Exporting a stack from TrackEM2

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Exporting a stack from TrackEM2

Ed Siefker
I have aligned two normalized, 16-bit images in TrackEM2.  I want to
export them as a tiff stack.

The right click menu has an "Export" option, but in that submenu
there's no option that does this.

It does have a "Make flat image..." option.  I'd be fine getting my
images as individual images and recreating the stack myself.
Unfortunately, it doesn't export 16-bit images.  It also doesn't seem
to work.

I have one image visible in the "Patches" tab. Right click, Export,
Make flat image.  I get a nice monochrome image of reasonable
intensity(Max=226).  Then I deselect that image, and make the other
one visible.  Right click, Export, Make flat image.  This image is
much, much darker. (Max=29).

My input images have identical max intensities (65332).  Why is this
happening?  What's the right way to do this?  Is this covered in the
manual somewhere? I couldn't find it.
-Ed

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Re: Exporting a stack from TrackEM2

Albert Cardona-2
Would be happy to address this question by Sept 6. Please remind me. Thanks.

Albert


> On Aug 21, 2018, at 4:50 PM, Ed Siefker <[hidden email]> wrote:
>
> I have aligned two normalized, 16-bit images in TrackEM2.  I want to
> export them as a tiff stack.
>
> The right click menu has an "Export" option, but in that submenu
> there's no option that does this.
>
> It does have a "Make flat image..." option.  I'd be fine getting my
> images as individual images and recreating the stack myself.
> Unfortunately, it doesn't export 16-bit images.  It also doesn't seem
> to work.
>
> I have one image visible in the "Patches" tab. Right click, Export,
> Make flat image.  I get a nice monochrome image of reasonable
> intensity(Max=226).  Then I deselect that image, and make the other
> one visible.  Right click, Export, Make flat image.  This image is
> much, much darker. (Max=29).
>
> My input images have identical max intensities (65332).  Why is this
> happening?  What's the right way to do this?  Is this covered in the
> manual somewhere? I couldn't find it.
> -Ed
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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