MicroArray Image Aanalysis software

[huan]

Hello
Now I am doing the DNA microarray image analysis by using different analysis software, but the experimental results are not very satisfactory. I want to get the Maximum Pixel intensity of every spot. Could anybody introduce a software to achieve this purpose.
I would appreciate if somebody could introduce a DNA microarray image analysis software to ge the the Maximum Pixel intensity of every spot.
thanks,
huan

[mbblack]

What kind of arrays? To get the raw intensity values, you need the native output files from the instrument that generated the scans. For example, Affymetix CEL files contain the raw intensity and standard deviation for every feature on the array. You can extract those values with Affy's own instrument software, or with commercial software (e.g. Partek, GeneSpring) or open source software (eg. the Affy package in BioConductor).

But every instrument already outputs feature summarized intensity values, not individual pixel values (even the images one normally sees are feature summarized, not pixel by pixel data). To get individual pixel values, I don't know how you'd even do that, but you would need to get them somehow from the original raw scan data collected by the array scanner itself (if that information is even kept - many modern insturments do image processing in real time in RAM, and only write out to file the feature summarized data). Again, for Affy arrays, the data, if available would be in the *.DAT files, but Affy's own AGCC instrument software processes that data into feature data for the CEL file output that gets written to disk.

[huan]

Dear mbblack,
Thanks a lot for your reply. My analysis is to deal with the *.tif microarray images. The images are produced by ImageQuant LAS 4000 scanner. Now I analyze the images with GenePix Pro, but I can only get the mean and median feature pixel intensity. The resuts are not satisfactory. So I wonder if there is another software I can get the Maximum Pixel intensity of each spot.
Thanks a lot!
huan

[TiborNagy]

ImageJ is a microscopy program, but it has a microarray plugin and it can calculates Maximum Pixel intensity.

[huan]

Dear TiborNagy,
Thanks a lot for your reply! I have got the ImageJ software, but how can I get the microarray plugin? Since I'm not familiar with this software, would you mind introducing the microarray plugin to me in detail?
Thank you very much for your kindness!
huan

[huan]

hi all,
To deal with the *.tif microarray images, I have tried a plugin called AGScan in ImageJ. But the export results don't include the Maximum Pixel intensity of the spot. So I'm wondering if there is another software or plugin I could use to compute the Pixel intensity of the spot