Herbie, Thanks for your results and good advice.
In speculating that the low-pass prefiltering might help, I was allowing for the possibility it might be irrelevant. Jeff -----Original Message----- From: Gluender <[email protected]> Sent: Friday, August 8, 2025 1:06 AM To: [email protected] Subject: Re: Registering objects to a rectangular area Yes Jeff, meanwhile I did a more thorough investigation using the two sample slices provided by the OP. It turns out that e.g. binarization or smoothing of the slice images has little to no effect on the shift parameters. Here are the shifts in pixels that I get when starting with 512x512 stacks: X Y original: 18 88 gauss r=8: 16 88 binarized: 17 87 Consequently, there appears to be no need for pre-processing the slice images. An ImageJ-macro that processes whole stacks is only about 20 code lines long and runs really fast, even for 1024x1024 slice images. Best Herbie ::::::::::::::::::::::::::::::::::::::::: Am 08.08.25 um 05:28 schrieb Jeff Stokes: > Herbie, > > Looks like it worked pretty well, from the images you sent. > > Jeff > > > -----Original Message----- > From: Gluender <[email protected]> > Sent: Thursday, August 7, 2025 1:02 AM > To: [email protected] > Subject: Re: Registering objects to a rectangular area > > 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]> >> 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]> >> >* >> >> -- >> ImageJ mailing list: >> https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!MX >> faZl3l!em9oCMotdAaa5j-SbsTMB-ZWu34WIAd_fy6C67JpL9IgdWpDzuwUu-MP7Yr2sN >> czfZBafYBV6blHF0a6lRQew8i9qjp6B_U$ >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. 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