Measuring Radishes

[AgricStudent]

Hello,

I'm an undergrad student and I'm currently working on the effect of two fertilisers at varying rates and the consequent developmental effect on root crops produced. So far I have managed to quantify the total area of root crops in the photo of each group and the different component areas of the root crop (approx 30 in each sample image).

However I was hoping that some person, who is more imagej savvy might be able to instruct me how I might be able to quantify the shapes in each image. I've tried understanding skeletonising or medial axis, but put simply I wondered if there was a straight-forward process to quantify the mean shape so that the samples could be numerically quantified and compared against each other, to show a trend?

Thanks in advance

ARAG

[Anderson, Charles (DNR)]

The general approach to obtaining shape measurements is simple: Go to Analyze | Set Measurements and check options of interest. Then threshold the image to segment out the parts of interest. Run Analyze | Analyze Particles on the thresholded image.  The options of interest will be reported for each particle.   Completely segmenting the parts of interest may be the most difficult step (but that is a different question and might require you attach an image).

You might also read
C. Igathinathane et al. 2008. Shape identification and particles size distribution from basic shape parameters using ImageJ. Computers and electronics in agriculture 63:168-182.  The three measurements he found useful can be calculated directly from the Analyze Particle outputs. You might find it easier to  do the additional calculations with a stats program or spreadsheet than writing a macro for ImageJ.  Note that there are several errors in the published code at the end of the paper.

Good luck.

C

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of AgricStudent
Sent: Thursday, November 14, 2013 1:30 PM
To: [hidden email]
Subject: Measuring Radishes

Hello,

I'm an undergrad student and I'm currently working on the effect of two fertilisers at varying rates and the consequent developmental effect on root crops produced. So far I have managed to quantify the total area of root crops in the photo of each group and the different component areas of the root crop (approx 30 in each sample image).

However I was hoping that some person, who is more imagej savvy might be able to instruct me how I might be able to quantify the shapes in each image. I've tried understanding skeletonising or medial axis, but put simply I wondered if there was a straight-forward process to quantify the mean shape so that the samples could be numerically quantified and compared against each other, to show a trend?

Thanks in advance

ARAG



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[Cheng Zhang]

Actually, the skeleton is different to medial axis. You could find the answer from numerical articles. To generate a good skeleton, you need to shape (in a binary image) the roots well. You may apply different filters to sharp the edges (I found equalization is a useful one). Once you have a good shape binary image, you can apply process->binary->skeletonize. You need set up binary options before applying skeletonize function. Good luck.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Anderson, Charles (DNR)
Sent: November 14, 2013 14:10
To: [hidden email]
Subject: Re: Measuring Radishes

The general approach to obtaining shape measurements is simple: Go to Analyze | Set Measurements and check options of interest. Then threshold the image to segment out the parts of interest. Run Analyze | Analyze Particles on the thresholded image.  The options of interest will be reported for each particle.   Completely segmenting the parts of interest may be the most difficult step (but that is a different question and might require you attach an image).

You might also read
C. Igathinathane et al. 2008. Shape identification and particles size distribution from basic shape parameters using ImageJ. Computers and electronics in agriculture 63:168-182.  The three measurements he found useful can be calculated directly from the Analyze Particle outputs. You might find it easier to  do the additional calculations with a stats program or spreadsheet than writing a macro for ImageJ.  Note that there are several errors in the published code at the end of the paper.

Good luck.

C

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of AgricStudent
Sent: Thursday, November 14, 2013 1:30 PM
To: [hidden email]
Subject: Measuring Radishes

Hello,

I'm an undergrad student and I'm currently working on the effect of two fertilisers at varying rates and the consequent developmental effect on root crops produced. So far I have managed to quantify the total area of root crops in the photo of each group and the different component areas of the root crop (approx 30 in each sample image).

However I was hoping that some person, who is more imagej savvy might be able to instruct me how I might be able to quantify the shapes in each image. I've tried understanding skeletonising or medial axis, but put simply I wondered if there was a straight-forward process to quantify the mean shape so that the samples could be numerically quantified and compared against each other, to show a trend?

Thanks in advance

ARAG



--
View this message in context: http://imagej.1557.x6.nabble.com/Measuring-Radishes-tp5005566.html
Sent from the ImageJ mailing list archive at Nabble.com.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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