ImageJ

Method to plot RGB pixel values?

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

11 messages Options

Henry Barwood

Method to plot RGB pixel values?

While reviewing an article on cathodoluminesce, I found an interesting
technique where the 0-255 values for RGB pixels were plotted to obtain
information about the provenance of some mineral grains. Is it possible to
do something like this in ImageJ ? The plots were basically red pixel value
plotted on blue pixel value because the green value did not vary a great
deal (for this specific investigation). If there is a technique or plug-in
for this sort of plotting, please let me know. Thanks.

Henry Barwood

Associate Professor of Science, Earth Sciences

Department of Math and Physics

MSCX 312G

Troy University

Troy, Alabama

[hidden email]

Michael Schmid

Re: Method to plot RGB pixel values?

Hi Henry,

you may have a look at the 3D Color Inspector/Color Histogram

http://rsb.info.nih.gov/ij/plugins/color-inspector.html

It plots the occurrence of pixels in three-dimensional R-G-B
space.

If you also want to do segmentation, you will need some type
of principal component analysis (PCA) plugin, just google up
"PCA" and "ImageJ". PCA plugins may require that you split the
RGB channels and create a stack.

Michael
________________________________________________________________

On 22 Jun 2007, at 16:08, Henry Barwood wrote:

> While reviewing an article on cathodoluminesce, I found an interesting
> technique where the 0-255 values for RGB pixels were plotted to obtain
> information about the provenance of some mineral grains. Is it
> possible to
> do something like this in ImageJ ? The plots were basically red
> pixel value
> plotted on blue pixel value because the green value did not vary a
> great
> deal (for this specific investigation). If there is a technique or
> plug-in
> for this sort of plotting, please let me know. Thanks.
>
>
>
> Henry Barwood
>
> Associate Professor of Science, Earth Sciences
>
> Department of Math and Physics
>
> MSCX 312G
>
> Troy University
>
> Troy, Alabama
>
> [hidden email]
>
>

dscho

Re: Method to plot RGB pixel values?

In reply to this post by Henry Barwood

Hi,

On Fri, 22 Jun 2007, Henry Barwood wrote:

> While reviewing an article on cathodoluminesce, I found an interesting
> technique where the 0-255 values for RGB pixels were plotted to obtain
> information about the provenance of some mineral grains. Is it possible to
> do something like this in ImageJ ? The plots were basically red pixel value
> plotted on blue pixel value because the green value did not vary a great
> deal (for this specific investigation). If there is a technique or plug-in
> for this sort of plotting, please let me know. Thanks.

I do not completely understand your question, but this might be what you
want:

http://rsb.info.nih.gov/ij/plugins/color-histogram.html

Hth,
Dscho

Henry Barwood

Re: Method to plot RGB pixel values?

In reply to this post by Michael Schmid

Hi Michael,

I tried this, and it certainly shows different color/intensity zones within
my images. By rotating the image, it is easy to visualize fields of CL
luminescence by mineral grains. Is there any way to extract data from the 3D
plot as an XY field (something like an XY plot of just the RG data)?

Henry

Henry Barwood
Associate Professor of Science, Earth Sciences
Department of Math and Physics
MSCX 312G
Troy University
Troy, Alabama
[hidden email]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Michael Schmid
Sent: Friday, June 22, 2007 9:48 AM
To: [hidden email]
Subject: Re: Method to plot RGB pixel values?

Hi Henry,

you may have a look at the 3D Color Inspector/Color Histogram

http://rsb.info.nih.gov/ij/plugins/color-inspector.html

It plots the occurrence of pixels in three-dimensional R-G-B
space.

If you also want to do segmentation, you will need some type
of principal component analysis (PCA) plugin, just google up
"PCA" and "ImageJ". PCA plugins may require that you split the
RGB channels and create a stack.

Michael
________________________________________________________________

On 22 Jun 2007, at 16:08, Henry Barwood wrote:

Joel Sheffield

Re: Method to plot RGB pixel values?

Here's a possiblity. Use the Image>Colors>RGB split to generate
separate images of each channel. You can then use the Image
Correlator plugin to create an xy plot of any image pair.

