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Hi Yang,

Looks like very tissue oriented so far. How about extending to 
subcellular features - maybe combine with what these papers are doing 
(the 2010 paper has ImageJ plugins at 
http://www.cytoo.com/cytoo_images_analysis.php   ... though the cytoo 
web page is boring compared to their www.CELLebrate.fr ):

Duong T, Goud B, Schauer K. Closed-form density-based framework for 
automatic detection of cellular morphology changes. Proc Natl Acad Sci U 
S A. 2012 May 29;109(22):8382-7.  PubMed PMID: 22586080; PubMed Central 
PMCID: PMC3365204.

Schauer K, Duong T, Bleakley K, Bardin S, Bornens M, Goud B. 
Probabilistic density maps to study global endomembrane organization. 
Nat Methods. 2010;7(7):560-6. Epub 2010 May 30. PubMed PMID: 20512144.

Hopefully Prof. Schauer can send you full resolution data from cells on 
micropatterns (and.or you can buy some micropattern coverglasses and 
image on a CHLA confocal).

You are doing three color analysis now, can you extend this to 10plex? 
42plex?


George
p.s. please say hello to Rex for me and please send me the paper or a 
link to it when it is online.

On 6/19/2012 6:55 PM, Yang Tang wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> CellPie is a celluar images analysis tool dedicated for spatial pattern analysis
> using image processing technique.
> New features were added in this version (v1.2):
>
> new features:
> (1)color channel analysis (RGB, H&E, H DAB, PB..)
> (2)individual cell recognition
> (3)clustering analysis
> (4)Uniformity evaluation
>
> the tool now can be free download through its project website:
> http://www.pedimg.org/cellpie/software.html
>
> Any feedback and suggestions are welcome.
> Please connect to [log in to unmask]
>
>
> Yang Tang
> Radiology Department
> Children's Hospital Los Angeles
> University of Southern California
>
>