merging IHC image from different slides

[Martino Bosco]

I have taken IHC images from different slides (of course, with different antibodies) using the same chromogen (DAB).
How can I merge these image in one image in order to obtain a "virtual multicolour immunohistochemistry)? In particular, how can I use internal Landmarks to obtain a correct overlap between two or more image of the same histological field?
Thanks for any help

Martino Bosco, MD
Anatomia Patologica
Alba (CN), Italy

[Saalfeld, Stephan]

You can place the landmarks manually using the multi-point tool or try
automatic feature extraction:

http://fiji.sc/Feature_Extraction

Then, you can transform or warp the slices into a reference using this
plugin

http://fiji.sc/Landmark_Correspondences

Without seeing the images this is all I can tell.

Cheers,
Stephan



On Wed, 2016-02-24 at 00:53 -0800, Martino Bosco wrote:

> I have taken IHC images from different slides (of course, with
> different
> antibodies) using the same chromogen (DAB).
> How can I merge these image in one image in order to obtain a
> "virtual
> multicolour immunohistochemistry)? In particular, how can I use
> internal
> Landmarks to obtain a correct overlap between two or more image of
> the same
> histological field?
> Thanks for any help
>
> Martino Bosco, MD
> Anatomia Patologica
> Alba (CN), Italy
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/mergin
> g-IHC-image-from-different-slides-tp5015699.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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[Richard Mort-2]

Hi All,

I can no longer get the following to work:

roiManager("Select", 1);
setKeyDown("Shift");
roiManager("Select", 2);
roiManager("Or");
roiManager("Add");

It only selects one of the ROI's. I seem to remember this used to be a
problem but thought it was fixed.

I'm on Linux with Fiji upto date (IJ v1.50g)

Best
R

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[gankaku]

Hi Richard,

Try...
roiManager("select", newArray (1,2));

Should do the job.
Regards,
Jan
Am 24.02.2016 12:39 schrieb "Richard Mort" <[hidden email]>:

> Hi All,
>
> I can no longer get the following to work:
>
> roiManager("Select", 1);
> setKeyDown("Shift");
> roiManager("Select", 2);
> roiManager("Or");
> roiManager("Add");
>
> It only selects one of the ROI's. I seem to remember this used to be a
> problem but thought it was fixed.
>
> I'm on Linux with Fiji upto date (IJ v1.50g)
>
> Best
> R
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Richard Mort-2]

Yes, thanks that works perfectly.

Best wishes

Richard


On 24/02/16 11:55, BioVoxxel wrote:
> roiManager("select", newArray (1,2));

--
Dr Richard Mort
Research Fellow
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU

Tel: [phone]


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[Bill Christens-Barry-2]

Hi,

On MacOS 10.7.5, Java 1.6, and ImageJ 1.50h5, I find that only the first ROI becomes selected after:

    roiManager("select", newArray (1,2));

After playing with several variants of this, it seems that only the first listed ROI ("1" in this example) becomes selected. Shift- or command- selecting multiple ROIs in the ROI manager works as expected.

Bill Christens-Barry

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[Richard Mort-2]

Hi Bill,

Do you mean when you use the


setKeyDown("Shift");

Command? Sounds like this is working differently between linux and mac.

R


On 24/02/16 14:53, Bill Christens-Barry wrote:

> Hi,
>
> On MacOS 10.7.5, Java 1.6, and ImageJ 1.50h5, I find that only the first ROI becomes selected after:
>
>      roiManager("select", newArray (1,2));
>
> After playing with several variants of this, it seems that only the first listed ROI ("1" in this example) becomes selected. Shift- or command- selecting multiple ROIs in the ROI manager works as expected.
>
> Bill Christens-Barry
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Dr Richard Mort
Research Fellow
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU

Tel: [phone]


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Scotland, with registration number SC005336.

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[Michael Schmid]

Hi Bill,

sorry, I cant reproduce the problem. The following macro works well for me:

newImage("Untitled", "8-bit ramp", 512, 512, 1);
makeRectangle(57, 43, 84, 40);    //1st roi
roiManager("Add");
makeRectangle(153, 110, 75, 33);  //2nd roi
roiManager("Add");
makeRectangle(237, 162, 65, 30);  //3rd roi
roiManager("Add");
roiManager("select", newArray (1,2));
roiManager("OR");

Note that roiManager("select", newArray (1,2)) selects the 2nd and 3rd roi; the first one has index 0.

ImageJ 1.50g; Java 1.6.0_65 [64-bit]; Mac OS X 10.6.8.

Michael
________________________________________________________________
On Feb 24, 2016, at 15:53, Bill Christens-Barry wrote:

> Hi,
>
> On MacOS 10.7.5, Java 1.6, and ImageJ 1.50h5, I find that only the first ROI becomes selected after:
>
>    roiManager("select", newArray (1,2));
>
> After playing with several variants of this, it seems that only the first listed ROI ("1" in this example) becomes selected. Shift- or command- selecting multiple ROIs in the ROI manager works as expected.
>
> Bill Christens-Barry
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Martino Bosco]

Thank you. I will try the plugin you recommended.
For example, I acclude two histological  images from the same tissue block, separeted four microns (along the y axis) each other.
The overlap (using: Image J>image>colours> merge channels) shows that the two markers are expressed in differet areas but, as you can see, the overlap between the two images is incorrect, of course.

Thank you very much!

[Bill Christens-Barry-2]

Richard,

No, I encountered the problem when I tried to select more than one ROI in the ROI manager list. However, after Michael Schmid kindly responded that he didn't encounter this problem, I found that after restarting my computer the problem cleared up.

In short, the problem was local to me alone.

hth,

Bill Christens-Barry

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