Non-Planar Unroll of Tiff Stack

[Lintfur]

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?




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[Michael Schmid]

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?

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[Lintfur]

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.  



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[Olivier Burri]

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.  



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