Re: flattening a layer from z-stacks of thick uneven tissue

Posted by Glen MacDonald-2 on Oct 13, 2009; 4:57pm
URL: http://imagej.273.s1.nabble.com/flattening-a-layer-from-z-stacks-of-thick-uneven-tissue-tp3690504p3690514.html

As mentioned by Gabriel, thresholding may help.  Deconvolution or  
imaging with higher NA will also reject more of the out of focus light.

Glen
On Oct 13, 2009, at 2:02 AM, Mark Krebs wrote:

> Thanks for the suggestion.
>
> I've tried enhanced depth of field (EDF) plugins from http://bigwww.epfl.ch/demo/edf/ 
> , but so far I'm
> unable to mask the fluorescence contributed by nuclei that are below  
> the top layer.  EDF creates a
> sharper image, but it appears to merge all of the z-stack, which is  
> what I'm trying to avoid.  The
> examples at the EDF website seem to be brightfield images of opaque  
> objects (fly eye, mineral, laser
> weld, mouse intestine) or of a transparent object with a single  
> layer (retinal pigment epithelium).  My
> images are of a transparent object with fluorescent nuclei in many  
> layers.   How can EDF be used to
> reduce fluorescence contributions from layers under the top layer of  
> nuclei?