redirect sampling

[Glen MacDonald-2]

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An 8-bit mask was created from a 16-bit image by Find Maxima with output = Segmented particles.   When this mask used in a macro to redirect Analyze Particles to the original image, an error message states the "source image is not a valid choice for "Redirect to:".  But, if I manually set measurements to target redirect sampling to the original image and then run Analyze Particles, it works.
I even set the macro to delete all intermediate images, so only the mask and target remain.  

I could work around by multiplying the mask and the source image, but that is slower.  
Can someone offer some insight to  my problem?

Thanks
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]

[Cameron Nowell-2]

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Hi Glen,

That's a bit weird and should work fine. I just had a go myself with the two images you can copy from here

https://dl.dropboxusercontent.com/u/11163658/analyse%20particles%20test.zip

using this code and it worked fine

selectWindow("Nuclei.tif");
run("Find Maxima...", "noise=400 output=[Segmented Particles] exclude");
run("Set Measurements...", "area mean display redirect=Cell.tif decimal=3");
selectWindow("Nuclei.tif Segmented");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing display summarize");

I am running the current up to date version of Fiji if that makes any difference

Cheers

Cam



Cameron J. Nowell
Centre for Dynamic Imaging
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville, Victoria 3052
Australia

Phone: [phone]
Mobile: [phone]
Fax: [phone]

Facility Website
LinkedIn Profile



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Glen MacDonald
Sent: Tuesday, 23 April 2013 8:14 AM
To: [hidden email]
Subject: redirect sampling

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To join, leave or search the confocal microscopy listserv, go to:
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*****

An 8-bit mask was created from a 16-bit image by Find Maxima with output = Segmented particles.   When this mask used in a macro to redirect Analyze Particles to the original image, an error message states the "source image is not a valid choice for "Redirect to:".  But, if I manually set measurements to target redirect sampling to the original image and then run Analyze Particles, it works.
I even set the macro to delete all intermediate images, so only the mask and target remain.  

I could work around by multiplying the mask and the source image, but that is slower.  
Can someone offer some insight to  my problem?

Thanks
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]

______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________

[Glen MacDonald-2]

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Hi Cameron,
Found it.  The user has '#' in the file names (not to mention ridiculously long names).  Set Measurements will not allow # in the redirected file name,regardless of whether hard coded, using a variable or an array pointer.  

Regards,
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]
[hidden email]





On Apr 22, 2013, at 8:52 PM, Cameron Nowell <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Glen,
>
> That's a bit weird and should work fine. I just had a go myself with the two images you can copy from here
>
> https://dl.dropboxusercontent.com/u/11163658/analyse%20particles%20test.zip
>
> using this code and it worked fine
>
> selectWindow("Nuclei.tif");
> run("Find Maxima...", "noise=400 output=[Segmented Particles] exclude");
> run("Set Measurements...", "area mean display redirect=Cell.tif decimal=3");
> selectWindow("Nuclei.tif Segmented");
> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing display summarize");
>
> I am running the current up to date version of Fiji if that makes any difference
>
> Cheers
>
> Cam
>
>
>
> Cameron J. Nowell
> Centre for Dynamic Imaging
> The Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade
> Parkville, Victoria 3052
> Australia
>
> Phone: [phone]
> Mobile: [phone]
> Fax: [phone]
>
> Facility Website
> LinkedIn Profile
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Glen MacDonald
> Sent: Tuesday, 23 April 2013 8:14 AM
> To: [hidden email]
> Subject: redirect sampling
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> An 8-bit mask was created from a 16-bit image by Find Maxima with output = Segmented particles.   When this mask used in a macro to redirect Analyze Particles to the original image, an error message states the "source image is not a valid choice for "Redirect to:".  But, if I manually set measurements to target redirect sampling to the original image and then run Analyze Particles, it works.
> I even set the macro to delete all intermediate images, so only the mask and target remain.  
>
> I could work around by multiplying the mask and the source image, but that is slower.  
> Can someone offer some insight to  my problem?
>
> Thanks
> 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]
>
> ______________________________________________________________________
> The information in this email is confidential and intended solely for the addressee.
> You must not disclose, forward, print or use it without the permission of the sender.
> ______________________________________________________________________