Manual registration of two images

[David Strachan]

Hi,

I am trying to find a plugin to allow registration of two images (RGB) but to do this manually. The two images are serial sections with different staining and so it is not that easy to see the common points in each image. I was hoping to find something that could show one image with transparent background overlaid on the other image and then allow me to manually move in x and y dir and rotation until I have them overlaid.

There seems to be lots of options preinstalled in FIJI (all with no instructions so although it may do exactly what I want I don't know) I have tried faffing around with these but time is of the essence, I need the analysis results by this Friday.

There was one plugin that sound the most promising in that I draw a line in one image between two points and then draw a line in the other image between the same tow landmark points and then it came up with loads of errors as It was then trying to do something automatically and the images are not similar enough.

Does anyone know if a macro where I can either interactively move one image over another to align or alternatively select 2 points in one image then select the matching two points in the other image and then get these images to orientate themselves to be the same.

I do not want the image to be overlaid permanently as I want to use the staining on one mage as a mask for subsequent measurement on the second image.


David Strachan

Beatson Institute for Cancer Research
Garscube Estate,
Switchback Road,
Glasgow, G61 1BD
Scotland
U.K.

Tel [phone]


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[Christian Goosmann-2]

Dear David
you could use the TrakEM 2 plugin, generate a project with 2 z-planes,
import one of your images in each plane. It is a bit of a learning curve
but doable till Friday, there are good tutorials. You can set the first
plane so it blends into your second plane (control the transparency in
'Layers' tab) and then manually shift the image in the second plane
around until it fits. From the project you can export a stack of both
images with image two translated/rotated in the step before. I can't
tell you all controls, but most things in TrakEM 2 work by using the
context menus you get with right-click. TrakEM2 is included in FIJI.
Hth
Christian

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: [phone]

David Strachan wrote:

> Hi,
>
> I am trying to find a plugin to allow registration of two images (RGB) but to do this manually. The two images are serial sections with different staining and so it is not that easy to see the common points in each image. I was hoping to find something that could show one image with transparent background overlaid on the other image and then allow me to manually move in x and y dir and rotation until I have them overlaid.
>
> There seems to be lots of options preinstalled in FIJI (all with no instructions so although it may do exactly what I want I don't know) I have tried faffing around with these but time is of the essence, I need the analysis results by this Friday.
>
> There was one plugin that sound the most promising in that I draw a line in one image between two points and then draw a line in the other image between the same tow landmark points and then it came up with loads of errors as It was then trying to do something automatically and the images are not similar enough.
>
> Does anyone know if a macro where I can either interactively move one image over another to align or alternatively select 2 points in one image then select the matching two points in the other image and then get these images to orientate themselves to be the same.
>
> I do not want the image to be overlaid permanently as I want to use the staining on one mage as a mask for subsequent measurement on the second image.
>
>
> David Strachan
>
> Beatson Institute for Cancer Research
> Garscube Estate,
> Switchback Road,
> Glasgow, G61 1BD
> Scotland
> U.K.
>
> Tel [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[CARL Philippe (LBP)]

Dear David,
In order to make a manual registration, just make a color channel
(Image->Color->Merge_Channels...) where you put one picture in red and the
other in green.
Then you select all (Ctrl + A), copy one channel (Ctrl + C), paste it (Ctrl
+ V) and then you can drag a channel with the arrow keys with respect to the
other one.
It is straight forward and working quite well...
Nevertheless you have only a precision of +/- 1 pixel and you can't go below
with this method.
So now I use either the StackReg or JavaSIFT plugins and they are making the
job much easier...
My best regards,
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de David
Strachan
Envoyé : mercredi 3 décembre 2014 14:24
À : [hidden email]
Objet : Manual registration of two images

Hi,

I am trying to find a plugin to allow registration of two images (RGB) but
to do this manually. The two images are serial sections with different
staining and so it is not that easy to see the common points in each image.
I was hoping to find something that could show one image with transparent
background overlaid on the other image and then allow me to manually move in
x and y dir and rotation until I have them overlaid.

There seems to be lots of options preinstalled in FIJI (all with no
instructions so although it may do exactly what I want I don't know) I have
tried faffing around with these but time is of the essence, I need the
analysis results by this Friday.

There was one plugin that sound the most promising in that I draw a line in
one image between two points and then draw a line in the other image between
the same tow landmark points and then it came up with loads of errors as It
was then trying to do something automatically and the images are not similar
enough.

Does anyone know if a macro where I can either interactively move one image
over another to align or alternatively select 2 points in one image then
select the matching two points in the other image and then get these images
to orientate themselves to be the same.

I do not want the image to be overlaid permanently as I want to use the
staining on one mage as a mask for subsequent measurement on the second
image.


David Strachan

Beatson Institute for Cancer Research
Garscube Estate,
Switchback Road,
Glasgow, G61 1BD
Scotland
U.K.

