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From: ImageAnalyst <imageanalyst@mailinator.com>
Newsgroups: comp.soft-sys.matlab
Subject: Re: Need algorithm help: molecule length from an image
Date: Mon, 12 May 2008 11:19:32 -0700 (PDT)
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On May 11, 7:12=A0pm, rober...@ibd.nrc-cnrc.gc.ca (Walter Roberson)
wrote:
> In article <g07jfi$af...@fred.mathworks.com>,
>
> Roger Stafford <ellieandrogerxy...@mindspring.com.invalid> wrote:
> > =A0Note to ImageAnalyst: In my opinion the length of the shape's perimet=
er
> >(presumably divided by 2) is not a reliable measure of what Adrian is see=
king
> >as the over-all length of a molecule. =A0Its outline is likely to be a so=
mewhat
> >jagged affair as is characteristic of long-chain molecules with differing=
 kinds
> >of structures and would tend to give too large and inconsistent a value.
>
> Hmmm, that triggers the throught that the molecule may have significant
> 3 dimensional components; unless we have at least two views of it
> in different planes, we would not be able to tell whether the molecule
> just happens to be shorter in the direction of view, but long into
> or out of the direction of view.
> --
> =A0 "The quirks and arbitrariness we observe force us to the
> =A0 conclusion that ours is not the only universe." -- Walter Kistler

----------------------------------------------------------------------------=
----------------
Well Walter, I believe you're exactly right.  I imagine that, assuming
the molecule is the string-like object in the scene, that if you took
a picture of it at one time, at another time the molecule could have
squiggled to a completely different shape, and since it's probably
floating around in 3D in some liquid, its projected shape (onto a 2D
image) and length could be completely different from one image to the
next.  This change is called "repeatability" and is how this one
molecule specimen changes from one snap of that one molecule to the
next.  There's also something called "reproducibility" which is a
different specimen of the same species of molecule but imaged as a
separate sample on perhaps a different microscope.  So because of all
this, it's possible that the molecule could have different "lengths"
depending on when you snapped the picture because you're seeing just a
2D projection of it.

And another thing . . . when you take a look at the image he posted,
let's say the "head" of the molecule is that wad of curled up stuff
plus the loop, and the tail is the other end.  Now exactly where does
the tail end?  You can see that it's not so easy to answer.  Maybe it
curls around down below and heads back to the right.  (It's not as
obvious now - I think he replaced the with a smaller version of what
he used to have).  But the tail seems to sort of fade away and it's
not really clear where it ends.  It is sort of a judgement call.  And
what about the head?  Is there a bunch of length there that is all
tangled up into a ball so that you can't really know the "true"
length?

And Adrian didn't say what kind of precision he needs.  Maybe a fully
automated method with sub-pixel precision is needed, but maybe just
hand-tracing the line is good enough especially if the length changes
a lot from one snapshot to the next.

Because of all this, it probably doesn't make sense to go overboard
with fancy algorithms to get the length of the molecule in that one
single, specific picture with sub-pixel precision when the "length" of
the molecule may vary by tens or hundreds of pixels from one picture
to the next.

Hey Adrian, are you ever going to check back here for answers to your
question, and answer some of the issues brought up?
Regards,
ImageAnalyst