[BioC] plate image processing and analysis with R

[J.delasHeras at ed.ac.uk]

As Wolfgang says, some of teh software designed for microarray  
analysis may be useful for this purpose.

I used TIGR Spotfinder for some time. It's free and easy to use:
http://www.tm4.org/spotfinder.html

GenePix is also very good, in some ways it may be better. The  
grid-finding algorithm is great, although for teh sizes we're talking  
about here a manual approach would be okay. GenePix requires a  
license... but it's still functional without one, it just restricts  
the amount of data you can export. I think it's restricted to teh  
first 1000 spots, which would be enough for your purposes.
http://www.moleculardevices.com/pages/software/gn_genepix_pro.html

The sort of data these two tools provide varies, so you can check and  
see which one gives you more of what you want.

Also, as Wolfgang said, I don't think I would want a JPEG image (8-bit  
resolution). It will work if you can't do better, but if you can  
capture a 16-bit image (typically TIFF format) that will be best.  
Incidentally, both Spotfinder and Genepix work with 16-bit TIFF files  
only...

Jose



Quoting Wolfgang Huber <huber at ebi.ac.uk>:

> Dear Christian,
>
> such a functionality could certainly be developed on top of EBImage, but
> I am not aware of any instances.
>
> If you have a rectangular grid, then maybe also some of the image
> analysis software that was developed for quantitating spotted microarray
> images could be adapted to your case?
>
> Please also note that .jpg may not always be ideal for quantitative
> analyses, you most likely want to avoid compression and want to use grey
> scale intensities that are proportional to what the CCD camera measured.
>
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
>
>
>> Hi,
>>
>> I am looking for a R library that would allow the analysis of images
>> of plates with colonies arranged on a regular grid on it, for
>> instance 32 rows X 48 columns or other densities. These are typically
>> used for large scale screen in yeast genetics and genomics where
>> different colonies are plated using a pin tool and growth rate are
>> estimated based on colony size or intensity from a .jpg image of the
>> plate. Has anyone seen this developed for R/Bioconductor? The
>> functions would serve to locate a grid on the plate and then extract
>> colony intensities or area, in an approach similar to the analysis of
>> microscopy screen available through EBIimage.
>>
>> Thanks for letting me know,
>>
>> Christian
>>
>
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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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