Multilevel Thresholding

[ijourneaux]

I have an image with dark and light particles that are distributed on  a flat surface. At this time flat surface is blue but it could be any color. I would like to characterize the area distribution of light and dark particles excluding any background area (blue) that is visible.

It would seem that this is an application for multilevel thresholding. I can't seem to get it to work. Usually the blue background gets confused with the light colored particles.

Once I do get a properly thresholded image, how do I do the area calculations?

Take Care

Ian Journeaux
Manager - Process Technology
NewPage Research
300 North Biron Drive
Wisconsin Rapids, Wisconsin   54495-8050

Phone:             [phone]
Cell:                 [phone]
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[ijourneaux]

Here is a sample picture I am trying to process. I have bark and wood on a blue background. Looking to get the area fraction of bark to wood ignoring the background.

http://www.imagecabin.com/?view=253819762b28b1bfac6b4cd4c


________________________________
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of IMAGEJ automatic digest system
Sent: Wednesday, September 23, 2009 11:00 PM
To: [hidden email]
Subject: IMAGEJ Digest - 22 Sep 2009 to 23 Sep 2009 (#2009-261)

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IMAGEJ Digest - 22 Sep 2009 to 23 Sep 2009 (#2009-261)

Table of contents:

 *   path on linux (4)
 *   Where to put .class files? (2)
 *   pan command in macro to display specified subregion? (3)
 *   Mean Linear Intercept
 *   Call multithreaded plugin from another plugin
 *   "Magnetic lasso"-like tool
 *   Remove slices from a virtual stack (6)
 *   problem in opening series with LOCI plug-in (2)
 *   How to release memory
 *   stack reverser (2)
 *   could not add a volume in imageJ3DViewer
 *   [SOLVED] RE: "Magnetic lasso"-like tool
 *   Bug when scaling VirtualStack to Stack

 1.  path on linux
    *   Re: path on linux<cid:[hidden email]> (09/22)
From: Johannes Schindelin <[hidden email]>
    *   Re: path on linux<cid:[hidden email]> (09/23)
From: "Vera, Pedro L." <[hidden email]>
    *   Re: path on linux<cid:[hidden email]> (09/23)
From: Johannes Schindelin <[hidden email]>
    *   Re: path on linux<cid:[hidden email]> (09/23)
From: Benoit Zuber <[hidden email]>
 2.  Where to put .class files?
    *   Where to put .class files?<cid:[hidden email]> (09/22)
From: Daniel Kalthoff <[hidden email]>
    *   Re: Where to put .class files?<cid:[hidden email]> (09/23)
From: Ben Tupper <[hidden email]>
 3.  pan command in macro to display specified subregion?
    *   pan command in macro to display specified subregion?<cid:[hidden email]> (09/23)
From: Bill Christens-Barry <[hidden email]>
    *   Re: pan command in macro to display specified subregion?<cid:[hidden email]> (09/23)
From: Gluender <[hidden email]>
    *   Re: pan command in macro to display specified subregion?<cid:[hidden email]> (09/23)
From: Bill Christens-Barry <[hidden email]>
 4.  Mean Linear Intercept
    *   Re: Mean Linear Intercept<cid:[hidden email]> (09/23)
From: Michael Doube <[hidden email]>
 5.  Call multithreaded plugin from another plugin
    *   Re: Call multithreaded plugin from another plugin<cid:[hidden email]> (09/23)
From: Michael Doube <[hidden email]>
 6.  "Magnetic lasso"-like tool
    *   Re: "Magnetic lasso"-like tool<cid:[hidden email]> (09/23)
From: Volker Baecker <[hidden email]>
 7.  Remove slices from a virtual stack
    *   Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: Michael Doube <[hidden email]>
    *   Re: Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: Michael Doube <[hidden email]>
    *   Re: Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: Bill Mohler <[hidden email]>
    *   Re: Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: "Dong, Hualing L." <[hidden email]>
    *   Re: Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: Wayne Rasband <[hidden email]>
    *   Re: Remove slices from a virtual stack<cid:[hidden email]> (09/23)
From: Michael Doube <[hidden email]>
 8.  problem in opening series with LOCI plug-in
    *   problem in opening series with LOCI plug-in<cid:[hidden email]> (09/23)
From: Berra Erkosar <[hidden email]>
    *   Re: problem in opening series with LOCI plug-in<cid:[hidden email]> (09/23)
From: Curtis Rueden <[hidden email]>
 9.  How to release memory
    *   How to release memory<cid:[hidden email]> (09/23)
From: Eddie Iannuccelli <[hidden email]>
 10. stack reverser
    *   stack reverser<cid:[hidden email]> (09/22)
From: Jane <[hidden email]>
    *   Re: stack reverser<cid:[hidden email]> (09/23)
From: Wayne Rasband <[hidden email]>
 11. could not add a volume in imageJ3DViewer
    *   could not add a volume in imageJ3DViewer<cid:[hidden email]> (09/23)
From: Thomas Boudier <[hidden email]>
 12. [SOLVED] RE: "Magnetic lasso"-like tool
    *   [SOLVED] RE: "Magnetic lasso"-like tool<cid:[hidden email]> (09/23)
From: "Vera, Pedro L." <[hidden email]>
 13. Bug when scaling VirtualStack to Stack
    *   Bug when scaling VirtualStack to Stack<cid:[hidden email]> (09/24)
From: Adrian <[hidden email]>

