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Hi Krzysztof, 
Just to clarify, Volocity will generate the exact output that you require, the individual distance from each red spot to the nearest green spot.  These distances can be displayed as feedback on the image, and plotted as a histogram. The distance can be calculated from either centroids, or nearest edges.  Distances can be calculated in voxels, calibrated units, or normalized to the longest axis of the containing nucleus. 

We're really delighted with the developments we've made to Volocity recently and would be happy to demonstrate them so please contact us off list for further details. 
Regards,
Andrew




> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[log in to unmask]] On Behalf Of Julio Vazquez
> Sent: 24 July 2012 18:40
> To: [log in to unmask]
> Subject: Re: Spatial relationship between two events in cells
> 
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
> 
> Krzysztof, just an additional thought: I am not sure if Volocity will
> give you the individual distance values for each spot, which is what
> you would need to plot your Histograms, but probably only the averaged
> values for the whole population; for instance, you can get the average
> minimum distance of each green spot to the red spots (i.e. the average
> value of the distance of all green spots to their nearest red spot), or
> the average value of the distance of each green spot to all red spots,
> etc. Maybe other Volocity users, or a Volocity support person can
> comment on this. What Volocity (and other 3-D image analysis software
> such as Imaris) will give you, is the x,y,z location of the centroids
> of all the spots found. With those values, it should be possible and
> relatively easy for someone with programming skills to write a program
> to extract the center to center distances.
> 
> ImageJ has a plugin to segment and measure 3-D objects (3D object
> counter). This will also list the x,y,z coordinateds of the geometric
> and/or intensity center, which you coudl use to make your own distance
> measurements:
> 
> http://rsbweb.nih.gov/ij/plugins/track/objects.html
> 
> I have never tried them, but FIJI may have additional tools for 3-D
> segmentation, and like ImageJ is free. A list of other software for 3-D
> analysis can be found here:
> 
> http://www.andrewnoske.com/wiki/index.php?title=Tomography_software
> 
> some of these (and maybe other) packages have been discussed on the
> confocal listserver.
> 
> 
> --
> Julio Vazquez,
> Fred Hutchinson Cancer Research Center
> Seattle, WA 98109-1024
> 
> 
> http://www.fhcrc.org
> 
> ===
> 
> 
> On Jul 23, 2012, at 12:15 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