Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I'd have to agree with Jim here.
My suspicion is that this is one of the most common errors in
colocalisation studies, and one I have to deal with constantly amongst
our users.
To link with the "automation" thread, the ease with which programs can
do manipulations like through-projections / stack-flattening and then
count various classes of pixels means that there is an obligation not
only learn how the images are collected, but then how they are
processed... once again, automation is great, but you really need to
know what the programs are doing.
Which brings me to an underlying grip about the lack of appropriate
documentation that some manufacturers provide. I know this issue has
been discussed on the list many times before. But if some combination
of hardware and software is going to be automated, we need to know how
it is being done, what algorithms are used, and what, if any,
processing steps are involved. Otherwise, it's not science...
hope that helps
IAN
On Wednesday, May 16, 2007, at 05:47 AM, James Pawley wrote:
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hi Andrea,
>
>
>
> I have used MetaMorph to perform colocalisation in 3d stacks also. I
> created a 3d image from the stack of each color, then flattened each
> by using stack arithrimatic, then used the colocalization application
> with the coorelation plot. I compared to actually using a journal
> that ran through each of the images in the stack, using the same way
> you discussed on your web page. The data was very similar. Try it,
> and see what you come up with.
>
>
>
> Cheers!
>
>
>
> Michelle Sutorik
>
>
>
> This plan may work for some stain distributions (i.e., when the stain
> is only in a plane or when no stained feature is behind, or in front
> of, any other stained feature) but is VERY MUCH TO BE DISCOURAGED in
> the general case.
>
> Objects actually located above and below each other will score as
> co-localized when they should not do so.
>
> This is about the worst shortcut you can take.
>
> I would automatically reject any paper in which such a plan was
> described.
>
> Sorry to be so grumpy...
>
> Jim Pawley
>
>
>
>
* * * * * * * * * * *
Prof Ian Gibbins
Anatomy & Histology
Flinders University
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