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

Posted by Przemko on Nov 10, 2009; 7:58am
URL: http://imagej.273.s1.nabble.com/flattening-a-layer-from-z-stacks-of-thick-uneven-tissue-tp3690504p3690506.html

Damon Poburko wrote:
> Sorry to beat a dead horse, but did you try the 3D-modeling version of
> Extended depth of field? I will also reduce your stack to single plain,
> but it does a pretty solid job of removing out of focus fuzz. I'm using
> this to gather fluorescent puncta on multiple plain into a single image.
> Deconvolution before had might also be helpfull, as per Glen's suggestion.
>
> Damon
>
>  

I tried that. I also tried extended depth of field in Adobe Photoshop
CS4. I must say InageJ failed. I have photos of zebrafish and got to
stitch a few of them together because of the thickness of the embryo,
not all planes are in focus. I tried different versions and settings of
Extended depth of field in ImageJ and got terrible results. Then I did
CS4 and presto. 4 clicks and I was there. I guess the main thing is that
CS4 aligns the sections. When you change focus to get different parts of
fish sharp the entire specimen shifts a bit (normal). ImageJ is however
unable to adjust for that. CS4 first aligns then does the rest. The
results are great. Any idea how to achieve that in ImajgeJ
Przemko

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Przemko Tylzanowski PhD
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