Posted by
Stephan Saalfeld on
URL: http://imagej.273.s1.nabble.com/Sensitive-Thresholding-tp3690288p3690290.html
Hi,
that's not my field really, but did you try to align the images first as
suggested in your previous post?
See, e,g,
http://pacific.mpi-cbg.de/wiki/index.php/Register_Virtual_Stack_Slicesincluded in Fiji or, if that fails (usually it does not) you could try
it manually, setting some control points in image a and corresponding
points in image b and then use `Plugins->Transform->Landmark
Correspondences' to register using these points.
An even easier way: `Plugins->Registration->Linear Stack Alignment with
SIFT', the ancestor of the previously mentioned registration plugin.
For that functionality, you need mpicbg_.jar
http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=blob_plain;f=precompiled/mpicbg_.jarwhich is included in Fiji but works for ImageJ too. Only
Register_Virtual_Stack_Slices has too many dependencies across Fiji to
install it without serious headache ;)
I am telling this because my first Google-hit for `extended depth of
focus' got me to this page:
http://www.janrik.net/ptools/ExtendedFocusPano12/index.htmlthat clearly makes a point about the need of ideally perfect
registration
Best,
Stephan
On Mon, 2009-11-30 at 12:47 +0100, Przemko wrote:
> Wilson R S (AT) wrote:
> > I am trying to develop system whereby I can piece together in focus
> > segments from each colour image in a stack to a single image(like a
> > jigsaw puzzle if you will). The stack is of the same particle taken at
> > different Z values.
> >
> > I have tried using the plugins "stack focuser" and "extended depth of
> > focus", however both result in a "fuzzy" image.
> >
> > My initial idea was to use a thresholding method, however this seams to
> > pick out the out of focus sections first. I have tried a few different
> > thresholding methods, colour and greyscale (on green channel seems to be
> > the best), but nothing I get is useful.
> >
> >
> Hi!
> I posted on the same topic but got no reply. Basically, extended depth
> of focus plugin failed me completely. I tried two different variants of
> the plugin and played with the parameter. The images I got would range
> from bad, through poor to disastrous. I tried Photoshop CS4 (the
> previous ones do not have it) extended depth of focus tool and got a
> great image the first time, and without fiddling. So my question, as a
> follow up to yours, is why the extended depth of focus does not work in
> ImageJ? Look at my previous post for more detail
>
> Cheers!
> Przemko
>
>