Tel [phone]


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[Malgorzata Swider]

Hi David,
you can try a "Template Matching'" plugin.
it allows you to select a rectangle region as a landmark on a reference
image.
sometimes it works pretty well, depending on images.
Best,
Gosia

------------------------------------------------
Malgorzata Swider, Ph.D.
Research Specialist
Scheie Eye Institute, University of Pennsylvania
51 North 39th St, Philadelphia PA 19104, USA
Ph: [phone]

--------------------------------------------------
From: "David Strachan" <[hidden email]>
Sent: Wednesday, December 03, 2014 8:24 AM
To: <[hidden email]>
Subject: Manual registration of two images

> Hi,
>
> I am trying to find a plugin to allow registration of two images (RGB) but
> to do this manually. The two images are serial sections with different
> staining and so it is not that easy to see the common points in each
> image. I was hoping to find something that could show one image with
> transparent background overlaid on the other image and then allow me to
> manually move in x and y dir and rotation until I have them overlaid.
>
> There seems to be lots of options preinstalled in FIJI (all with no
> instructions so although it may do exactly what I want I don't know) I
> have tried faffing around with these but time is of the essence, I need
> the analysis results by this Friday.
>
> There was one plugin that sound the most promising in that I draw a line
> in one image between two points and then draw a line in the other image
> between the same tow landmark points and then it came up with loads of
> errors as It was then trying to do something automatically and the images
> are not similar enough.
>
> Does anyone know if a macro where I can either interactively move one
> image over another to align or alternatively select 2 points in one image
> then select the matching two points in the other image and then get these
> images to orientate themselves to be the same.
>
> I do not want the image to be overlaid permanently as I want to use the
> staining on one mage as a mask for subsequent measurement on the second
> image.
>
>
> David Strachan
>
> Beatson Institute for Cancer Research
> Garscube Estate,
> Switchback Road,
> Glasgow, G61 1BD
> Scotland
> U.K.
>
> Tel [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html 

--
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[Saalfeld, Stephan]

Hi Philippe, Christian and David,

with the copy option in composite images, you would not be able to
rotate.

Christian already mentioned TrakEM2.  Instructions are here:

http://www.ini.uzh.ch/~acardona/trakem2_manual.html#layer_overlays

http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch

Another, much simpler option using manually set point correspondences is
this plugin:

http://fiji.sc/Landmark_Correspondences

You just have both channels open as independent images, mark
corresponding points with the multiple-point selection tool (in
corresponding order, i.e. 1 corresponds to 1, 2 corresponds to 2, ...),
call the plugin to transform one image such that it matches the other
with your choice of transformation.  I bet you'll figure it out from the
available instructions.

Best,
Stephan



On Wed, 2014-12-03 at 15:15 +0100, Philippe CARL wrote:

> Dear David,
> In order to make a manual registration, just make a color channel
> (Image->Color->Merge_Channels...) where you put one picture in red and the
> other in green.
> Then you select all (Ctrl + A), copy one channel (Ctrl + C), paste it (Ctrl
> + V) and then you can drag a channel with the arrow keys with respect to the
> other one.
> It is straight forward and working quite well...
> Nevertheless you have only a precision of +/- 1 pixel and you can't go below
> with this method.
> So now I use either the StackReg or JavaSIFT plugins and they are making the
> job much easier...
> My best regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Biophotonique et Pharmacologie
> UMR 7213 CNRS - Université de Strasbourg
> Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : [phone]
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de David
> Strachan
> Envoyé : mercredi 3 décembre 2014 14:24
> À : [hidden email]
> Objet : Manual registration of two images
>
> Hi,
>
> I am trying to find a plugin to allow registration of two images (RGB) but
> to do this manually. The two images are serial sections with different
> staining and so it is not that easy to see the common points in each image.
> I was hoping to find something that could show one image with transparent
> background overlaid on the other image and then allow me to manually move in
> x and y dir and rotation until I have them overlaid.
>
> There seems to be lots of options preinstalled in FIJI (all with no
> instructions so although it may do exactly what I want I don't know) I have
> tried faffing around with these but time is of the essence, I need the
> analysis results by this Friday.
>
> There was one plugin that sound the most promising in that I draw a line in
> one image between two points and then draw a line in the other image between
> the same tow landmark points and then it came up with loads of errors as It
> was then trying to do something automatically and the images are not similar
> enough.
>
> Does anyone know if a macro where I can either interactively move one image
> over another to align or alternatively select 2 points in one image then
> select the matching two points in the other image and then get these images
> to orientate themselves to be the same.
>
> I do not want the image to be overlaid permanently as I want to use the
> staining on one mage as a mask for subsequent measurement on the second
> image.
>
>
> David Strachan
>
> Beatson Institute for Cancer Research
> Garscube Estate,
> Switchback Road,
> Glasgow, G61 1BD
> Scotland
> U.K.
>
> Tel [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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