[BioC] Image analysis for single channel macro arrays

Peter Wilkinson pwilkinson at videotron.ca
Fri Jul 30 08:01:41 CEST 2004

Well, I have looked deeply into this and I am not impressed with any 
software out there. Genepix is rather good but is painfully log because its 
mostly manual.  Quantarray is poor at segmenting, and its adaptive 
algorithm is poor. The histogram method is only good for well defined 
spots, or high quality runs. Its automated feature does not work well at 
all. I thought Spot uses a histogram .... but I don't remember, and its not 

The problem with ALL the software I have seen is that if you put the 
software in different technician's hands you will get different results.

I do have a demo of Arraypro analyser that I have not tried it yet, but 
this one boats reproduceability between users. You can find a demo of that 
one. However after talking with their scientists about the segmenting .... 
I was not that impressed.

I don't think any commercial software has a chance if you have diffusion. I 
can not imagine anything being good enough for dealing with that the way 
one might expect

As far as background, unless you are dealing with radioisotopes, background 
subtraction can be over-rated, and should not be done.

I am always on the hunt for good segmenting software .... soon I hope to 
find the time to write my own.

Have a go with Array Pro  and good luck .... we all need it.


At 11:26 PM 7/29/2004, Nicholas Lewin-Koh wrote:
>Does anyone have any insight into what works well for spot
>and quantification for membrane arrays? I tried Spot but it only seems
>to work on dual channel
>arrays. Most of the other commercial programs don't seem to be very
>good, the features
>of interest to me are automatic gridding, good treatment of overlapping
>spots (they diffuse more on membrane
>arrays), and good backgound estimation.
>Thanks for any insight/help.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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