How to align images manually and merge them into a multi-channel composite image?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

How to align images manually and merge them into a multi-channel composite image?

Jiseok
Hi,

I have 4 images taken in 4 different days.

I want to manually align the 4 images, because there are small shifts and
movements each time I image.

Then I want to merge the 4 aligned images into a 4-channel composite image,
where each day image corresponds to a different channel. For example,
day1=R, day2=G, day3=B, day4=gray.

Can anyone kindly give me any advice how I can do this?

I don’t think I can use any automatic method for aligning, since the images
are quite complicated and need human eye inspection to decide matching
points.

I attached the 4 images, if anyone wants to see what they’re like.

Thank you very much!

Day1
<http://imagej.1557.x6.nabble.com/file/t381950/day1.jpg>

Day2
<http://imagej.1557.x6.nabble.com/file/t381950/day2.jpg>

Day3
<http://imagej.1557.x6.nabble.com/file/t381950/day3.jpg>

Day4
<http://imagej.1557.x6.nabble.com/file/t381950/day4.jpg>



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

G. Esteban Fernandez
Hi!

You can create a composite image from your unaligned images, then
copy-paste one channel. After pasting, you can click and drag to whatever
arbitrary position you want. Make sure you activate Composite mode in
Channels Tool (Ctrl-Shift-Z) so you can see the other channels while you
move the active channel.

-Esteban


On Tue, May 22, 2018, 1:23 PM Jiseok <[hidden email]> wrote:

> Hi,
>
> I have 4 images taken in 4 different days.
>
> I want to manually align the 4 images, because there are small shifts and
> movements each time I image.
>
> Then I want to merge the 4 aligned images into a 4-channel composite image,
> where each day image corresponds to a different channel. For example,
> day1=R, day2=G, day3=B, day4=gray.
>
> Can anyone kindly give me any advice how I can do this?
>
> I don’t think I can use any automatic method for aligning, since the images
> are quite complicated and need human eye inspection to decide matching
> points.
>
> I attached the 4 images, if anyone wants to see what they’re like.
>
> Thank you very much!
>
> Day1
> <http://imagej.1557.x6.nabble.com/file/t381950/day1.jpg>
>
> Day2
> <http://imagej.1557.x6.nabble.com/file/t381950/day2.jpg>
>
> Day3
> <http://imagej.1557.x6.nabble.com/file/t381950/day3.jpg>
>
> Day4
> <http://imagej.1557.x6.nabble.com/file/t381950/day4.jpg>
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

Kenneth Sloan-3
In reply to this post by Jiseok
I recommend Plugins->Registration->Align Image by Roi.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On 22 May 2018, at 15:19 , Jiseok <[hidden email]> wrote:
>
> Hi,
>
> I have 4 images taken in 4 different days.
>
> I want to manually align the 4 images, because there are small shifts and
> movements each time I image.
>
> Then I want to merge the 4 aligned images into a 4-channel composite image,
> where each day image corresponds to a different channel. For example,
> day1=R, day2=G, day3=B, day4=gray.
>
> Can anyone kindly give me any advice how I can do this?
>
> I don’t think I can use any automatic method for aligning, since the images
> are quite complicated and need human eye inspection to decide matching
> points.
>
> I attached the 4 images, if anyone wants to see what they’re like.
>
> Thank you very much!
>
> Day1
> <http://imagej.1557.x6.nabble.com/file/t381950/day1.jpg>
>
> Day2
> <http://imagej.1557.x6.nabble.com/file/t381950/day2.jpg>
>
> Day3
> <http://imagej.1557.x6.nabble.com/file/t381950/day3.jpg>
>
> Day4
> <http://imagej.1557.x6.nabble.com/file/t381950/day4.jpg>
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

Stephan.Preibisch@mdc-berlin.de
In reply to this post by Jiseok
Hi,

This can be automatically aligned using the Descriptor-based series registration … check the result here:

http://preibischlab.mdc-berlin.de/download/aligned.zip

Using these parameters (for longer time series use regularization with a rigid model)

http://preibischlab.mdc-berlin.de/download/params.zip

All the best,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
Robert-Rössle-Str. 10
13125 Berlin

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de
twitter: http://twitter.com/preibischs

On May 22, 2018, at 10:19 PM, Jiseok <[hidden email]<mailto:[hidden email]>> wrote:

Hi,

I have 4 images taken in 4 different days.

