[BioC] Imaging of Protein Array

Saroj Mohapatra smohapat at vbi.vt.edu
Mon Jun 26 17:35:45 CEST 2006

Hi Shizuka:

Which software are you using for segmentation of the images? Some 
software (e.g., ImaGene) provide a way of increasing or decreasing the 
circle size to cover the area of the spot manually. But manually finding 
spot area is  (1) too time-consuming. (2)visual judgment can be 
misleading, it is influenced by the levels of brightness, contrast etc. 
(3) the spots might be irregular in shape, so fitting a circle would be 

It is best to automate the whole process and only check at the end to 
see if any obvious mistake was done.

Spot uses a slightly different algorithm (from ImaGene) and, I think 
(others might give better opinion) produces more realistic values for 
the spot intensities. You could download an evaluation copy of 
Spot(http://spot.cmis.csiro.au/spot/index.php) and try it out.

Best wishes,


> Dear list members:
> Hello.  I am trying to convert the tiff images of RayBio Cytokine 
> Antibody Array (http://www.raybiotech.com/product.htm) into numbers in 
> order to compare them numerically.
> The problem I am having now is that how to define the area of a spot.  
> Do any of you have experience with working with protein arrays?  Any 
> help is appreciated.  Thank you very much for your help in advance.
> Shizuka
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