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__;!!MXfaZl3l!em9oCMotdAaa5j-SbsTMB-ZWu34WIAd_fy6C67JpL9IgdWpDzuwUu-MP7Yr2sNczfZBafYBV6blHF0a6lRQew8i9qjp6B_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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