create a color intensity map

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create a color intensity map

Thiago
Hi,

I have done some fluorescence experiments as a function of the time, and I need merge the images (Image left) and create a map with the fluorescence intensity (image right). Anyone knows if it is possible to do this using Imaje J? Or other software that I can do it.

fluorescence

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Re: create a color intensity map

John Oreopoulos
Thiago,

Look at the Analyze->Tools->Calibration bar function of ImageJ which is documented here:

http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.14

specifically sub-section 30.14.7

Maybe that helps,

John Oreopoulos
Staff Scientist
Spectral Applied Research Inc.
A Division of Andor Technology
Richmond Hill, Ontario
Canada
www.spectral.ca


On 2013-11-25, at 12:15 PM, Thiago wrote:

> Hi,
>
> I have done some fluorescence experiments as a function of the time, and I
> need merge the images (Image left) and create a map with the fluorescence
> intensity (image right). Anyone knows if it is possible to do this using
> Imaje J? Or other software that I can do it.
>
> <http://imagej.1557.x6.nabble.com/file/n5005697/Montage.jpg>
>
> <http://imagej.1557.x6.nabble.com/file/n5005697/EtOH_onset.png>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/create-a-color-intensity-map-tp5005697.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: create a color intensity map

Joel Sheffield
In reply to this post by Thiago
Hi Thiago, It seems to me that what you need is to convert the image to
8-bit, and then provide a look-up-table that will change color in
proportion to the intensity.   Basically, you should:
1. convert the image to 8-bit. (Image>type>8-bit), adjust contrast and
brightness if necessary.
2.  apply a look-up-table from the selection that comes from ImageJ or
create your own,
  a,  go to Image>color>display LUTS
  b.  note the LUT that you think will be best for your data.  (I used the
ICA lut)
  c.  go to File>import>lut, and select that lut  (It will be in the ImageJ
directory>luts
3.  Convert the image back to RGB color (Image>type>RGB color)
4.  Resave it

You should get something like the one I have attached.

This will not be a quantitative display, since the brightness has been
adjusted, but it is possible to set up some standards so that specific
colors correspond to specific intensities --Be aware of all of the caveats,
generously scattered through this list, about quantitating fluorescence.




On Mon, Nov 25, 2013 at 12:15 PM, Thiago <[hidden email]> wrote:

> Hi,
>
> I have done some fluorescence experiments as a function of the time, and I
> need merge the images (Image left) and create a map with the fluorescence
> intensity (image right). Anyone knows if it is possible to do this using
> Imaje J? Or other software that I can do it.
>
> <http://imagej.1557.x6.nabble.com/file/n5005697/Montage.jpg>
>
> <http://imagej.1557.x6.nabble.com/file/n5005697/EtOH_onset.png>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/create-a-color-intensity-map-tp5005697.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

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

Montage map.jpg (596K) Download Attachment
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Re: create a color intensity map

Thiago
Thanks Joel. I got it!!!
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Re: create a color intensity map

Thiago
In reply to this post by John Oreopoulos
Thanks John, It was really helpful!!! I got what I wanted