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I should add that I don't know if or how well Fiji will import the
Leica confocal image format, you might have to export everything to
TIFF.  Also, you will have to stitch each plane separately.  I wrote
an ImageJ macro at some point to automate the plane-by-plane
stitching, so if you do go this route let me know and I'll dig the
macro out for you.

-Esteban


On Thu, Aug 16, 2012 at 1:18 AM, David Johnston <[log in to unmask]> wrote:
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> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I should add that Leica's later SP5 software also does tile scan differently to
> earlier incarnations. In the older versions, you got a seperate Z series for each
> field of view in the experiment file, plus the tiled image (provided you set the
> options correctly to retain raw images). In the later incarnations you get a
> single series containing XYZ of all tiles, making tile based operations more
> awkward (if you then have to manually crop out each tile, one by one).
>
> In defense of the stitching ability of Leica's software, I guess that it is trying
> to stitch by image content rather than simply by stage coordinates and in our
> samples there isn't a huge area of signal in each field for it to work with, in our
> experience it works well with more information rich samples.
>
> Cheers,
>
> DAJ