http://imagej.273.s1.nabble.com/StereoView-after-StackFocuser-tp3699767p3699771.html
I am going to work on Stack_Focuser. I shall try to introduce a different edge
detector. If you have any questions or suggestions -- let me know.
> I just realized that if I use Sobel or Variance as Sharpness Estimator on
> the EDF, I get similar results to stackfocuser! But If I use Real or
> Complex Wavelets, the topology gets mixed.
>
> Kind of obvious since Stack Focuser uses Sobel... :-)
>
> On 4/13/07, NeLaS <
[hidden email]> wrote:
> > Hi Gabriel!
> >
> > Maybe you are seeing the results of different methods to decide what is
> > on
> >
> > > focus when you use semi-transparent objects.
> > >
> > > These plugins would work perfectly on stacks of images of opaque
> > > objects. The
> > > problem with semi-transparent objects (like those cells) is that they
> > > can be
> > > on focus at several places in the z plane. The plugins try to maximise
> > > some
> > > focus function in the z direction. Depending on the implementation this
> > > may
> > > be found at different places.
> >
> > Hum, interesting point!
> >
> > Just curious, which of the topology maps give you the best focused
> > result?
> >
> >
> > That's a difficult question, but I think the stack focuser plugin is
> > giving better ones. If I use kernel size of 3, the focused image turns
> > out "average" because of the abundance of "noise", final image is grainy.
> > If I use kernels bigger than 100 I get really nice resolved focus in most
> > areas of the image, but the kernel patches appear explicitly (while using
> > smaller kernels these patches are so small they look like noise).
> >
> > The stack focuser seems to interpret the stack's focus information as I
> > would expect, but EDF apparently mix the onfocus information (maybe
> > because of the opacity of images?). I have tried other configurations for
> > EDF, on the advanced mode, but the resulting images were not too
> > different regarding the topology.
> >
> > Can you upload the stack for testing?
> >
> >
> > sure! the .zip can be downloaded
> > here<
http://filexoom.com/files/12783/2cell.zip>. It contains the stack
> > (8bit), a focused image processed with k=3 and another with k=150
> > (StackFocuser), and the output image from Extended Depth of Field (Easy
> > mode -> Speed/quality "high").
> >
> > thanks!
> >
> > bruno
> >
> > On 4/13/07, Gabriel Landini <
[hidden email]> wrote:
> > > On Friday 13 April 2007 02:23:44 NeLaS wrote:
> > > > doing the sequence:
> > > > >Open image sequence
> > > > >Run Extended Depth of Field Plugin (EDF)
> > > > >Run Anaglyph plugin (G.Landini) and mark to generate a stereo image
> > > >
> > > > However, the topology map created by EDF does not seem to reflect the
> > > > stack's resulting topology, but only the single output image's
> > >
> > > topology.
> > >
> > > Maybe you are seeing the results of different methods to decide what is
> > > on
> > > focus when you use semi-transparent objects.
> > >
> > > These plugins would work perfectly on stacks of images of opaque
> > > objects. The
> > > problem with semi-transparent objects (like those cells) is that they
> > > can be
> > > on focus at several places in the z plane. The plugins try to maximise
> > > some
> > > focus function in the z direction. Depending on the implementation this
> > > may
> > > be found at different places.
> > >
> > > Just curious, which of the topology maps give you the best focused
> > > result?
> > >
> > > Can you upload the stack for testing?
> > >
> > > > I tried to use Anaglyph plugin with the Height Map, but with no
> > >
> > > success!
> > >
> > > > The resulting image is absolutely distorted. I assigned the output
> > > > and heightmap to 32bit and 8bit, but it made no difference.
> > > >
> > > > ps: sorry for my ignorance, but is heightmap = topology ?
> > >
> > > Yes, although the heightmap is not guaranteed to be meaningful
> > > (measure-wise)
> > > unless your stacks are all taken at the same step depth.
> > >
> > > Regards
> > >
> > > G.
> >
> > --
> > Bruno C. Vellutini
> > organelas.com
> >
> > Centro de Biologia Marinha (CEBIMar)
> > Universidade de São Paulo
> > Av. Manoel H. do Rego km 131,5
> > 11600-000 São Sebastião, SP, Brasil
> >
http://www.usp.br/cbm/