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Dear Krzysztof and Jurek,

The Huygens software may be very useful for you. Especially if you want 
to analyze many images. The Huygens Object Analyzer is an extensive tool 
which measures distances within channels as well as between channels. 
Distances from CM to CM (center of mass), from CM to surface and/or 
surface to surface are reported in real units by taking the sampling 
into account. Nearest neighbor objects are automatically detected, if 
requested. By analyzing all objects at once a direct histogram can be 
obtained from the distances. Of course all statistics can be exported to 
make your own histograms or graphs.

The Huygens software is very suitable for analyzing many images. 
Template support across the Huygens tools allow you to carry out the 
exact same analysis on multiple images. Additionally, scripting 
functionalities allow more advanced users and programmers to make the 
analysis fully automatic.

The best way to determine if the Huygens Software works for you is to 
simply test the software, which you can download at www.svi.nl/download. 
We will gladly provide you with a test license and manuals.

Good luck with your research! And if we can be of any help, please do 
not hesitate to contact us.

Marja van Aken
Scientific Software Developer
SVI, makers of the Huygens software
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On 07/23/2012 09:15 PM, Krzysztof Berniak wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear List Members,
>
> We are looking for an image analysis/cytometry tool that can perform
> the following job:
>
> We have a 3D image stack that consists of several hundred green and
> red foci (they represent two nuclear processes that occur in many
> little spots). We need to find the center of mass of each red 3D
> focus, and measure the distance (in 3D) to the nearest green spot, and
> repeat the process for all red spots in one 3D stack. Next, we need to
> repeat this job in a large number of nuclei. Eventually, we need to
> obtain a histogram of distances between the red spots and their the
> nearest green spot neighbor in a large population of 3D objects.
>
> Does anyone know a ready-to-use image analysis tool that can do this
> job for us? We have started to work on our own algorithm, but maybe
> there are solutions to this problem available already. Any advice
> about a software package that could this work would be much
> appreciated.
>
> Thank you very much for your help,
>
> Krzysztof Berniak, Jurek Dobrucki
> Jagiellonian University
>