Re: automatic detection out-of-focus images

Posted by Gabriel Landini on Apr 08, 2011; 8:48am
URL: http://imagej.273.s1.nabble.com/JACoP-parameter-and-PSF-tp3685080p3685084.html

On Friday 08 Apr 2011 01:40:05 you wrote:

> > The key issue is that it is not the whole Image (Field of View) that is
> > out of focus but some parts of it, because sample of "thick" for the
> > objective focus depth .
> >
> > We have tried avaialbe ImageJ plugings from here but none of tham
>
> ... yes?
>
> The bigger issue is: how do _you_ differentiate between out-of-focus and
> naturally blurry parts of an image?

That is usually resolved by comparing the features across the Z axis for each
pixel. The real problem is that autofocus implies finding "the" most in focus
pixel in the z axis and this works fine for opaque objects (like in real world
photograhps) however in (well, brightfield at least) microscopy, objects are
not opaque but semi transparent, and therefore is it possible (for a fixed
focal length objective travelling along the z axis) to find more than one area
with "in focus" objects.

So the problem is not the same as with other types of imagery. There is no
guarantee (with autofocus algorithms) that the final image is the best one.
One needs a different type of autofocusing that takes partial/semi-transparent
occlusion into account.

Of course, with thicker sections this issue becomes more relevant.


Cheers

Gabriel