Joel

Date sent: Fri, 22 Jun 2007 10:53:37 -0500
Send reply to: ImageJ Interest Group <[hidden email]>
From: Henry Barwood <[hidden email]>
Subject: Re: Method to plot RGB pixel values?
To: [hidden email]

> Hi Michael,
>
> I tried this, and it certainly shows different color/intensity zones within
> my images. By rotating the image, it is easy to visualize fields of CL
> luminescence by mineral grains. Is there any way to extract data from the 3D
> plot as an XY field (something like an XY plot of just the RG data)?
>
> Henry
>
> Henry Barwood
> Associate Professor of Science, Earth Sciences
> Department of Math and Physics
> MSCX 312G
> Troy University
> Troy, Alabama
> [hidden email]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Michael Schmid
> Sent: Friday, June 22, 2007 9:48 AM
> To: [hidden email]
> Subject: Re: Method to plot RGB pixel values?
>
> Hi Henry,
>
> you may have a look at the 3D Color Inspector/Color Histogram
>
> http://rsb.info.nih.gov/ij/plugins/color-inspector.html
>
> It plots the occurrence of pixels in three-dimensional R-G-B
> space.
>
> If you also want to do segmentation, you will need some type
> of principal component analysis (PCA) plugin, just google up
> "PCA" and "ImageJ". PCA plugins may require that you split the
> RGB channels and create a stack.
>
> Michael
> ________________________________________________________________
>
> On 22 Jun 2007, at 16:08, Henry Barwood wrote:
>
> > While reviewing an article on cathodoluminesce, I found an interesting
> > technique where the 0-255 values for RGB pixels were plotted to obtain
> > information about the provenance of some mineral grains. Is it
> > possible to
> > do something like this in ImageJ ? The plots were basically red
> > pixel value
> > plotted on blue pixel value because the green value did not vary a
> > great
> > deal (for this specific investigation). If there is a technique or
> > plug-in
> > for this sort of plotting, please let me know. Thanks.
> >
> >
> >
> > Henry Barwood
> >
> > Associate Professor of Science, Earth Sciences
> >
> > Department of Math and Physics
> >
> > MSCX 312G
> >
> > Troy University
> >
> > Troy, Alabama
> >
> > [hidden email]
> >
> >

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs

Catherine Degnin

RG2B colocalization plugin

In reply to this post by Michael Schmid

I would like to download Chris Mauer's RG2B Colocalization plugin.
When downloading from the NIH website I pull down the script, but not
a packaged .class file. Since I am not a computer junkie, I have no
idea what to do with this information. Should this be packaged in a
downloadable file or do I need to convert the script (and how to do
this) inorder to place this in my plugin folder?

Thanks,
Catherine

Michael Schmid

Re: RG2B colocalization plugin

On 23 Jun 2007, at 02:16, Catherine Degnin wrote:

> I would like to download Chris Mauer's RG2B Colocalization plugin.
> When downloading from the NIH website I pull down the script, but
> not a packaged .class file.

Hi Catherine,

if you see a file starting with "import ij.*;" it is not a script but
Java code.

If you see already the java code, select File>Save Page As... to save
it.

Another way of doing it:
Before getting there, either right-click the
"RG2B_Colocalization.java" link and select "Save link as..." (or
whatever your Web browser calls that option), or click it with the
alt key down, which should also download the file on most browsers.

As the text on the web page tells, put the file into the ImageJ/
plugins folder (or a subfolder therof), then select "Compile and Run"
from the ImageJ menu and select this file. This creates a .class file.
After closing and reopening Image, it will be installed in the
"Plugins" menu (because it has an underscore in its name).

Michael

Catherine Degnin

Re: RG2B colocalization plugin

Michael,

I'm a Mac user, so no right-click, but I could open the file with the
alt key down. I moved it into the plugins folder, opened imageJ, ran
"compile and run" but got the following message:

Note: sun.tools.javac.Main has been deprecated.
error: Can't write: /Applications/ImageJ/plugins/
RG2B_Colocalization.class
1 error, 1 warning

I'm assuming this is a problem with my computer. Any clue what I
need to do to fix? I have a Mac G5 with the Tiger operating system ~

Thanks,
Catherine

On Jun 25, 2007, at 2:33 AM, Michael Schmid wrote:

