select a specific 16 bit grayscale intensity for filling a ROI

[Gabriel Acevedo]

Hello,
  I am trying to fill a ROI in a stack of 16 bit DICOM images with a
specific grayscale value, but in the 16bit range. The default color picker
only gives an 8-bit range. Is there a way to assign a specific fill "color"
outside of the 0-256 range? I've tried selecting the 8-bit "equivalent" but
it is not translating into 16 bits too well.
Thanks in Advance,

Gabriel Acevedo-Bolton

[Wayne Rasband]

> Hello,
>   I am trying to fill a ROI in a stack of 16 bit DICOM images
> with a specific grayscale value, but in the 16bit range. The
> default color picker only gives an 8-bit range. Is there a way
> to assign a specific fill "color" outside of the 0-256 range?
> I've tried selecting the 8-bit "equivalent" but it is not
> translating into 16 bits too well.

This macro fills the ROI in all images in a stack with the value 1234.

   setColor(1234);
   for (i=1; i<=nSlices; i++) {
       setSlice(i);
       fill();
   }

-wayne

[Jerome Mutterer]

Gabriel,

You can install the following tool macroset. Double click on it's icon  
to set the fill value, then click on the image to fill it. If a Roi is  
active it will be filled.

Jerome.


// fill image or ROI with specified value.

var value=100;

macro "Fill16bits Tool -  
C000D08D09D17D1aD26D2bD31D32D33D34D35D3cD40D44D4dD50D53D57D5dD61D62D63D64D65D66D68D6cD73D77D7bD84D8aD8cD94D95D99D9bD9cD9dD9eD9fDa5Da6Da7Da8Da9DaaDb6Db7Db8Db9DbcDbdDbeDcbDcdDcfDde"{
setColor(value);
fill();
}

macro "Fill16bits Tool Options" {
value = getNumber("Fill value ",value);
}

Quoting Gabriel Acevedo <[hidden email]>:

> Hello,
>   I am trying to fill a ROI in a stack of 16 bit DICOM images with a
> specific grayscale value, but in the 16bit range. The default color picke=
> r
> only gives an 8-bit range. Is there a way to assign a specific fill "colo=
> r"
> outside of the 0-256 range? I've tried selecting the 8-bit "equivalent" b=
> ut
> it is not translating into 16 bits too well.
> Thanks in Advance,
>
> Gabriel Acevedo-Bolton
>

[Jonathan Jackson-2]

Jerome,
This tool will be very useful indeed, thanks for submitting it.  Others
installing this tool may wish to enable the 'Undo' function. I also added
introduced the calibrate() function in order to work with signed 16 bit
images. The modified macro is:

var value=100;
macro "Fill16bits Tool -
C000D08D09D17D1aD26D2bD31D32D33D34D35D3cD40D44D4dD50D53D57D5dD61D62D63D64D65D66D68D6cD73D77D7bD84D8aD8cD94D95D99D9bD9cD9dD9eD9fDa5Da6Da7Da8Da9DaaDb6Db7Db8Db9DbcDbdDbeDcbDcdDcfDde"{
setupUndo();                     // requires 1.32g
setColor(value - calibrate(0));  // calibrate Requires 1.34h.
fill();
}

I also have a comment for Wayne - when the cursor moves over an ROI, the
icon changes (I see it change from a cross-hair to a pointer) indicating
that the tool operates on the ROI.  This is appropriate for the ROI editing
tools, but I'd like to be able to keep the cross cursor for a tool such as
this which draws on the image.  Would it be possible to add a macro / tool
function which sets whether or not the pointer changes within an ROI?

Thanks,
Jon

>Gabriel,
>
>You can install the following tool macroset. Double click on it's icon
>to set the fill value, then click on the image to fill it. If a Roi is
>active it will be filled.
>
>Jerome.
>
>
>// fill image or ROI with specified value.
>
>var value=100;
>
>macro "Fill16bits Tool -
>C000D08D09D17D1aD26D2bD31D32D33D34D35D3cD40D44D4dD50D53D57D5dD61D62D63D64D65D66D68D6cD73D77D7bD84D8aD8cD94D95D99D9bD9cD9dD9eD9fDa5Da6Da7Da8Da9DaaDb6Db7Db8Db9DbcDbdDbeDcbDcdDcfDde"{
>setColor(value);
>fill();
>}
>
>macro "Fill16bits Tool Options" {
>value = getNumber("Fill value ",value);
>}
>

[Wayne Rasband]

> Jerome,
> This tool will be very useful indeed, thanks for submitting it.
> Others installing this tool may wish to enable the 'Undo' function.
> I also added introduced the calibrate() function in order to work
> with signed 16 bit images. The modified macro is:
>
> var value=100;
> macro "Fill16bits Tool -
> C000D08D09D17D1aD26D2bD31D32D33D34D35D3cD40D44D4dD50D53D57D5dD61D62D63D
> 64D65D66D68D6cD73D77D7bD84D8aD8cD94D95D99D9bD9cD9dD9eD9fDa5Da6Da7Da8Da9
> DaaDb6Db7Db8Db9DbcDbdDbeDcbDcdDcfDde"{
> setupUndo();                     // requires 1.32g
> setColor(value - calibrate(0));  // calibrate Requires 1.34h.
> fill();
> }

This should be changed to setColor(value) with ImageJ 1.37e or later,  
which fixes setColor() so it works with signed 16-bit images.

> I also have a comment for Wayne - when the cursor moves over
> an ROI, the icon changes (I see it change from a cross-hair
> to a pointer) indicating that the tool operates on the ROI.
> This is appropriate for the ROI editing tools, but I'd like
> to be able to keep the cross cursor for a tool such as this
> which draws on the image.  Would it be possible to add a
> macro / tool function which sets whether or not the pointer
> changes within an ROI?

With ImageJ 1.37h and later,  the cursor does not change shape when it  
is over an ROI if you are using a macro tool.

-wayne