Matrix operation for ImageJ

[Pang, Zhengyu (GE Global Research)]

Dear all,

Could I read an image and convert image into a matrix, and then perform
some calculation on the matrix. I know that Matlab Image Processing
Toolbox can read an image into a metrice using A=imread() function.
Could ImageJ perfom similarly?

Thanks!

Zhengyu
> g Global Research Center
>
> ______________________________________________________________________
>
>           Zhengyu Pang, Ph.D.
                        Bioanalytics and Protein Science Laboratory
                        Biosciences Global Technology Organization
> One Research Circle, K1 5B37A
> Niskayuna, NY12309
> * [hidden email]
> *[phone]
>
>

[Joachim Wesner]

Hi Zhenyu,

are you talking Macro or Java/Plugin code?

ImageJ is slighltly less "automated" than MatLab here, but in a plugin you
can get a reference to the image data
as a 1D array (getPixels()) and convert it to any nD-matrix structure you
like with a simple loop or work directly on the
data using proper indexing.

General Matrix processing again is not a part of ImageJ, but there are a
zillion of free Java packages (MTFMatrix, JAMA, ....)
that can be integrated easily!

Sincerely

Joachim

ImageJ Interest Group <[hidden email]> schrieb am 24.06.2008 06:21:56:

> Dear all,
>
> Could I read an image and convert image into a matrix, and then perform
> some calculation on the matrix. I know that Matlab Image Processing
> Toolbox can read an image into a metrice using A=imread() function.
> Could ImageJ perfom similarly?
>
> Thanks!
>
> Zhengyu
> >       g Global Research Center
> >
> > ______________________________________________________________________
> >
> >           Zhengyu Pang, Ph.D.
>          Bioanalytics and Protein Science Laboratory
>          Biosciences Global Technology Organization
> >       One Research Circle, K1 5B37A
> >       Niskayuna, NY12309
> >       * [hidden email]
> >       *[phone]
> >
> >

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[Marcel]

I recently i anounced a new version of the software Bio7 (Window, Linux will follow later!) which is capable to transfer image data from an embedded imageJ version as a matrix with the help of a server to R. R itself is very powerful for matrix calculations.
In addition Bio7 offers an R shell to work directly with the transfered data in the R workspace.
The manipulated data then can be sent back to imageJ or evaluated and statistical analysed with R.

http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/imagetransfer.htm

Typical things that you can do with R and imageJ are to classify data , interpolate
spatial data or visualize matrix data from R.

The software can be downloaded here:

http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/links/index.html

Only if you don't know R:
The R language itself is an interpreted language but frequently uses compiled c,c++,fortran code to accomplish a task which makes it also very usable for image data.

With kind regards

M.Austenfeld