Have I lost my mind?

[Philip Ershler]

I have an file from a Zeiss Confocal (.lsm). I open it and it comes in as a 2 channel hyperstack. I use the Hyperstacks->Reduce Dimensionality to extract the channel of interest. Next I define an ROI and select it in the ROI manager. Then I choose Stacks->Plot Z Axis Profile and I get essentially a blank graph. If I click the Live button on the graph I get a blue line which will move back and forth on the blank graph as I scroll back and forth through the stack. What am I doing wrong? BTW, I am running ImageJ64 1.49n on OS X 10.1.1.

Thanks, Phil
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[Jeff Spector-2]

HI,
 I'm using imageJ 1.49m on  OS X10.8.5. I have noticed that the "plot z
axis profile" only seems to work if the image knows the  "time" between
frames. If I go to image->properties and it says 0 sec intervals then I
always get a blank graph. Perhaps this is your issue?  It would be nice if
it has a 0 interval if it would then plot it simply by "frames" instead of
giving an empty graph...
-Jeff

On Tue, Jan 6, 2015 at 4:27 PM, Philip Ershler <[hidden email]>
wrote:

> I have an file from a Zeiss Confocal (.lsm). I open it and it comes in as
> a 2 channel hyperstack. I use the Hyperstacks->Reduce Dimensionality to
> extract the channel of interest. Next I define an ROI and select it in the
> ROI manager. Then I choose Stacks->Plot Z Axis Profile and I get
> essentially a blank graph. If I click the Live button on the graph I get a
> blue line which will move back and forth on the blank graph as I scroll
> back and forth through the stack. What am I doing wrong? BTW, I am running
> ImageJ64 1.49n on OS X 10.1.1.
>
> Thanks, Phil
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Philip Ershler]

Thank you very much. That does the trick,

Phil

> On Jan 6, 2015, at 3:17 PM, Jeff Spector <[hidden email]> wrote:
>
> HI,
> I'm using imageJ 1.49m on  OS X10.8.5. I have noticed that the "plot z
> axis profile" only seems to work if the image knows the  "time" between
> frames. If I go to image->properties and it says 0 sec intervals then I
> always get a blank graph. Perhaps this is your issue?  It would be nice if
> it has a 0 interval if it would then plot it simply by "frames" instead of
> giving an empty graph...
> -Jeff
>
> On Tue, Jan 6, 2015 at 4:27 PM, Philip Ershler <[hidden email]>
> wrote:
>
>> I have an file from a Zeiss Confocal (.lsm). I open it and it comes in as
>> a 2 channel hyperstack. I use the Hyperstacks->Reduce Dimensionality to
>> extract the channel of interest. Next I define an ROI and select it in the
>> ROI manager. Then I choose Stacks->Plot Z Axis Profile and I get
>> essentially a blank graph. If I click the Live button on the graph I get a
>> blue line which will move back and forth on the blank graph as I scroll
>> back and forth through the stack. What am I doing wrong? BTW, I am running
>> ImageJ64 1.49n on OS X 10.1.1.
>>
>> Thanks, Phil
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Rasband, Wayne (NIH/NIMH) [E]]

On Jan 6, 2015, at 4:27 PM, Philip Ershler <[hidden email]> wrote:
>
> I have an file from a Zeiss Confocal (.lsm). I open it and it comes in as a 2 channel hyperstack. I use the Hyperstacks->Reduce Dimensionality to extract the channel of interest. Next I define an ROI and select it in the ROI manager. Then I choose Stacks->Plot Z Axis Profile and I get essentially a blank graph. If I click the Live button on the graph I get a blue line which will move back and forth on the blank graph as I scroll back and forth through the stack. What am I doing wrong? BTW, I am running ImageJ64 1.49n on OS X 10.1.1.

The latest ImageJ daily build (1.49o14) fixes a bug that caused Image>Stacks>Plot Z-axis Profile to create a blank graph when the frame interval was 0.

-wayne

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[Philip Ershler]

Thanks Wayne!

> On Jan 6, 2015, at 5:12 PM, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]> wrote:
>
>> On Jan 6, 2015, at 4:27 PM, Philip Ershler <[hidden email]> wrote:
>>
>> I have an file from a Zeiss Confocal (.lsm). I open it and it comes in as a 2 channel hyperstack. I use the Hyperstacks->Reduce Dimensionality to extract the channel of interest. Next I define an ROI and select it in the ROI manager. Then I choose Stacks->Plot Z Axis Profile and I get essentially a blank graph. If I click the Live button on the graph I get a blue line which will move back and forth on the blank graph as I scroll back and forth through the stack. What am I doing wrong? BTW, I am running ImageJ64 1.49n on OS X 10.1.1.
>
> The latest ImageJ daily build (1.49o14) fixes a bug that caused Image>Stacks>Plot Z-axis Profile to create a blank graph when the frame interval was 0.
>
> -wayne
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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