On Fri, 12 Dec 1997, Chris Pudney wrote:
Hi folks

>Other than that there seems to have been fairly little work done on
>segmenting confocal stacks.  There are the occassional papers on
>segmenting stacks restricted to a specific problem domain, e.g.
>segmenting a particular type of cell, but little in the way of general
>approaches to segmenting confocal stacks.  This is probably because the
>problem is very difficult, maybe even more so than segmenting image
>volumes from other modalities such as MR or CT.

Not true.  There is quite a bit of literature on segmentation and
contouring.  Application of contouring and segmentation techniques to
confocal microscopic images has not been a priority as it has been
presumed that the AOIs (Areas of interest) are well defined.  However, a
common method is the use of the "Snakes" algorithm.  A version of Snakes
is available from the NIH-Image web page.  Our lab has developed a
contouring method based on adjustable thresholding.  We are in the process
of developing an appropriate segmentation technique to used with Java.
The segmentation algorithm is in C++ as is the contouring algorithm.  Also
this contouring algorithm can handle 24 bit PICTS-usually not a
requirement for confocal images.

I am also looking to determine if using a Snakes algorithm will do any
better than our current thresholding method.  I will be redeveloping some
source code for a modified Snakes algorithm.  If anyone is interested,
please e-mail me directly.
Cheers, geoff

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