________________________________
[http://LIST.NIH.GOV/archives/lpowered.gif]<http://www.lsoft.com/LISTSERV-powered.html> Browse the IMAGEJ online archives.<http://list.nih.gov/cgi-bin/wa?LIST=IMAGEJ>

This electronic message contains information from NewPage Corporation or subsidiary companies,
which may be confidential, privileged or otherwise protected from disclosure. The information is
intended to be used solely by the recipient(s) named. If you are not an intended recipient, be
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contents is prohibited. If you have received this transmission in error, please notify NewPage
immediately at [hidden email].

[Joel Sheffield]

Hi,

If you run Image>colors>split colors, you will get the three color
channels as separate images.  In the "blue" channel, the background
appears white.  I don't know enough to tell you which is bark and
wood in the image, but there are two levels of intensity that you
should be able to isolate.

Best of Luck,

Joel

> Here is a sample picture I am trying to process. I have bark and
> wood on a blue background. Looking to get the area fraction of bark
> to wood ignoring the background.
>
> http://www.imagecabin.com/?view=253819762b28b1bfac6b4cd4c
>
>
> ________________________________
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
> Of IMAGEJ automatic digest system
> Sent: Wednesday, September 23, 2009 11:00 PM
> To: [hidden email]
> Subject: IMAGEJ Digest - 22 Sep 2009 to 23 Sep 2009 (#2009-261)
>
> [https://list.nih.gov/LISTSERV_WEB/IMAGES/nihlogo.gif]
>
> [https://list.nih.gov/LISTSERV_WEB/IMAGES/listserv.gif]
>
>
> IMAGEJ Digest - 22 Sep 2009 to 23 Sep 2009 (#2009-261)
>
> Table of contents:
>
>  *   path on linux (4)
>  *   Where to put .class files? (2)
>  *   pan command in macro to display specified subregion? (3)
>  *   Mean Linear Intercept
>  *   Call multithreaded plugin from another plugin
>  *   "Magnetic lasso"-like tool
>  *   Remove slices from a virtual stack (6)
>  *   problem in opening series with LOCI plug-in (2)
>  *   How to release memory
>  *   stack reverser (2)
>  *   could not add a volume in imageJ3DViewer
>  *   [SOLVED] RE: "Magnetic lasso"-like tool
>  *   Bug when scaling VirtualStack to Stack
>
>  1.  path on linux
>     *   Re: path on linux<cid:[hidden email]> (09/22)
> From: Johannes Schindelin <[hidden email]>
>     *   Re: path on linux<cid:[hidden email]> (09/23)
> From: "Vera, Pedro L." <[hidden email]>
>     *   Re: path on linux<cid:[hidden email]> (09/23)
> From: Johannes Schindelin <[hidden email]>
>     *   Re: path on linux<cid:[hidden email]> (09/23)
> From: Benoit Zuber <[hidden email]>
>  2.  Where to put .class files?
>     *   Where to put .class files?<cid:[hidden email]> (09/22)
> From: Daniel Kalthoff <[hidden email]>
>     *   Re: Where to put .class files?<cid:[hidden email]>
> (09/23)
> From: Ben Tupper <[hidden email]>
>  3.  pan command in macro to display specified subregion?
>     *   pan command in macro to display specified
> subregion?<cid:[hidden email]> (09/23)
> From: Bill Christens-Barry <[hidden email]>
>     *   Re: pan command in macro to display specified
> subregion?<cid:[hidden email]> (09/23)
> From: Gluender <[hidden email]>
>     *   Re: pan command in macro to display specified
> subregion?<cid:[hidden email]> (09/23)
> From: Bill Christens-Barry <[hidden email]>
>  4.  Mean Linear Intercept
>     *   Re: Mean Linear Intercept<cid:[hidden email]> (09/23)
> From: Michael Doube <[hidden email]>
>  5.  Call multithreaded plugin from another plugin
>     *   Re: Call multithreaded plugin from another
> plugin<cid:[hidden email]> (09/23)
> From: Michael Doube <[hidden email]>
>  6.  "Magnetic lasso"-like tool
>     *   Re: "Magnetic lasso"-like tool<cid:[hidden email]>
> (09/23)
> From: Volker Baecker <[hidden email]>
>  7.  Remove slices from a virtual stack
>     *   Remove slices from a virtual stack<cid:[hidden email]>
> (09/23)
> From: Michael Doube <[hidden email]>
>     *   Re: Remove slices from a virtual
