Posted by
Stanislav Vitha on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Mosaic-with-optical-sectoning-tp590526p590529.html
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocalHi Rachael,
you do not mention what instrument you are using; For multi-area time
lapse Z-stack data from our Olympus FV1000 confocal I have recently been
using the ImageJ mosaicking plug-in from the good people at NCMIR, which
can import the Olympus confocal files and also understands the XY mosaic
log file.
download at
http://www.ncmir.ucsd.edu/Software/imagej_mosaicking_plugins.htminstructions at
http://www.ncmir.ucsd.edu/~skchow/rts2000/mosaicprocess.htmlWith our scope I set up acquisition of overlapping tiles (or for 3D,
overlapping z-stacks). The confocal software acquires the z-stacks and
also saves a log file with XY coordinates of each z-stack.
The mosaicking plugin reads the log file and based on the XY coordinates
of each tile assembles them into a mosaic. You end up with assembled
mosaic for each z-slice. Their file format is tiled tiff, which can be
read by some, but not all software.
Stan Vitha
Microscopy and Imaging Center
Texas A&M University
BSBW 119
College Station, TX 77843-2257
On Wed, 17 Oct 2007 15:57:07 +0800, Rachael Lim <
[hidden email]>
wrote:
>Hi! We are trying to run an experiment that requires image acquisition of
a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed
by
>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export
out
>and compile them with another software. Does any of you have any
suggestion
>of possible software that has the capability of compiling individual
planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim
>=========================================================================