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]>
Sent: Wednesday, August 6, 2025 1:48 PM
To: [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/
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]>
http://nyulmc.org/micros 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]>
>
Sent: Wednesday, August 6, 2025 3:24 PM
To: [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]>
<[email protected] <mailto:[email protected]> >
[email protected] <mailto:[email protected]>
<[email protected] <mailto:[email protected]> >*
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