Path: news.mathworks.com!not-for-mail
From: "Ken Campbell" <campbeks@gmail.com>
Newsgroups: comp.soft-sys.matlab
Subject: Re: Need algorithm help: molecule length from an image
Date: Tue, 13 May 2008 04:26:03 +0000 (UTC)
Organization: University of Kentucky
Lines: 142
Message-ID: <g0b58r$lqo$1@fred.mathworks.com>
References: <g023qb$j0m$1@fred.mathworks.com> <g07jfi$afk$1@fred.mathworks.com>  <7d6b1108-5156-49cb-84bf-423bb11b437a@k13g2000hse.googlegroups.com>
Reply-To: "Ken Campbell" <campbeks@gmail.com>
NNTP-Posting-Host: webapp-05-blr.mathworks.com
Content-Type: text/plain; charset="ISO-8859-1"
Content-Transfer-Encoding: 8bit
X-Trace: fred.mathworks.com 1210652763 22360 172.30.248.35 (13 May 2008 04:26:03 GMT)
X-Complaints-To: news@mathworks.com
NNTP-Posting-Date: Tue, 13 May 2008 04:26:03 +0000 (UTC)
X-Newsreader: MATLAB Central Newsreader 534287
Xref: news.mathworks.com comp.soft-sys.matlab:468049


ImageAnalyst <imageanalyst@mailinator.com> wrote in message 
<7d6b1108-5156-49cb-84bf-
423bb11b437a@k13g2000hse.googlegroups.com>...
> 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

I would be interested in Adrian's comments too but I've 
enjoyed following the thread and thinking about the 
different ways of approaching the problem. There have been 
some good ideas.

I am wary of answering questions that Adrian really needs 
to answer but I think the image shows a molecule that has 
been deposited on a surface and then stained with something 
to increase the contrast for electron microscopy. This 
means that the molecule is deposited 'flat' on a surface  
and doesn't cross over itself. I agree that the problem is 
harder if this isn't the case. For what it's worth I don't 
think that you can do electron microscopy on molecules 'in 
solution'.

I've seen people talk about similar images in seminars I've 
attended and I'd be surprised if Adrian needs to 'unravel' 
the ball or requires 'sub-pixel' methods. I think 
the 'perimeter' approach is probably the most appropriate 
idea that's been suggested so far for this type of work.

But as ImageAnalyst points out, that's really for Adrian to 
decide.

Ken