Standard way to perform calculations, stats, exclusions on individual pixels?

[Jacob Keller]

Dear List,

let's say I have an image stack and I want to apply various mathematical
filters of some sort or another, such as "remove (or set = 0, etc) all
pixels with standard deviation across the stack of > 20 (or 1 sigma above
mean, etc)"--can this be done easily in imageJ? Seems like a common enough
thing to do, but I can't find the right resource to tell me how to do it.

Jacob

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*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

On Sep 13, 2012, at 21:29, Jacob Keller wrote:

> Dear List,
>
> let's say I have an image stack and I want to apply various mathematical
> filters of some sort or another, such as "remove (or set = 0, etc) all
> pixels with standard deviation across the stack of > 20 (or 1 sigma above
> mean, etc)"--can this be done easily in imageJ? Seems like a common enough
> thing to do, but I can't find the right resource to tell me how to do it.
>
> Jacob
________________________________________________________________

Hi Jacob,

you can use Image>Stacks>Z Project to get the standard deviation of columns across the stack.
Same with "Average intensity", if you want to calculate (std deviation)/mean.
Then threshold it, Edit>Selection>Create Selection, transfer the selection to the stack (either using the ROI Manager or simply "Restore Selection" on the Stack.
Then do whatever operation you want to do on the selection.

For operations that are not supported by Image>Stacks>Z Project:
Image>Stacks>Reslice the stack with 90° Rotation selected, then do your desired operation on the lines of the new image (e.g. a macro or using the Fast Filters Plugin, which allows you to work on horizontal lines only). Reslice it back to the original.

Michael

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[Jacob Keller]

Hi Michael,

thanks very much for these suggestions--I am going to try to put them to
use in a macro, if possible, which should be great.

Gratefully,

Jacob

On Fri, Sep 14, 2012 at 3:35 AM, Michael Schmid <[hidden email]>wrote:

> On Sep 13, 2012, at 21:29, Jacob Keller wrote:
>
> > Dear List,
> >
> > let's say I have an image stack and I want to apply various mathematical
> > filters of some sort or another, such as "remove (or set = 0, etc) all
> > pixels with standard deviation across the stack of > 20 (or 1 sigma above
> > mean, etc)"--can this be done easily in imageJ? Seems like a common
> enough
> > thing to do, but I can't find the right resource to tell me how to do it.
> >
> > Jacob
> ________________________________________________________________
>
> Hi Jacob,
>
> you can use Image>Stacks>Z Project to get the standard deviation of
> columns across the stack.
> Same with "Average intensity", if you want to calculate (std
> deviation)/mean.
> Then threshold it, Edit>Selection>Create Selection, transfer the selection
> to the stack (either using the ROI Manager or simply "Restore Selection" on
> the Stack.
> Then do whatever operation you want to do on the selection.
>
> For operations that are not supported by Image>Stacks>Z Project:
> Image>Stacks>Reslice the stack with 90° Rotation selected, then do your
> desired operation on the lines of the new image (e.g. a macro or using the
> Fast Filters Plugin, which allows you to work on horizontal lines only).
> Reslice it back to the original.
>
> Michael
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

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