How to count cells in stacks? (tried 3D object counter)

[KerL]

Hi all,

I have a stack of images that I would like to quantify. Some cells appear in more than 1 z-slice, therefore the possibility of counting a cell twice remains. Is there a macro that allows me to solve this problem, preferably one that allows me to use the regular ROI manager. I have tried using the 3D object counter plugin, but the 3D ROI manager does not allow me to look at the counted object in the original image.

[Glen MacDonald-2]

Dear Kevin,
Try the Cell Counter Plugin.
Select the ‘Show All’ option to leave a marker visible on other slices so that you can avoid double counts.  ROIs from the manager may applied to the initialized stack but cannot be created on the initialized stack.  So leave the original stack open with, or to create ROIs.


Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]







On Feb 5, 2015, at 2:04 PM, KerL <[hidden email]> wrote:

> Hi all,
>
> I have a stack of images that I would like to quantify. Some cells appear in
> more than 1 z-slice, therefore the possibility of counting a cell twice
> remains. Is there a macro that allows me to solve this problem, preferably
> one that allows me to use the regular ROI manager. I have tried using the 3D
> object counter plugin, but the 3D ROI manager does not allow me to look at
> the counted object in the original image.
>
> <http://imagej.1557.x6.nabble.com/file/n5011466/Capture.png>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/How-to-count-cells-in-stacks-tried-3D-object-counter-tp5011466.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Anda Cornea]

I just happened upon this paper today and I thought it may help you:

 http://journal.frontiersin.org/Journal/10.3389/fnana.2014.00027/full?utm_source=newsletter&utm_medium=email&utm_campaign=Neuroscience-w21-2014

Good luck!



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of KerL
Sent: Thursday, February 05, 2015 2:05 PM
To: [hidden email]
Subject: How to count cells in stacks? (tried 3D object counter)

Hi all,

I have a stack of images that I would like to quantify. Some cells appear in more than 1 z-slice, therefore the possibility of counting a cell twice remains. Is there a macro that allows me to solve this problem, preferably one that allows me to use the regular ROI manager. I have tried using the 3D object counter plugin, but the 3D ROI manager does not allow me to look at the counted object in the original image.

<http://imagej.1557.x6.nabble.com/file/n5011466/Capture.png>



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View this message in context: http://imagej.1557.x6.nabble.com/How-to-count-cells-in-stacks-tried-3D-object-counter-tp5011466.html
Sent from the ImageJ mailing list archive at Nabble.com.

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[Thomas Boudier]

Hi,

With 3DManager, you can import segmented image ("Add image") from
3DCounter and view the objects contours as overlay on the current image
("Live roi").

Thomas

On 06/02/15 06:04, KerL wrote:

> Hi all,
>
> I have a stack of images that I would like to quantify. Some cells appear in
> more than 1 z-slice, therefore the possibility of counting a cell twice
> remains. Is there a macro that allows me to solve this problem, preferably
> one that allows me to use the regular ROI manager. I have tried using the 3D
> object counter plugin, but the 3D ROI manager does not allow me to look at
> the counted object in the original image.
>
> <http://imagej.1557.x6.nabble.com/file/n5011466/Capture.png>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/How-to-count-cells-in-stacks-tried-3D-object-counter-tp5011466.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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[Mauricio Aguirre Morales]

Hi Kevin,
Try this plug in maybe it is not exactly what you were asking in the
initial e-mail but hopefully it could help somehow!
http://www.optinav.com/MeasureStack.htm

El 05/02/2015 a las 11:04 p.m., KerL escribió:

> Hi all,
>
> I have a stack of images that I would like to quantify. Some cells appear in
> more than 1 z-slice, therefore the possibility of counting a cell twice
> remains. Is there a macro that allows me to solve this problem, preferably
> one that allows me to use the regular ROI manager. I have tried using the 3D
> object counter plugin, but the 3D ROI manager does not allow me to look at
> the counted object in the original image.
>
> <http://imagej.1557.x6.nabble.com/file/n5011466/Capture.png>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/How-to-count-cells-in-stacks-tried-3D-object-counter-tp5011466.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Sincerely
Mauricio Aguirre Morales

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