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Dear list,

I've recently become involved in a project that is going to require a large
number of images to be analyzed for multiple antigens. The images will be
section series (approx. 6 - 12 um deep) of porcine tissue captured on a
Leica confocal system, indirectly stained using 3 different fluorophores. I
will need to retrieve volume measurements from the section series. From the
number of tissues I will receive, I will be acquiring hundreds of images.

My usual method for smaller workloads has been to load the raw .tiff files
into Nikon Elements, and go through the time-consuming process of telling
the software how to handle the series (wavelengths, steps, etc.), manually
calibrate the image from the Leica text output, apply median filter,
threshold and run measurements. I have as many of those steps as possible
rolled into one macro. Also, Elements has the ability to automatically
reconstruct the section series based on file name, but this is unreliable
with files captured using a sequential scan.

Does anyone out there have experience with a similar situation and found a
method that is more efficient for dealing with such a large number of
images? Is there a better software alternative? I think the biggest
time-hog is having to take raw image files from a Leica system and
reconstruct them in Nikon Elements. Perhaps Leica has an analysis package
better suited for this?

Just wanted to see if anyone else has fought this battle.

Thank you all in advance.

Keith Prater
Research Technician II
Center for Environmental Biotechnology
University of Tennessee-Knoxville