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Dear Rachael Lim,

Imaris (bitplane AG) has recently implemented functionality to handle huge image files (no commercial interest from my side). If you want to just merge the mosaics into a projection image, this could already be achieved with -for example- ImageJ. Aaron Ponti from our group has recently developed (MatLab based) software for a 3d alignment and shading correction of stacks from mosaics.

Dont hesitate to contact me for further detail.

Cheers, jens

Dr. Jens Rietdorf
head of microscopy unit 
Friedrich-Miescher-Institute, wro-1066.2.32
Maulbeerstr.66, CH-4058 Basel, Switzerland
http://www.fmi.ch/  Phone +41 (61) 697-5172


-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]]On
Behalf Of Rachael Lim
Sent: Wednesday, October 17, 2007 9:57 AM
To: [log in to unmask]
Subject: Mosaic with optical sectoning


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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