multimeasure problem

[Jeremy Adler]

When I open a stack with 32 images and run multi measure I get one line of measurements, not the 32 I expected.

The problem seems to be that ImageJ does not recognize that the image is a stack - nSlices correctly reports the number of images in the stack and I can run through the stack manually but Show Info reports a bit depth of only 1.
If the stack is broken down into images (stack to images) and reformed (images to stack) then Show Info correctly reports the depth as 32 and multi measure runs properly.

The stack came from micromanager and I am running version 1.50g

any suggestions.
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[Ramon Silva]

Hi Jeremy,

if i understood your problem, i guess that you could try PROCESS > BATCH >
MEASURE...

2016-03-06 16:41 GMT-03:00 Jeremy Adler <[hidden email]>:

>
> When I open a stack with 32 images and run multi measure I get one line of
> measurements, not the 32 I expected.
>
> The problem seems to be that ImageJ does not recognize that the image is a
> stack - nSlices correctly reports the number of images in the stack and I
> can run through the stack manually but Show Info reports a bit depth of
> only 1.
> If the stack is broken down into images (stack to images) and reformed
> (images to stack) then Show Info correctly reports the depth as 32 and
> multi measure runs properly.
>
> The stack came from micromanager and I am running version 1.50g
>
> any suggestions.
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

*Ramon Costa Silva*

*Graduando em Ciência da Computação.*

*Voluntário: Laboratório Aprendizagem Computacional e Métodos de Otimização
e Robótica - LACMOR.*

*Estagiário: Núcleo de Tecnologia da Informação - NTI.*
*Universidade Federal do Maranhão - UFMA.*

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Hi Jeremy,

If you add the line to ROI (press 't' button) and then try the
multi-measure(ROImanager/More/Multi Measure...).

This should be able to solve your problem.


Bin

On Sun, Mar 6, 2016 at 2:41 PM, Jeremy Adler <[hidden email]> wrote:

>
> When I open a stack with 32 images and run multi measure I get one line of
> measurements, not the 32 I expected.
>
> The problem seems to be that ImageJ does not recognize that the image is a
> stack - nSlices correctly reports the number of images in the stack and I
> can run through the stack manually but Show Info reports a bit depth of
> only 1.
> If the stack is broken down into images (stack to images) and reformed
> (images to stack) then Show Info correctly reports the depth as 32 and
> multi measure runs properly.
>
> The stack came from micromanager and I am running version 1.50g
>
> any suggestions.
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--


[image: --]
BIN WEI
[image: https://]about.me/jimmywei
<https://about.me/jimmywei?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>

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[Swayne, Theresa C.]

Hi Jeremy,

Is the data perhaps being read as a composite image (stack of channels with a C next to the slice selector)? MultiMeasure will only measure only the current channel of a composite image, even though other “stack” commands (e.g. Set Slice…) will interpret each channel as a “slice.”

If this is the case, you can run Stack to Hyperstack and re-configure the stack as a z stack (swap the numbers appearing in the Channels and Slices boxes).

If that doesn’t solve the problem, it might be helpful to post the problem stack somewhere.

Hope this helps,
Theresa


On Mar 6, 2016, at 2:41 PM, Jeremy Adler <[hidden email]<mailto:[hidden email]>> wrote:


When I open a stack with 32 images and run multi measure I get one line of measurements, not the 32 I expected.

The problem seems to be that ImageJ does not recognize that the image is a stack - nSlices correctly reports the number of images in the stack and I can run through the stack manually but Show Info reports a bit depth of only 1.
If the stack is broken down into images (stack to images) and reformed (images to stack) then Show Info correctly reports the depth as 32 and multi measure runs properly.

The stack came from micromanager and I am running version 1.50g

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

------------------------------------
Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: [phone]
[hidden email]<mailto:[hidden email]>


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[Jeremy Adler]

Hi Theresa,

You have hit the solution, it is not a simple stack of images - running Hyperstack to Stack solves the problem.
Oddly the original does not show a C next to the slider.

Thanks for clearing up this minor problem and thanks to Bin and Ramon for their suggestions.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Swayne, Theresa C.
Sent: den 7 mars 2016 17:03
To: [hidden email]
Subject: Re: multimeasure problem


Hi Jeremy,

Is the data perhaps being read as a composite image (stack of channels with a C next to the slice selector)? MultiMeasure will only measure only the current channel of a composite image, even though other “stack” commands (e.g. Set Slice…) will interpret each channel as a “slice.”

If this is the case, you can run Stack to Hyperstack and re-configure the stack as a z stack (swap the numbers appearing in the Channels and Slices boxes).

If that doesn’t solve the problem, it might be helpful to post the problem stack somewhere.

Hope this helps,
Theresa


On Mar 6, 2016, at 2:41 PM, Jeremy Adler <[hidden email]<mailto:[hidden email]>> wrote:


When I open a stack with 32 images and run multi measure I get one line of measurements, not the 32 I expected.

The problem seems to be that ImageJ does not recognize that the image is a stack - nSlices correctly reports the number of images in the stack and I can run through the stack manually but Show Info reports a bit depth of only 1.
If the stack is broken down into images (stack to images) and reformed (images to stack) then Show Info correctly reports the depth as 32 and multi measure runs properly.

The stack came from micromanager and I am running version 1.50g

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

------------------------------------
Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: [phone]
[hidden email]<mailto:[hidden email]>


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