http://imagej.273.s1.nabble.com/Segmentation-of-granular-stuff-tp3698915p3698916.html
> On 6 Jul 2007, at 20:42, Jolien Connor wrote:
>
>> Hi,
>>
>> I am trying to do something similar to what many try
>> to do with thresholding -- find a way for the software
>> to pick out my pixels of interest away from the
>> background. In my case, it is granular "stuff" that
>> are intracellular inclusions in the brain. We have
>> many image montages taken of mouse brain sections and
>> we are trying to quantitate the percentage of specific
>> brain regions occupied by the inclusions (percent
>> volume). Some of the monochrome images are here:
>>
>> www.waisman.wisc.edu/cmn/mutant high load.tif
>> www.waisman.wisc.edu/cmn/mutant high load and
>> faint.tif
>> www.waisman.wisc.edu/cmn/mutant low load and faint.tif
>> www.waisman.wisc.edu/cmn/control.tif
>>
>> They are very large since they are montages; contact
>> me at
[hidden email] if you want them and
>> can't get them.
>>
>> If you look at the pictures of the mutants compared
>> with the control, you can see what they are -- the
>> bright granular stuff all over the place. Cells that
>> contain the inclusions sometimes have processes that
>> show up, and we only want to pick out the brightest,
>> most granular stuff, which are the inclusions. We
>> want a method that can tell the difference between
>> mutants and controls, as well as between high load
>> mutants and low load mutants (lots of them versus just
>> a few).
>>
>> The biggest problem right now seems to be that some of
>> our pictures are faint, possibly because the stain
>> weakened, our mercury bulb Atto Arc controller is
>> dying, or some other reason. As humans, we can still
>> pick them out, but we don't have a thresholding
>> algorithm that can handle this problems.
>>
>> We have been using the Subtract Background function,
>> then thresholding the image, and can't get consistent
>> results. We use a brightfield image that lines up
>> with each monochrome image to trace our regions, then
>> have ImageJ calculate the % Area occupied by pixels
>> above threshold. There's no threshold we could pick
>> that would correctly differentiate between controls,
>> low load mutants and high load mutants. Any ideas?
>>
>> Thanks,
>>
>> Jolien Connor
>> University of Wisconsin
>
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