> stack<cid:[hidden email]> (09/23)
> From: Michael Doube <[hidden email]>
>     *   Re: Remove slices from a virtual
> stack<cid:[hidden email]> (09/23)
> From: Bill Mohler <[hidden email]>
>     *   Re: Remove slices from a virtual
> stack<cid:[hidden email]> (09/23)
> From: "Dong, Hualing L." <[hidden email]>
>     *   Re: Remove slices from a virtual
> stack<cid:[hidden email]> (09/23)
> From: Wayne Rasband <[hidden email]>
>     *   Re: Remove slices from a virtual
> stack<cid:[hidden email]> (09/23)
> From: Michael Doube <[hidden email]>
>  8.  problem in opening series with LOCI plug-in
>     *   problem in opening series with LOCI
> plug-in<cid:[hidden email]> (09/23)
> From: Berra Erkosar <[hidden email]>
>     *   Re: problem in opening series with LOCI
> plug-in<cid:[hidden email]> (09/23)
> From: Curtis Rueden <[hidden email]>
>  9.  How to release memory
>     *   How to release memory<cid:[hidden email]> (09/23)
> From: Eddie Iannuccelli <[hidden email]>
>  10. stack reverser
>     *   stack reverser<cid:[hidden email]> (09/22)
> From: Jane <[hidden email]>
>     *   Re: stack reverser<cid:[hidden email]> (09/23)
> From: Wayne Rasband <[hidden email]>
>  11. could not add a volume in imageJ3DViewer
>     *   could not add a volume in
> imageJ3DViewer<cid:[hidden email]> (09/23)
> From: Thomas Boudier <[hidden email]>
>  12. [SOLVED] RE: "Magnetic lasso"-like tool
>     *   [SOLVED] RE: "Magnetic lasso"-like
> tool<cid:[hidden email]> (09/23)
> From: "Vera, Pedro L." <[hidden email]>
>  13. Bug when scaling VirtualStack to Stack
>     *   Bug when scaling VirtualStack to
> Stack<cid:[hidden email]> (09/24)
> From: Adrian <[hidden email]>
>
> ________________________________
> [http://LIST.NIH.GOV/archives/lpowered.gif]<http://www.lsoft.com/LIS
> TSERV-powered.html> Browse the IMAGEJ online
> archives.<http://list.nih.gov/cgi-bin/wa?LIST=IMAGEJ>
>
> This electronic message contains information from NewPage
> Corporation or subsidiary companies,
> which may be confidential, privileged or otherwise protected from
> disclosure. The information is
> intended to be used solely by the recipient(s) named. If you are not
> an intended recipient, be
> aware that any review, disclosure, copying, distribution or use of
> this transmission or its
> contents is prohibited. If you have received this transmission in
> error, please notify NewPage
> immediately at [hidden email].
>

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
[phone], fax [phone]
http://astro.temple.edu/~jbs

[Michael Schmid]

Hi Ian,

if you have nice color contrast as in your sample image, convert it  
to HSB:
Image>Type>HSB stack.
Then you can threshold the Hue channel; Edit>Selection>Create  
Selection selects only the foreground.
In the Brightness channel, you can threshold bright or dark areas and  
use "Measure" (with "Area Fraction" enabled in the Measurement Options).

Michael
________________________________________________________________

On 24 Sep 2009, at 21:18, Journeaux, Ian wrote:


> Here is a sample picture I am trying to process. I have bark and  
> wood on a blue background. Looking to get the area fraction of bark  
> to wood ignoring the background.
>
> http://www.imagecabin.com/?view=253819762b28b1bfac6b4cd4c
>

On 24 Sep 2009, at 18:59, Journeaux, Ian wrote:

> I have an image with dark and light particles that are distributed  
> on  a flat surface. At this time flat surface is blue but it could  
> be any color. I would like to characterize the area distribution of  
> light and dark particles excluding any background area (blue) that  
> is visible.
>
> It would seem that this is an application for multilevel  
> thresholding. I can't seem to get it to work. Usually the blue  
> background gets confused with the light colored particles.
>
> Once I do get a properly thresholded image, how do I do the area  
> calculations?
>
> Take Care
>
> Ian Journeaux
> Manager - Process Technology
> NewPage Research
> 300 North Biron Drive
> Wisconsin Rapids, Wisconsin   54495-8050