Dear colleague,
good to hear that you've found a solution.
However, it doesn't differ that much from the suggested one as it is
based on cross-correlations as well.
Regards
Herbie
:::::::::::::::::::::::::::::::::::::::::::::
Am 07.08.25 um 23:08 schrieb AR.M. AlHinnawi:
Thank you all (Michael, Jeff, Herbie) for proposing solutions.
The problem is solved.
After research, I came across a plugin "Template Matching Align Slices
in Stack". It is quite useful and has adequately solved the problem. It
asks the user to opn a stack and draw a rectangle confining the object
of interest, then it searches all the remaining slices to spot similar
"matches" and align them in the same rectangular coordinates. Here are
the links:
https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin?authuser=0#h.xnfrro37ykki
<https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin?authuser=0#h.xnfrro37ykki>
https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin/tuto1?authuser=0
<https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin/tuto1?authuser=0>
Additionally, I came across a plugin called "TurboReg", but I didn't
explore it extensively.
I am sharing the above solution/s in case you may be interested.
It would be an honor if you wish to launch a research collaboration.
Thank you again.
Kind Regards
Abdel-Razzak
/*Abdel-Razzak Al-Hinnawi, (Full Prof.) (B.Sc., M.Sc., Ph.D. Medical
Imaging Sciences & Digital Image Processing & Biomedical Engineering)*/
/*Faculty of Allied Medical Sciences*/
/*ISRA University*/
/*11622, Amman, *//*JORDAN*/
/*phone: +962 780515199*/
/*e-mail: *[email protected]
<mailto:[email protected]>[email protected]
<mailto:[email protected]>_/
On Thu, 7 Aug 2025 at 11:06, Gluender <[email protected]
<mailto:[email protected]>> wrote:
Greetings Jeff!
"cross-correlate two frames"
That's exactly what I did to obtain the result shown in my earlier
reply.
Regards
Herbie
:::::::::::::::::::::::::::::::::::::::::
Am 07.08.25 um 02:22 schrieb Jeff Stokes:
> Prof. Al-Hinnawi,
>
> It looks like you're trying to register multiple frames
containing a fairly noisy feature, in order to produce a lower-noise
final image. The obvious thought is to cross-correlate two frames of
find the appropriate x-y shift needed to add them together. You have
to be mindful of the edges of the frames; it's best if the feature
is well surrounded by zeros or a constant value. (When I've done
this, I pad the frame with zeros out to image size 3+ times the
maximum width of the feature.) Given the very noisy nature of each
individual image, the cross correlation might not indicate the true
shift needed accurately enough. Perhaps smoothing (low-pass filter)
each frame first before performing the autocorrelations will yield
more nearly correct shifts. Then add the unfiltered frames together
using the shifts thus determined. These processes are all
mathematical, i.e. can be done automatically with code. If they
can't be done in ImageJ or ImageJ macros, they are easily done in
Matlab, with the final images saved for viewing with ImageJ.
>
> As Michael suggests below, tabulating the center of the
object in each slice is promising. It may be that the mathematical
centroid of the object in the image will give you its 'position' as
well or better than a manual method and of course will be faster.
Again, if not ImageJ, then Matlab, Python, etc.
> I don't claim my ideas above are better than or as good as
the registration tools Michael pointed you to below. (I have not
explored them.)
> Best of luck.
> Jeff Stokes
> San Diego, USA
>
>
> -----Original Message-----
> From: Cammer, Michael
<[email protected]
<mailto:[email protected]>>
> Sent: Wednesday, August 6, 2025 1:48 PM
> To: [email protected] <mailto:[email protected]>
> Subject: Re: Registering objects to a rectangular area
>
> If you are willing to click on the center of the object of
interest in each of the 400 slices, then it is simple to write a
macro that with each click, the XY coordinates are saved and the
macro progresses to the next slice automatically, and at the end all
images are repositioned to center on the XY locations.
>
> Or you could try one of the registration tools such as
https://bigwww.epfl.ch/thevenaz/stackreg/
<https://bigwww.epfl.ch/thevenaz/stackreg/>
>
> Cheers-
>
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, New York, NY 10016
> Office: RB (formerly Skirball) 4-102 -- call if door is locked
(phone near elevators)
> Office: 646-501-0567 Cell (voice only, not text): 914-309-3270
[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> http://nyulmc.org/micros
<http://nyulmc.org/micros> http://microscopynotes.com/
<http://microscopynotes.com/> Scheduling the time you want is far
more reliable by phone call. Why not provide your phone number?
>
>
>
>
> -----Original Message-----
> From: AR.M. AlHinnawi <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>> >
> Sent: Wednesday, August 6, 2025 3:24 PM
> To: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
> Subject: Registering objects to a rectangular area
>
> [EXTERNAL]
>
> Dear ImageJ
>
> I have a stack of 400 images. They all show the same objects but
at different settings, resulting in irregular displacements.
>
> The interested objects can be confined in a rectangular area in
the first slice (a rectangular area that can be drawn manually).
>
> I aim to make similar objects in all remaining slices to fit in
the rectangle. For example, I attached the first and last slice.
>
> It doesn't seem easy.
>
> Please, can you advise?
>
> Thank you
>
> *Abdel-Razzak Al-Hinnawi, (Full Prof.) (B.Sc., M.Sc., Ph.D.
Medical Imaging Sciences & Digital Image Processing & Biomedical
Engineering)* *Faculty of Allied Medical Sciences* *ISRA University*
*11622, Amman, **JORDAN*
> *phone: +962 780515199*
> *e-mail: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>> >
> [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>> >*
>
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