About thresholding

[yuanchen]

Dear all friends

I am now trying to threshold my 16 bits tiff image sequence by grayscale
value. This was done by using imageJ ' threshold' command.  But this seems
can only allow you to save images as binary. Say pixel that about GV 24340
will be 1 , the rest of them will be 0.

Is there any way to threshold images, but still save them as the 16 bits
images ( with the graycalue ranged 0 -65525) :)

Best wishes

Yuan Chen

University of Sheffield

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[Krs5]

Dear Yuan Chen,

Alternatively, you could try the macro code below.

       
        title1 = getTitle;
        getDimensions(width, height, channels, slices, frames);
        run("Duplicate...", "title=[duplicate] duplicate range=1-"+slices);
        run("Threshold...");
        title = "Message";
                msg="Set threshold then click \"OK\"";
                waitForUser(title, msg);
        run("Convert to Mask");
        setBatchMode(true);
        run("Analyze Particles...", "size=1-Infinity circularity=0.00-1.00 show=Nothing add stack");
        for (i=0;i<roiManager("count");i++){
                selectWindow(title1);
                roiManager("Select", i);
                run("Copy");
                selectWindow("duplicate");
                roiManager("Select", i);
                run("Paste");
        }
        run("Select None");
        roiManager("Show None");
        setBatchMode("exit and show");

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
University of Leicester
http://www.le.ac.uk/biochem/microscopy/home.html



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Yuan Chen
Sent: 28 April 2013 20:08
To: [hidden email]
Subject: About thresholding

Dear all friends

I am now trying to threshold my 16 bits tiff image sequence by grayscale value. This was done by using imageJ ' threshold' command.  But this seems can only allow you to save images as binary. Say pixel that about GV 24340 will be 1 , the rest of them will be 0.

Is there any way to threshold images, but still save them as the 16 bits images ( with the graycalue ranged 0 -65525) :)

Best wishes

Yuan Chen

University of Sheffield

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

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

[yuanchen]

Thanks very much Mike :)

BW

Yuan


On 29 April 2013 08:02, Michael Epping <[hidden email]> wrote:

> Hello Yuan Chen,
>
> it is possible to preserve the grayvalues when thresholding. But you have
> to convert your 16-bit images to 32-bit. Then run the thresholding command
> and IJ will ask you to "Set Background Pixels to NaN". When you use a macro
> the commands
> > setAutoThreshold("Default dark"); // or select your favourite method
> > run("NaN Background");
> will do the trick.
>
> Best regards
> Michael Epping
>
> Am 28.04.2013 21:08, schrieb Yuan Chen:
>
>> Dear all friends
>>
>> I am now trying to threshold my 16 bits tiff image sequence by grayscale
>> value. This was done by using imageJ ' threshold' command.  But this seems
>> can only allow you to save images as binary. Say pixel that about GV 24340
>> will be 1 , the rest of them will be 0.
>>
>> Is there any way to threshold images, but still save them as the 16 bits
>> images ( with the graycalue ranged 0 -65525) :)
>>
>> Best wishes
>>
>> Yuan Chen
>>
>> University of Sheffield
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

... [show rest of quote]

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[yuanchen]

Dear Kees

Thanks very much , I will give it a go :)

BW

Yuan


On 29 April 2013 09:16, Straatman, Kees R. (Dr.) <[hidden email]>wrote:

> Dear Yuan Chen,
>
> Alternatively, you could try the macro code below.
>
>
>         title1 = getTitle;
>         getDimensions(width, height, channels, slices, frames);
>         run("Duplicate...", "title=[duplicate] duplicate range=1-"+slices);
>         run("Threshold...");
>         title = "Message";
>                 msg="Set threshold then click \"OK\"";
>                 waitForUser(title, msg);
>         run("Convert to Mask");
>         setBatchMode(true);
>         run("Analyze Particles...", "size=1-Infinity circularity=0.00-1.00
> show=Nothing add stack");
>         for (i=0;i<roiManager("count");i++){
>                 selectWindow(title1);
>                 roiManager("Select", i);
>                 run("Copy");
>                 selectWindow("duplicate");
>                 roiManager("Select", i);
>                 run("Paste");
>         }
>         run("Select None");
>         roiManager("Show None");
>         setBatchMode("exit and show");
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> University of Leicester
> http://www.le.ac.uk/biochem/microscopy/home.html
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Yuan Chen
> Sent: 28 April 2013 20:08
> To: [hidden email]
> Subject: About thresholding
>
> Dear all friends
>
> I am now trying to threshold my 16 bits tiff image sequence by grayscale
> value. This was done by using imageJ ' threshold' command.  But this seems
> can only allow you to save images as binary. Say pixel that about GV 24340
> will be 1 , the rest of them will be 0.
>
> Is there any way to threshold images, but still save them as the 16 bits
> images ( with the graycalue ranged 0 -65525) :)
>
> Best wishes
>
> Yuan Chen
>
> University of Sheffield
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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