I want to manually align the 4 images, because there are small shifts and
movements each time I image.

Then I want to merge the 4 aligned images into a 4-channel composite image,
where each day image corresponds to a different channel. For example,
day1=R, day2=G, day3=B, day4=gray.

Can anyone kindly give me any advice how I can do this?

I don’t think I can use any automatic method for aligning, since the images
are quite complicated and need human eye inspection to decide matching
points.

I attached the 4 images, if anyone wants to see what they’re like.

Thank you very much!

Day1
<http://imagej.1557.x6.nabble.com/file/t381950/day1.jpg>

Day2
<http://imagej.1557.x6.nabble.com/file/t381950/day2.jpg>

Day3
<http://imagej.1557.x6.nabble.com/file/t381950/day3.jpg>

Day4
<http://imagej.1557.x6.nabble.com/file/t381950/day4.jpg>



--
Sent from: http://imagej.1557.x6.nabble.com/

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


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

Jiseok
In reply to this post by G. Esteban Fernandez
Thanks a lot, this was super helpful!
By the way, I can only move the channel image in X-Y direction, but I cannot
rotate it to align, right?



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

Michael Elbaum
You might also try the nice manual alignment tool in TomoJ.
http://www.cmib.fr/en/download/softwares/TomoJ.html
Michael


________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Jiseok [[hidden email]]
Sent: Wednesday, May 23, 2018 20:52
To: [hidden email]
Subject: Re: How to align images manually and merge them into a multi-channel composite image?

Thanks a lot, this was super helpful!
By the way, I can only move the channel image in X-Y direction, but I cannot
rotate it to align, right?



--
Sent from: http://imagej.1557.x6.nabble.com/

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

Kenneth Sloan-3
In reply to this post by Jiseok
With which tool?

The one I recommended (align with line ROI) does translation, uniform scale, and rotation.

Most of the ones I saw suggested will offer a choice of possible transformations, usually including:

*translation only
*translation and rotation
*translation, rotation, and uniform scaling
*and more...up to arbitrary rubber-sheet warping

I had a rather nice (but crude) version that allows you to manually specify 1, 2, or 3 landmark pairs, and
then selects the type of transformation based on your choice.  I was about to make it bullet-proof, when
I discovered "align with line ROI", which does everything I need (short of automatic registration) at the moment.

The major problem I have in automatic registration is that my images tend to be multi-modal, meaning that the shapes and the
intensity values are radically different from image to image.  Things like SIFT work great...until they don't.

Since I'm lazy, and I only write the code, and not use it - I'm not unhappy pushing the task off on the poor image reader.

My current guideline is that I will use auto methods if:

a) the imaging is fairly consistent, with the major difference being the position of the camera wrt the scene, or
b) there are more than 20 images in a given stack to be aligned (in these cases, I try to process away the
   imaging differences so that the registration plugin can handle it.

Otherwise: my current standard is "align with line ROI".  Most of my "customers" spend a long time examining
the images, so the extra time to locate 2 landmarks (in each image) is not onerous.  Your milage may vary.



--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On 23 May 2018, at 12:52 , Jiseok <[hidden email]> wrote:
>
> Thanks a lot, this was super helpful!
> By the way, I can only move the channel image in X-Y direction, but I cannot
> rotate it to align, right?
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: How to align images manually and merge them into a multi-channel composite image?

G. Esteban Fernandez
In reply to this post by Jiseok
Right, with the basic method I suggested you cannot manually rotate.
You'd have to copy the channel out to a different window with Image >
Duplicate (Ctrl-Shift-D), then rotate it (Image > Transform > Rotate)
and paste it back into the composite image.  You'd have to do multiple
iterations of this duplicate-rotate-paste at different angles.

-Esteban

On Wed, May 23, 2018 at 10:52 AM, Jiseok <[hidden email]> wrote:

> Thanks a lot, this was super helpful!
> By the way, I can only move the channel image in X-Y direction, but I cannot
> rotate it to align, right?
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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