Re: Getting more information on ImageJ algorithms

Posted by Adam Hughes on Nov 24, 2013; 8:37pm
URL: http://imagej.273.s1.nabble.com/Getting-more-information-on-ImageJ-algorithms-tp5005673p5005682.html

On Sat, Nov 23, 2013 at 10:18 PM, Jim Passmore <[hidden email]> wrote:

> Adam,
>
> One of the beautiful things about ImageJ is it is open source--most of
> the core is public domain I think, with some other open source
> licenses for different plugins.  Therefore you can browse the code at
> http://rsbweb.nih.gov/ij/developer/source/index.html
> and the API, at http://rsbweb.nih.gov/ij/developer/api/index.html
> (Requires learning some Java, but learning to *read* java is a lot
> easier than learning to code projects!)
>
> On Fri, Nov 22, 2013 at 4:51 PM, Adam Hughes <[hidden email]>
> wrote:
> > I was hoping to learn a bit more about what goes on under the hood in
> these
> > processes.  In particular, how does the automatic threshold choose it's
> > region on the histogram?
>
> This one is actually in the FAQ
> http://rsbweb.nih.gov/ij/docs/faqs.html#auto

Thanks, sorry I had overlooked this!

>
>
>
> > Is Despeckle the common name for this method, and
> > what exactly does it compute?
> Not sure of other names, but again, look at the actual Java and the
> API.  You'll see a that despeckle runs a median with a radius of 1.
>
> > Same for Analyze Particles.  Are these
> > methods unique to ImageJ, or are they based on some generally accepted
> > methods in image analysis.  If so, what other names to they go by? I'm
> > hoping to get a better sense of where this fits in to the bigger picture
> of
> > image analysis, so any context is quite helpful.
>
> If you have trouble finding the right Java class, method, etc., try
> using the "command finder" in ImageJ.  Press ctrl-L, and type the
> command into the search field.  For example, "Analyze Particles" is in
> ij.plugin.filter.ParticleAnalyzer.  This requires some effort, but
> you'll definitely understand what's happening "under the hood."
> You'll then have to research what other methods are found in
> literature & other software.  Beware this information might not be
> available for commercial packages.  That's why many on this list use
> ImageJ.
>

Thanks for the tip with ctrl-L.  I had looked at the API before but
couldn't find what I was looking for.  I wish I was more fluent in Java,
but certainly have a better idea now, thank you.

>
> It will get quite interesting, so have fun!
>
>
> --
> Jim Passmore
> Research Associate
> Sealed Air Corporation
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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