How to not associate ROI with specific image in a z stack file?

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How to not associate ROI with specific image in a z stack file?

Jiseok
Hi, I opened a z-stack image (ZEISS .czi file) in imageJ, and drew ROIs for
one of the z plane, and saved. Then I wanted to open the saved ROIs in
another z stack image, but the ROIs are associated with specific z plane
number, and whenever I select the ROIs it will keep going to the wrong z
plane. How do I fix this?

Thank you.



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Re: How to not associate ROI with specific image in a z stack file?

fabrice senger-2
Hi ! for each ROI you have 3 numbers. First number is Z or T. Suppress this
one ( chosse ROI Properties and suppress) next the ROI is no longer
associated with specific Z or T.

2018-03-09 23:26 GMT+01:00 Jiseok <[hidden email]>:

> Hi, I opened a z-stack image (ZEISS .czi file) in imageJ, and drew ROIs for
> one of the z plane, and saved. Then I wanted to open the saved ROIs in
> another z stack image, but the ROIs are associated with specific z plane
> number, and whenever I select the ROIs it will keep going to the wrong z
> plane. How do I fix this?
>
> Thank you.
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: How to not associate ROI with specific image in a z stack file?

Kenneth Sloan-3
I have a related (I think) question.

I have a Java plugin that uses a class that extends ImageStack, and a class that extends StackWindow, to manage the display of a stack, monitor cursor movement, display overlays, etc.

As written, the Overlay is applied to every slice in the stack.  Up until now, that has been the desired
behavior.  But...I now feel the need to apply the Overlay to only one slice in the stack.

In previous plugins, I have done this by re-drawing the Overlay every time the displayed slice changes.
Before I do that here, I thought I'd ask - is there an easy way to attach an Roi (added to an overlay) so that that Roi is displayed ONLY when a particular slice is displayed?

In particular, I have an ImageRoi used to color code an image on a pixel-by-pixel basis.  I'd like to restrict that effect to a single slice in the stack.  Right now, I simply add the ImageRoi to a single Overlay which applies to the entire stack.

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Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On 10 Mar 2018, at 04:35 , Fabrice Senger <[hidden email]> wrote:
>
> Hi ! for each ROI you have 3 numbers. First number is Z or T. Suppress this
> one ( chosse ROI Properties and suppress) next the ROI is no longer
> associated with specific Z or T.
>
> 2018-03-09 23:26 GMT+01:00 Jiseok <[hidden email]>:
>
>> Hi, I opened a z-stack image (ZEISS .czi file) in imageJ, and drew ROIs for
>> one of the z plane, and saved. Then I wanted to open the saved ROIs in
>> another z stack image, but the ROIs are associated with specific z plane
>> number, and whenever I select the ROIs it will keep going to the wrong z
>> plane. How do I fix this?
>>
>> Thank you.
>>
>>
>>
>> --
>> 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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html