> On 23 Jun 2007, at 02:16, Catherine Degnin wrote:
>
>> I would like to download Chris Mauer's RG2B Colocalization
>> plugin. When downloading from the NIH website I pull down the
>> script, but not a packaged .class file.
>
> Hi Catherine,
>
> if you see a file starting with "import ij.*;" it is not a script
> but Java code.
>
> If you see already the java code, select File>Save Page As... to
> save it.
>
> Another way of doing it:
> Before getting there, either right-click the
> "RG2B_Colocalization.java" link and select "Save link as..." (or
> whatever your Web browser calls that option), or click it with the
> alt key down, which should also download the file on most browsers.
>
> As the text on the web page tells, put the file into the ImageJ/
> plugins folder (or a subfolder therof), then select "Compile and
> Run" from the ImageJ menu and select this file. This creates
> a .class file.
> After closing and reopening Image, it will be installed in the
> "Plugins" menu (because it has an underscore in its name).
>
> Michael

Michael Schmid

Re: RG2B colocalization plugin

Hi Catherine,

looks like a permission problem - you have no write access to
the plugins directory.
Open the ImageJ directory in the finder, select "plugins",
type command-i (File>Get Info) and have a look at the
"Ownership&Permissions" at the bottom. With "Details" you
can see the "owner", "group" and "others" permission.
If there is only one user of the Mac (except the administrator),
it makes sense to change the owner into that user.
If there are several users of ImageJ on the Mac, it's easy if
they are in one group and you make this the group that owns the
directory. This group should have read&write access.

It may make sense to make other ImageJ directories (e.g. "macros")
writeable as well. For simplicity, I have the full ImageJ folder
including subfolders ("Apply to enclosed items" option) writeable
for me, than I can replace the ij.jar file with the newest
version without any authentication as administrator.

---
Don't care about the Note: "sun.tools.javac.Main has been
deprecated" message.

btw, if your mouse has no right button, command-click will do
the same as right-click (command is the "cloverleaf" key).

Michael
________________________________________________________________

On 25 Jun 2007, at 20:19, Catherine Degnin wrote:

> Michael,
>
> I'm a Mac user, so no right-click, but I could open the file with
> the alt key down. I moved it into the plugins folder, opened
> imageJ, ran "compile and run" but got the following message:
>
> Note: sun.tools.javac.Main has been deprecated.
> error: Can't write: /Applications/ImageJ/plugins/
> RG2B_Colocalization.class
> 1 error, 1 warning
>
> I'm assuming this is a problem with my computer. Any clue what I
> need to do to fix? I have a Mac G5 with the Tiger operating system ~
>
> Thanks,
> Catherine
>
>
> On Jun 25, 2007, at 2:33 AM, Michael Schmid wrote:
>
>> On 23 Jun 2007, at 02:16, Catherine Degnin wrote:
>>
>>> I would like to download Chris Mauer's RG2B Colocalization
>>> plugin. When downloading from the NIH website I pull down the
>>> script, but not a packaged .class file.
>>
>> Hi Catherine,
>>
>> if you see a file starting with "import ij.*;" it is not a script
>> but Java code.
>>
>> If you see already the java code, select File>Save Page As... to
>> save it.
>>
>> Another way of doing it:
>> Before getting there, either right-click the
>> "RG2B_Colocalization.java" link and select "Save link as..." (or
>> whatever your Web browser calls that option), or click it with the
>> alt key down, which should also download the file on most browsers.
>>
>> As the text on the web page tells, put the file into the ImageJ/
>> plugins folder (or a subfolder therof), then select "Compile and
>> Run" from the ImageJ menu and select this file. This creates
>> a .class file.
>> After closing and reopening Image, it will be installed in the
>> "Plugins" menu (because it has an underscore in its name).
>>
>> Michael

quantumlottie

upgrade

I have just upgraded my imagej and replaced the ij file in the imagej
folder with the new ij file. However now all my plugins don't work I
just get a message when I try to run them saying:

"This JVM does not include the javac compiler. Javac is included with
the Windows and Linux versions of ImageJ that are bundled with Java"

What have I done??

quantumlottie

Re: upgrade

Hello

I have solved my own problem. I deleted the compiler along with the old
version. I have no fixed it

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Holmes, Charlotte
Sent: 26 June 2007 14:29
To: [hidden email]
Subject: upgrade

I have just upgraded my imagej and replaced the ij file in the imagej
folder with the new ij file. However now all my plugins don't work I
just get a message when I try to run them saying:

"This JVM does not include the javac compiler. Javac is included with
the Windows and Linux versions of ImageJ that are bundled with Java"

What have I done??