Curve-Fitting All Pixels in Timelapse

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Curve-Fitting All Pixels in Timelapse

Jacob Keller-2
Dear Imagers,

is anyone aware of a way in IJ to fit each pixel in a timelapse series to a
given equation, then output a stack with those fitted curves? Seems very
parallel-izable, and pretty useful as well, say for bleach correction etc.
For my current purposes, I would just like to fit a (y=mx+b) line for each
pixel.

Thanks,

Jacob Keller

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Re: Curve-Fitting All Pixels in Timelapse

Herbie
Good day Jacob,

I see no reason why a macro couldn't do that but the main question
concerns your requirement:

"[...] then output a stack with those fitted curves?"

How do you imagine this stack?
Same temporal resolution as the original stack?

In the past we saw questions regarding pixel-wise, i.e. 1D FFT of a
stack and I even wrote a plugin that does this. So where do you see a
problem with fits?

If yes, this shouldn't pose big problems.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 04.05.18 um 04:47 schrieb Jacob Keller:

> Dear Imagers,
>
> is anyone aware of a way in IJ to fit each pixel in a timelapse series to a
> given equation, then output a stack with those fitted curves? Seems very
> parallel-izable, and pretty useful as well, say for bleach correction etc.
> For my current purposes, I would just like to fit a (y=mx+b) line for each
> pixel.
>
> Thanks,
>
> Jacob Keller
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Curve-Fitting All Pixels in Timelapse

Herbie
In reply to this post by Jacob Keller-2
Jacob,

if you want to go with a macro solution, I recommend to first transform
the stack so that its slices contain one spatial coordinate and the time
coordinate.

Then, for every slice, use "run("Image to Results")" and from this
matrix get 1D arrays as a function of time by the new table macro functions.

Then, for every slice, fit the 1D arrays with the macro fit function and
write the arrays back to the table by the new table macro functions.

Finally, for every slice, write the table with the new values back using
"run("Results to Image")".

Redo the transform.

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 04.05.18 um 04:47 schrieb Jacob Keller:

> Dear Imagers,
>
> is anyone aware of a way in IJ to fit each pixel in a timelapse series to a
> given equation, then output a stack with those fitted curves? Seems very
> parallel-izable, and pretty useful as well, say for bleach correction etc.
> For my current purposes, I would just like to fit a (y=mx+b) line for each
> pixel.
>
> Thanks,
>
> Jacob Keller
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: Curve-Fitting All Pixels in Timelapse

Michael Schmid-3
In reply to this post by Jacob Keller-2
Hi Jacob,

to start with, you can try the Stack Fitter
   http://imagejdocu.tudor.lu/doku.php?id=plugin:stack:stack_fitter:start

It is not parallelized (I did not have time for it), and its output is
not the fitted curves but a stack with the fit parameters.
In a macro, you can use Process>Math and Process>Image Calculator to
create a stack of the fit itself.
Or modify the source code for that kind of output.

Michael
________________________________________________________________
On 04/05/2018 04:47, Jacob Keller wrote:

> Dear Imagers,
>
> is anyone aware of a way in IJ to fit each pixel in a timelapse series to a
> given equation, then output a stack with those fitted curves? Seems very
> parallel-izable, and pretty useful as well, say for bleach correction etc.
> For my current purposes, I would just like to fit a (y=mx+b) line for each
> pixel.
>
> Thanks,
>
> Jacob Keller

--
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Re: Curve-Fitting All Pixels in Timelapse

Fred Damen
In reply to this post by Jacob Keller-2
Greetings,

If by 'fit each pixel in a timelapse series' you mean you would like to
process each voxel's values through the frame dimension.  I got tired of
rewriting this every time I needed, both processing and looking at trends, so
... see attached. (note: the listserv will not allow me to attach java files).

I was going to upload them to where all the other community provided plugins
are, although at present I could not find reference to how/where to upload
plugins.

Enjoy,

Fred


On Thu, May 3, 2018 9:47 pm, Jacob Keller wrote:
> Dear Imagers,
>
> is anyone aware of a way in IJ to fit each pixel in a timelapse series to a
given equation, then output a stack with those fitted curves? Seems very
parallel-izable, and pretty useful as well, say for bleach correction etc.
For my current purposes, I would just like to fit a (y=mx+b) line for each
pixel.
>
> Thanks,
>
> Jacob Keller
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html