Plugin for fluorsecent images

[jknowles]

Dear Imagej users

 

We have been wanting to take some fluorescent images using different colours
and merge or overlay. However one channel is very bright and the others very
feint. If there a plugin that allows you to put the three images together
and then for each channel to have an exposure adjust or maybe
brightness/contrast?

 

I had a look at the ones built in but they don't seem to do the above.

 

Many thanks

 

Jonathan

 

 

Professor J.C. Knowles BSc(hons), PhD, FIMMM, CEng, FRSC, CSci
Professor of Biomaterials Science
Head of Division of Biomaterials and Tissue Engineering,
UCL Eastman Dental Institute,
University College London,
256 Gray's Inn Road,
London WC1X 8LD. UK.
Telephone  [phone]
Fax [phone]
Mobile [phone]

Skype address: jknowles_edi
Editor, Journal of Biomaterials Applications
Email [hidden email]
Eastman website;  <http://www.eastman.ucl.ac.uk/>
http://www.eastman.ucl.ac.uk
Personal website;  <http://www.eastman.ucl.ac.uk/~jknowles>
http://www.homepages.ucl.ac.uk/~sfhvjck/
This email represents the views of the sender alone and must not be
construed as representing the views of the Eastman Dental Institute. It may
contain confidential information and may be protected by law as a legally
privileged document and copyright work. Its content should not be disclosed
and it should not be given or copied to anyone other than the person(s)
named or referenced above. If you have received this email in error, please
contact the sender.

 

 

[Juanjo Vega]

I think you want to smooth brightness for that channel, so they have similar intensity. Am I right?

Maybe you can try to make a stack with your three images, to normalize that stack with the bright&contrast tool, and then to combine the three images as channels for a new RGB one.

Or maybe you can develop a plugin to normalize the three channels according to their max and min values... I'm just guessing.

Of course, it might be more convenient for you to develop a plugin to automate all the stuff above once you know the steps that you need.

Hope that helps,

Juanjo.

On Oct 14, 2011, at 5:19 PM, Prof Jonathan Knowles wrote:

> Dear Imagej users
>
>
>
> We have been wanting to take some fluorescent images using different colours
> and merge or overlay. However one channel is very bright and the others very
> feint. If there a plugin that allows you to put the three images together
> and then for each channel to have an exposure adjust or maybe
> brightness/contrast?
>
>
>
> I had a look at the ones built in but they don't seem to do the above.
>
>
>
> Many thanks
>
>
>
> Jonathan
>
>
>
>
>
> Professor J.C. Knowles BSc(hons), PhD, FIMMM, CEng, FRSC, CSci
> Professor of Biomaterials Science
> Head of Division of Biomaterials and Tissue Engineering,
> UCL Eastman Dental Institute,
> University College London,
> 256 Gray's Inn Road,
> London WC1X 8LD. UK.
> Telephone  [phone]
> Fax [phone]
> Mobile [phone]
>
> Skype address: jknowles_edi
> Editor, Journal of Biomaterials Applications
> Email [hidden email]
> Eastman website;  <http://www.eastman.ucl.ac.uk/>
> http://www.eastman.ucl.ac.uk
> Personal website;  <http://www.eastman.ucl.ac.uk/~jknowles>
> http://www.homepages.ucl.ac.uk/~sfhvjck/
> This email represents the views of the sender alone and must not be
> construed as representing the views of the Eastman Dental Institute. It may
> contain confidential information and may be protected by law as a legally
> privileged document and copyright work. Its content should not be disclosed
> and it should not be given or copied to anyone other than the person(s)
> named or referenced above. If you have received this email in error, please
> contact the sender.
>
>
>
>

------------------------------------------------------------
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.csic.es

[phone]

"Las mejores almas son capaces de los mayores vicios como de las mayores
virtudes, y aquellos que caminan despacio por el camino recto pueden
llegar más lejos que los que corren pero se apartan de él." - Discurso
del Método, René Descartes.

[John Oreopoulos]

Jonathan,

Use the Image->Color->Merge Channels command to combine the three RGB images. Then use the Image->Adjust->Color Balance command to adjust the brightness and contrast of each color channel to the desired levels. You could also auto contrast each channel. If you want to automate this process, try using the macro recorder.

Perhaps there are better or alternate ways to do this as well. Surely someone must have created a similar plugin (???).

