Re: trouble specifying a ROI in ROI Manager

Posted by Joris FA Meys on Feb 13, 2009; 12:41pm
URL: http://imagej.273.s1.nabble.com/Macros-to-read-and-write-Complex-Fourier-Transform-tp3693680p3693685.html

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
> > >
> --
> Hugo Arruda de Moura Torres
> ==================================
> Departamento de Biofísica
> Universidade Federal de São Paulo
> Rua Botucatu 862 7o. andar
> CEP 04023-062 Vila Clementino
> São Paulo - SP - Brasil
> Tel:[phone] r.220
> Fax: [phone]
>