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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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