The best way to explain what I want to do is to imagine that my object in
question is a 100 page stack of printer paper, rolled in to a cylinder. If I take that rolled up cylinder of paper and then unroll it and lay it flat, and each paper represented an image/slice, how would I get to that point of having an image sequence of each paper representing a slice? -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi anonymous,
you could try something like the following: - If necessary, reslice [1] the stack such that the axis runs in z direction. - If necessary, crop to have the axis in the center - Use a plugin to convert from polar to Cartesian coordinates. I fear that the Polar Transformer [2] can do only single slices, not stacks, so you would need a macro to do it slice by slice and combine the slices into a stack. Maybe one could modify it to work with stacks, or there is a similar plugin that works with stacks? - Reslice the stack to get the 'paper sheets' Michael [1] https://imagej.nih.gov/ij/docs/guide/146-28.html#toc-Subsubsection-28.6.9 [2] https://imagej.nih.gov/ij/plugins/download/Polar_Transformer.java ________________________________________________________________ On 13/12/2017 19:03, Lintfur wrote: > The best way to explain what I want to do is to imagine that my object in > question is a 100 page stack of printer paper, rolled in to a cylinder. If > I take that rolled up cylinder of paper and then unroll it and lay it flat, > and each paper represented an image/slice, how would I get to that point of > having an image sequence of each paper representing a slice? -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
So I did something similar to what you are talking about and got it to
"work". However, it took 5 minutes to do one slice of a 300 slice stack. Granted, the time would decrease every time that I iterated to the next slice, as I started with the largest circumference, but this is unacceptable for what we're doing. The huge amount of time must be coming from the fact that ImageJ is having to open a 1.6 MB file every time - to get the left and right sides of the circle as a column of pixels. There must be a formula that can do the same thing but without having to open an image every time, I'm guessing. -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Lintfur,
Would it be possible to have an example dataset to test out and help you further? I have a macro that creates spirals that you can offset as needed and the reslicing is rather fast. But I don't understand what you mean by "ImageJ is having to open a file every time" so I'd need a dataset to get an example of your data structure... Best Oli -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lintfur Sent: Tuesday, December 19, 2017 3:19 PM To: [hidden email] Subject: Re: Non-Planar Unroll of Tiff Stack So I did something similar to what you are talking about and got it to "work". However, it took 5 minutes to do one slice of a 300 slice stack. Granted, the time would decrease every time that I iterated to the next slice, as I started with the largest circumference, but this is unacceptable for what we're doing. The huge amount of time must be coming from the fact that ImageJ is having to open a 1.6 MB file every time - to get the left and right sides of the circle as a column of pixels. There must be a formula that can do the same thing but without having to open an image every time, I'm guessing. -- 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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