Re: Particle Analysis

Posted by dpoburko on
URL: http://imagej.273.s1.nabble.com/Particle-Analysis-tp3690320p3690321.html

I had a similar problem so I wrote a macro to run multiple thresholds
based on user defined variables. I believe there are similar macros out
there, but this one works well for me. I've hesitated making it
available to the whole community for lack of polish. But you're welcome
to give it a try. The idea is that it will determine the max intensity
in your image, perform a series of thresholds. It then uses analyze
particles for each threshold. As defined particles grow, the macro will
stop counting a given particle when it hits a maximum size. This allows
it to find small particles of greatly varying intensity of local
background.

Anyhow, let me know if you would like to give it a try and I'll clean up
the code to make it more self-explanatory.

Cheers,
Damon


Florian Sedlmeir wrote:

> Hi,
>
> I want to analyse particle-like structures with ImageJ. The problem
> is, that these particles usually have a good contrast against their
> local environment, but globally there are too many areas with similar
> or same grey values to threshold the image. So i have a few questions
> concerning this:
>
> - Is there an easy way to threshold only selected areas in a picture
> (to threshold the whole picture step by step)?
>
> - My particles are easily distinguishable with the eye because they
> are not as rough as their environment (+usually  there is a local
> difference in contrast). ImageJ is able to find the edges with the
> "find edges" tool, but unfortunatly it doesn´t create closed areas (my
> plan was to find edges, threshold the resulting picture and analyse
> the resulting particles then) Is there a solution for this a problem?
>
> - One of my friends showed me the "magic wand" tool in Photoshop,
> which is able to determine my particles properly. Unfortunatly the
> same tool in ImageJ is not able to do this, it seems to be too
> sensitive. (Are there parameters which can be adjustet?)
> So my question is: Does a plugin exist, which is able to do the same
> task as Photoshop´s magic wand?
>
>
> Thank you and best regards.
> Florian