Card-carrying bioinformaticist here....

Are you positive you can't segment using GenePix or an equivalent? Their spot-segmentation algorithms are really very nicely done, and modern versions handle one, two, and four-colour arrays. You don't have to scan on an Axon scanning to use GenePix -- it should handle your Typhoon data no problem. The reason I suggest this is that segmentation is pretty tricky, and when you suggest "corresponding pixels in two spots" type comparisons, that means that even a one-pixel segmentation error will corrupt the comparison. If I reviewering a paper doing this I'd be extremely concerned, and would probably ask for: a direct comparison to an established quanting program on a spot-by-spot basis, direct comparison to an established quanting program on an overall results basis, and public release of the code used for your program. Just my two cents....

In reply to Re: Perl Image Analysis by Anonymous Monk
in thread Perl Image Analysis by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.