converting the image to greyscale and then binary) does not work for my photographs as the background here (bare soil) is not white and therefore this is not excluded when converting the image to black and white.
> If anyone can give me a bit of help / direction regarding 1) whether this is possible with Image J and 2) how I could go about doing this with my photos, it would be greatly appreciated.
>
> Many thanks in advance,
> Sarah
>
> <aerial_photo-1.JPG>

[Krs5]

Dear Sarah,

I agree with Michael; try to use the colour threshold. In the Hue set the top slider to something like 38. Now make a grey scale image (Image--Type-- 8 bit), followed by a threshold on this image. Play with the sliders till you get what you want. See attached image

Good luck

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of [hidden email]
Sent: 05 October 2010 12:07
To: [hidden email]
Subject: Re: Problems calculating 'proportion green' from pictures

Not an expert in this but here are a couple of ideas.

1. Use the colour threshold in imageJ to see if a green'ish portion of the image can be thresholded. ImageJ's partical analysis can then be used to calculate the portion of the image that was determined as being green.

2. If colour thresholding proves not suitable, split the image into red, green and blue, then integrate the intensity of each of the components and then calculate total green / (total red + total green + total blue) Tthis will give some crude measure to how overall green the image is.

Next apply the above to a selection of images and compare these results with the measurements you get by doing by hand. If there is a good correlation, then the quick and dirty measure of image greenness might be good enough for your needs.

Things to watch out for: does the soil (background) vary in hue significantly from sample to sample?

Just random Tuesday morning thoughst!


On 5 Oct 2010, at 11:40, sarah Al-beidh wrote:

> Hello all,
>
> I am new to the list and to Image J and would be really grateful if one of you could offer some advice / assistance.
> For a few months now, I have been trying to work out how to measure the vegetation cover from aerial photographs of 3m x3m plots (see attached photo for example). What I would like is a means of estimating the proportion of vegetation in each of my photographs wihtout having to draw lines around each green patch.
> I have located a pdf on the Image J website describing how to determine the photosynthetic portion of a variegated leaf; however, this method (involving converting the image to greyscale and then binary) does not work for my photographs as the background here (bare soil) is not white and therefore this is not excluded when converting the image to black and white.
> If anyone can give me a bit of help / direction regarding 1) whether this is possible with Image J and 2) how I could go about doing this with my photos, it would be greatly appreciated.
>
> Many thanks in advance,
> Sarah
>
> <aerial_photo-1.JPG>

[Cammer, Michael]

This misses the very bright plant in the upper right, but selects for a color range.

run("Smooth");
run("HSB Stack");
setAutoThreshold("Default");
//run("Threshold...");
run("Spectrum");
setThreshold(47, 68);
run("Convert to Mask", " ");
run("Histogram", "slice");

result:
255 53387

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of sarah Al-beidh [[hidden email]]
Sent: Tuesday, October 05, 2010 6:40 AM
To: [hidden email]
Subject: Problems calculating 'proportion green' from pictures

Hello all,

I am new to the list and to Image J and would be really grateful if one of you could offer some advice / assistance.
For a few months now, I have been trying to work out how to measure the vegetation cover from aerial photographs of 3m x3m plots (see attached photo for example). What I would like is a means of estimating the proportion of vegetation in each of my photographs wihtout having to draw lines around each green patch.
I have located a pdf on the Image J website describing how to determine the photosynthetic portion of a variegated leaf; however, this method (involving converting the image to greyscale and then binary) does not work for my photographs as the background here (bare soil) is not white and therefore this is not excluded when converting the image to black and white.
If anyone can give me a bit of help / direction regarding 1) whether this is possible with Image J and 2) how I could go about doing this with my photos, it would be greatly appreciated.

Many thanks in advance,
Sarah


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