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Re: special case of remove particle

Posted by chris elliott on May 11, 2010; 4:02pm
URL: http://imagej.273.s1.nabble.com/how-to-disable-results-window-and-log-table-tp3688351p3688353.html

Mtrack2 will require a particle to exist for N frames, and allow size
discrimination. it works nicely with fly larvae, so maybe it will have a
hint for you

http://valelab.ucsf.edu/~nico/IJplugins/MTrack2.html
chris

On 11/05/2010 16:35, Rodrigo Gonçalves wrote:

> Dear all,
>
> I'm observing particles in a stack. The stack was extracted from a VHS video, therefore some images contain outliers and "ghost" particles every one and then  (video signal artifacts).
>
> My goal is to automatize the counting and tracking for the whole stack (as I have several stacks). Therefore I'm trying to "erase" everything from the stack that is not relevant (i.e., non actual particles). I can do the 98% of the job using the directly available tools in ImageJ to erase minor particles and enhance the visibility of the particles I want (adjusting brightness, despeckle, find edge, etc.).
>
> BUT there are still a couple of dots in some frames (slices), which unfortunately are the same size as my particles and therefore I can not make ImageJ distinguish from the interest particles. The particularity of these evil dots is that they appear only in one or to consecutive slices, and then disappear. I can get rid of almost all the non-important particles with the
> Particle Remover plugin (which is great!), but still have these
> "transient" dots.
>
>
> My question: do you know of something like a Particle Remover but with a temporal (or stack-playback) function? The parameter would be not only circularity and size, but also minimal frames of existence or something like that.
>
> Or maybe I should try to create a macro in which I can tell the program that if the particle is present only in X consecutive frames (in my case, 2 as maximum), then delete those frames or mark them, etc.? I guess that this could be done with a macro or plugin (counting particles and comparing the number with the previous slice, etc.) but maybe some of you has already done it.
>
> Thanks a lot in advance for your time,
> Rodrigo
>
> ________________________
>
> Rodrigo J. Gonçalves
>
>
>
> Igualdad - Equality
>
> Libertad - Freedom
>
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> www.maketradefair.com
>
>     www.oxfam.org
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