Cheers,

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca


On 2011-10-14, at 11:49 AM, Juanjo Vega wrote:

> I think you want to smooth brightness for that channel, so they have similar intensity. Am I right?
>
> Maybe you can try to make a stack with your three images, to normalize that stack with the bright&contrast tool, and then to combine the three images as channels for a new RGB one.
>
> Or maybe you can develop a plugin to normalize the three channels according to their max and min values... I'm just guessing.
>
> Of course, it might be more convenient for you to develop a plugin to automate all the stuff above once you know the steps that you need.
>
> Hope that helps,
>
> Juanjo.
>
> On Oct 14, 2011, at 5:19 PM, Prof Jonathan Knowles wrote:
>
>> Dear Imagej users
>>
>>
>>
>> We have been wanting to take some fluorescent images using different colours
>> and merge or overlay. However one channel is very bright and the others very
>> feint. If there a plugin that allows you to put the three images together
>> and then for each channel to have an exposure adjust or maybe
>> brightness/contrast?
>>
>>
>>
>> I had a look at the ones built in but they don't seem to do the above.
>>
>>
>>
>> Many thanks
>>
>>
>>
>> Jonathan
>>
>>
>>
>>
>>
>> Professor J.C. Knowles BSc(hons), PhD, FIMMM, CEng, FRSC, CSci
>> Professor of Biomaterials Science
>> Head of Division of Biomaterials and Tissue Engineering,
>> UCL Eastman Dental Institute,
>> University College London,
>> 256 Gray's Inn Road,
>> London WC1X 8LD. UK.
>> Telephone  [phone]
>> Fax [phone]
>> Mobile [phone]
>>
>> Skype address: jknowles_edi
>> Editor, Journal of Biomaterials Applications
>> Email [hidden email]
>> Eastman website;  <http://www.eastman.ucl.ac.uk/>
>> http://www.eastman.ucl.ac.uk
>> Personal website;  <http://www.eastman.ucl.ac.uk/~jknowles>
>> http://www.homepages.ucl.ac.uk/~sfhvjck/
>> This email represents the views of the sender alone and must not be
>> construed as representing the views of the Eastman Dental Institute. It may
>> contain confidential information and may be protected by law as a legally
>> privileged document and copyright work. Its content should not be disclosed
>> and it should not be given or copied to anyone other than the person(s)
>> named or referenced above. If you have received this email in error, please
>> contact the sender.
>>
>>
>>
>>
>
> ------------------------------------------------------------
> Juanjo Vega ([hidden email])
>
> Unidad de Biocomputación. Laboratorio B-13.
> Centro Nacional de Biotecnología. CNB-CSIC.
> C\ Darwin, 3. Campus de Cantoblanco.
> Universidad Autónoma de Madrid.
> 28049, Madrid, Spain.
>
> http://www.cnb.csic.es
> http://www.biocomp.cnb.csic.es
>
> [phone]
>
> "Las mejores almas son capaces de los mayores vicios como de las mayores
> virtudes, y aquellos que caminan despacio por el camino recto pueden
> llegar más lejos que los que corren pero se apartan de él." - Discurso
> del Método, René Descartes.

[dscho]

Hi,

On Fri, 14 Oct 2011, Prof Jonathan Knowles wrote:

> We have been wanting to take some fluorescent images using different
> colours and merge or overlay. However one channel is very bright and the
> others very feint. If there a plugin that allows you to put the three
> images together and then for each channel to have an exposure adjust or
> maybe brightness/contrast?

Even better: use a macro. Macros are not really hard to understand and
fiddle with until they do exactly what you want to do.

Here is something you might want to use for starters (just click on
Plugins>New>Macro, paste the following and run it from the editor's menu):

-- snipsnap --
// open the blobs sample and make a ROI
run("Blobs (25K)");
run("Select All");

// open the boats sample and crop it to the same size as blobs
run("Boats (356K)");
run("Restore Selection");
run("Crop");

// do the same for the cell colony sample (and make it also 8-bit)
run("Cell Colony (31K)");
run("8-bit");
run("Restore Selection");
run("Crop");

// here comes the meat: merge the channels into a composite image
run("Merge Channels...", "red=boats.gif green=blobs.gif "
        + "blue=Cell_Colony.jpg gray=*None* create");

// virtually click Image>Adjust>Brightness & Contrast
run("Brightness/Contrast...");

// virtually click the "Auto" button in all the channels
Stack.getDimensions(dummy, dummy, nChannels, dummy, dummy);
for (channel = 1; channel <= nChannels; channel++) {
        Stack.setChannel(channel);
        run("Enhance Contrast", "saturated=0.35");
}

[Daniel James White]

Hi Jonathan,

Tell the merge tool to output a composite image instead of RGB

Composite image has a slider for channel, and can handle 16 bit images (RGB is 8 bit per channel)

then you can use the brightness contrast tool independently on the colour channels.

Read the nice new imageJ manual for more details.

Dan




On Oct 15, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Fri, 14 Oct 2011 16:19:51 +0100
> From:    Prof Jonathan Knowles <[hidden email]>
> Subject: Plugin for fluorsecent images
>
> Dear Imagej users
>
>
>
> We have been wanting to take some fluorescent images using different colours
> and merge or overlay. However one channel is very bright and the others very
> feint. If there a plugin that allows you to put the three images together
> and then for each channel to have an exposure adjust or maybe
> brightness/contrast?
>
>
>
> I had a look at the ones built in but they don't seem to do the above.
>
>
>
> Many thanks
>
>
>
> Jonathan

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
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( white (at) mpi-cbg.de )