*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

with the obvious bias of being one of the authors, I can just point you
toward
http://www.endrov.net
and the new high-throughput analysis tool.

I strongly recommend storing the images already at the source into a decent
file format, which better keeps track of the relationship between your
images. Only if you are at loss with this should you do a name based import
(why is it unreliable with your input images? if the naming is systematic,
it should not be). Maybe you also want to consider storing in OMERO while
you are at it, as a cleanup phase after the acquisition

/Johan



On Thu, Mar 14, 2013 at 3:15 PM, Keith Prater <[log in to unmask]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> 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
>



-- 
-- 
-----------------------------------------------------------
Johan Henriksson, PhD
Karolinska Institutet
Ecobima AB - Custom solutions for life sciences
http://www.ecobima.com  http://mahogny.areta.org  http://www.endrov.net

<http://www.endrov.net>