Image Stack Color Analysis

[ataulf]

Hello,

I have a few images of the same rock (a stack) with each of them revealing the presence of a certain element in a different color. So one of them will show bright green when Silicon is present, another may show dark red where Calcium is present, etc.

Is there any way to overlay these and be able to tell what is the concentration of all the minerals at a given point on the rock?

Thank you for your time.

Best regards,
A. Taulf

[Michael Schmid]

Hi A.,

probably the method of choice is creating a composite image from the stack:
Image>Color>Make Composite.

Then use the 'Channels' window to set the colors of the channels, etc.
See
  http://rsb.info.nih.gov/ij/docs/guide/146-28.html#sub:Channels...[Z]

For the concentrations, one option is to select the area and use the Roi Managers 'Multi Measure' (in the 'More>>' menu). It will only give you the channel number, not the channel name.

If you want to have more functionality, there are macros or plugins around, or you can write your own one. A simple starting point might be
  http://rsb.info.nih.gov/ij/macros/MeasureStack.txt

Michael
________________________________________________________________
On Mar 10, 2014, at 04:10, ataulf wrote:

> Hello,
>
> I have a few images of the same rock (a stack) with each of them revealing
> the presence of a certain element in a different color. So one of them will
> show bright green when Silicon is present, another may show dark red where
> Calcium is present, etc.
>
> Is there any way to overlay these and be able to tell what is the
> concentration of all the minerals at a given point on the rock?
>
> Thank you for your time.
>
> Best regards,
> A. Taulf

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

[Shameem Sampath]

Hi,
I'd like to come to the ImageJ 2014 conference in Luxembourg.
Does anyone know on which dates it'll be held?
Regards,
Shameem Sampath

Sent from my iPhone

> On 10 Mar 2014, at 13:49, Michael Schmid <[hidden email]> wrote:
>
> Hi A.,
>
> probably the method of choice is creating a composite image from the stack:
> Image>Color>Make Composite.
>
> Then use the 'Channels' window to set the colors of the channels, etc.
> See
>  http://rsb.info.nih.gov/ij/docs/guide/146-28.html#sub:Channels...[Z]
>
> For the concentrations, one option is to select the area and use the Roi Managers 'Multi Measure' (in the 'More>>' menu). It will only give you the channel number, not the channel name.
>
> If you want to have more functionality, there are macros or plugins around, or you can write your own one. A simple starting point might be
>  http://rsb.info.nih.gov/ij/macros/MeasureStack.txt
>
> Michael
> ________________________________________________________________
>> On Mar 10, 2014, at 04:10, ataulf wrote:
>>
>> Hello,
>>
>> I have a few images of the same rock (a stack) with each of them revealing
>> the presence of a certain element in a different color. So one of them will
>> show bright green when Silicon is present, another may show dark red where
>> Calcium is present, etc.
>>
>> Is there any way to overlay these and be able to tell what is the
>> concentration of all the minerals at a given point on the rock?
>>
>> Thank you for your time.
>>
>> Best regards,
>> A. Taulf
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Kevin W Eliceiri]

Dear Shameem,


The committee is working on dates and will be making announcement next month.


best
kevin

On 03/10/14, Shameem Sampath  wrote:

> Hi,
> I'd like to come to the ImageJ 2014 conference in Luxembourg.
> Does anyone know on which dates it'll be held?
> Regards,
> Shameem Sampath
>
> Sent from my iPhone
>
> > On 10 Mar 2014, at 13:49, Michael Schmid <[hidden email]> wrote:
> >
> > Hi A.,
> >
> > probably the method of choice is creating a composite image from the stack:
> > Image>Color>Make Composite.
> >
> > Then use the 'Channels' window to set the colors of the channels, etc.
> > See
> > http://rsb.info.nih.gov/ij/docs/guide/146-28.html#sub:Channels...[Z]
> >
> > For the concentrations, one option is to select the area and use the Roi Managers 'Multi Measure' (in the 'More>>' menu). It will only give you the channel number, not the channel name.
> >
> > If you want to have more functionality, there are macros or plugins around, or you can write your own one. A simple starting point might be
> > http://rsb.info.nih.gov/ij/macros/MeasureStack.txt
> >
> > Michael
> > ________________________________________________________________
> >> On Mar 10, 2014, at 04:10, ataulf wrote:
> >>
> >> Hello,
> >>
> >> I have a few images of the same rock (a stack) with each of them revealing
> >> the presence of a certain element in a different color. So one of them will
> >> show bright green when Silicon is present, another may show dark red where
> >> Calcium is present, etc.
> >>
> >> Is there any way to overlay these and be able to tell what is the
> >> concentration of all the minerals at a given point on the rock?
> >>
> >> Thank you for your time.
> >>
> >> Best regards,
> >> A. Taulf
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Kevin W. Eliceiri
Director, Laboratory for Optical and Computational Instrumentation (LOCI)
Departments Cell and Molecular Biology and Biomedical Engineering
Affiliate Principal Investigator, Morgridge Institute for Research (MIR)
Room 271 Animal Sciences, 1675 Observatory Drive, Madison, WI 53706
Phone: [phone]

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