Imitation microarray analysis

[ch-2]

Hi..

I'm a new user of ImageJ, and it shows; things are not intuitive yet.
So far, I've just been playing around with it, trying to get the hang of
it.  The first application I used it for was measuring lines on a gel,
and I was pleased to find the menu options for doing that.

Now I'm trying something trivial; I have a pseudo-microarray that I'd
like to convert into a spreadsheet.  The data is just a grid listing the
properties of the various amino acids, and it would have been far
quicker for me to type in the data than to use ImageJ, but I really want
to learn this program.  The image is the bottom half of
http://www.compbio.dundee.ac.uk/papers/amas/figure1.ps

So far, I've converted the postscript file to a pgm file using:
  gs -dNOPLATFONTS -sDEVICE=pgmraw -r204x196 -dNOPAUSE -dQUIET
     -sOutputFile=image%d.pgm figure1.ps -c quit

Then I loaded the image into imagej, selected the array, then did
'Image/Duplicate', which creates a separate image from the selection.

Then I did 'Analyze/Analyze particles', choosing the 'show outlines'
option.  Instantly, it selects all of the spots.

At this point I'm stuck.  I don't know what to do next to measure the
filledness of the dots, or how to write that information to a file that
would be useful to Excel or vi or something.

Another part of the problem is that the 'Analyze particles' plugin
doesn't number the selections sequentially, which makes turning dots
into data harder.  Also, in the original picture, the filled-in dots
have been shifted a little bit to the left compared to the empty dots.

Is there a plugin that reads scantron (fill-in-the-bubble) cards?  That
would be perfect for this.  Or even something free and simple for
analyzing microarray data, as this image looks somewhat like one.

I like ImageJ's line-graph data recovery tool, that was neat!

Thanks!

--
CH <[hidden email]>
First-year biotechnology student, old-style computer hacker