Re: trouble specifying a ROI in ROI Manager

Posted by Wayne Rasband on Feb 13, 2009; 8:56pm
URL: http://imagej.273.s1.nabble.com/Macros-to-read-and-write-Complex-Fourier-Transform-tp3693680p3693687.html

Here is a macro that creates a square selection that has the same area
as an existing selection.

   getSelectionBounds(x, y, width, height);
   getRawStatistics(area);
   size = sqrt(area);
   x2 = x + width/2 - size/2;
   y2 = y + height/2 - size/2;
   makeRectangle(x2, y2, size, size);

-wayne

On Feb 13, 2009, at 3:27 PM, Hugo A. M. Torres wrote:

> I tried that, didn't work. Maybe I am still having rounding issues
> because of the area being reported in micrometers.
>
> I am not experienced in writing macros, but would it be possible at
> least in principle to write a macro that specifies a square ROI
> according to an area value input?
>
> Hugo
>
> On Fri, 2009-02-13 at 13:41 +0100, joris meys wrote:
>> Ah, I see. Sorry for the misunderstanding.
>>
>> As far as I understand, the ROI measures inside its boundaries,
>> boundary not
>> included. So in fact you should extend the length and width of the
>> ROI with
>> 2 pixels if you want to have a square that covers the same area. I'm
>> not
>> 100% sure about this, but it might be worth a try.
>>
>> Kind regards
>> Joris
>>
>> On Fri, Feb 13, 2009 at 1:13 PM, Hugo A. M. Torres
>> <[hidden email]>wrote:
>>
>>> No Joris, I understand what you are saying, but the problem is the
>>> first
>>> ROI (used to measure the nucleus I am interested in) has a triangular
>>> shape, which will not fit in the background area unless I make it
>>> into a
>>> square of the same area as the triangle. Now, this should be very
>>> straightforward: just draw a square with sides whose lenght is the
>>> square root of the triangle area. It doesn't work if I use a
>>> calculator,
>>> possibly because of rounding issues, I don't know.
>>>
>>> I always get a smaller area in um^2 if I do this by hand. So I was
>>> wandering if it is possible to specify a square ROI by area value.
>>>
>>> Any ideas?
>>>
>>> Tganks
>>>
>>> On Fri, 2009-02-13 at 11:08 +0100, joris meys wrote:
>>>> The measurements should be fairly simple with the ROI manager. Just
>>>> click
>>> on
>>>> the roi you specified earlier, and drag it to where you want to
>>>> measure.
>>>> First click "Add", because otherwise the ROI manager will measure
>>>> at the
>>>> previous position. That should give you the results you want.
>>>>
>>>> Kind regards
>>>> Joris
>>>>
>>>>
>>>> On Fri, Feb 13, 2009 at 4:36 AM, Hugo A. M. Torres
>>>> <[hidden email]
>>>> wrote:
>>>>
>>>>> Hello listmates,
>>>>>
>>>>> I am trying to perform densitometry measurements according to this
>>>>> method:
>>>>>
>>>>> "The nucleus was encircled by free-hand drawing of a border around
>>>>> the
>>>>> outermost mRNA-expressing cells in the nucleus. The mean density
>>>>> and
>>> the
>>>>> area of the selection were measured. The mean density of the
>>>>> background
>>>>> was measured from a rectangular area of corresponding size in the
>>>>> immediate vicinity of the nucleus. The mean density of the
>>>>> background
>>>>> was subtracted from the mean density of the nucleus and..."
>>>>>
>>>>> Now, the problem is I can't specify a ROI of the same area of the
>>>>> place
>>>>> I measured previously. I tried taking the square root of the area
>>> (given
>>>>> in um^2) and specifying a square ROI with sides of this length but
>>>>> the
>>>>> resulting area measured is always smaller!
>>>>>
>>>>> Is it possible to specify a square ROI by inputing  an area value
>>>>> in
>>>>> square micrometers?
>>>>>
>>>>> Thanks
>>>>> --
>>>>> Hugo Arruda de Moura Torres
>>>>> ==================================
>>>>> Departamento de Biofísica
>>>>> Universidade Federal de São Paulo
>>>>> Rua Botucatu 862 7o. andar
>>>>>
>>> --
>>
>>
>