[ImageJ-devel] ROI -> Overlay bug

Albert Cardona sapristi at gmail.com
Mon May 14 07:53:33 CDT 2012

2012/5/11 Lee Kamentsky <leek at broadinstitute.org>:
> On 5/11/2012 2:10 PM, Albert Cardona wrote:
>> 2012/5/11 Gabriel Landini<G.Landini at bham.ac.uk>:
>>> On Thursday 10 May 2012 18:38:58 Senseney, Justin  [E] wrote:
>>>> Gabriel’s nice points brought up  the issue of bias in counting pixels
>>>> ...
>>> skype or discuss it at the Luxembourg conference).
>> I second Gabriel's views, a pixel is a point and considering it so
>> solves a lot of issues. If that's a break from IJ1, that's ok: it's
>> for the better.
> Brave man - I think that's how I interpreted it when I wrote the imglib
> ROIs. If you are to count pixels, it's by whole numbers and the criterion is
> whether the integer coordinate falls inside the region of interest, not how
> it's drawn. Area is a different measure and might very well be different
> than pixel count. Unfortunate as it is, maybe the visual representation is
> just illustrative, not normative.

Brave are the ImageJ 2 developers that are going to implement this
while having to interact with ImageJ 1. Shifting all ImageJ 1 ROIs by
0.5 in X and Y while preserving consistency in the measurements will
not be trivial. But ImageJ 1 never kept measurements consistent and
nobody ever complained too loudly that wasn't aware of the situation

Measuring areas is always tricky and there is where considering a
pixel a square is helpful. I think of the square as the domain over
which a pixel sample reigns. But of course measuring is not the same
as scaling. Preserving measurements across image scales is, as far as
I can tell, a field of mathematics, and a question always resolved
arbitrarily by convention. The point being that, as long as ImageJ 2.0
declares how it performs measurements clearly in the manual, then it's
all set.

Regarding the line not having any area: depends, that's your take. One
could consider the default width of a pixel to be 1, and therefore the
area of a line of 4 pixels is also 4. It's an arbitrary convention. I
just hope the manual will be clear about all measurements done by
ImageJ 2.0.



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