[ome-devel] Image analysis module using matlab

[Tom Macura]

Dear Anh,

Hi. Thanks for your interest in OME. Since release 2.4.0 we support 
writing, importing, and running MATLAB analysis modules. I am currently 
writing documentation explaining this process. The documentation will 
be posted on the website next week.

I understand that you have some MATLAB code that you would like to run 
against images in OME.
Please tell me what is your operating system and MATLAB version.

To run analysis modules in OME you must
(1) Define the Semantic Types (in XML)
(2) Write the Module definition (in XML)
	(a) Define the Formal Inputs and Formal Outputs of the module
	(b) Write the execution instructions (MATLAB dependent)
	(c) Write the module (in MATLAB/C/Perl)
(3) [OPTIONAL] Write a chain (in XML) using the module
(4a) Import STs, Module XML, Chain XML (if written) into OME database
[at command-line> ome help import

(4b) Copy MATLAB source code of module to proper directory. The 
directory is set during the installation process. You must elect to 
install the OME MATLAB specific perl modules. Often /OME/matlab is the 
correct directory.

(5) If you didn't do optional step 3, run the ChainBuilder Agent from 
the Shoola (Java) interface to OME. Use this agent to construct your 
chain.

(6) Execute the chain from the command line
[at command-line> ome help execute

I strongly suggest you look at some example Module and ST definitions 
to get a feel for the process.
I suggest you try to get the MatlabTestChain running before you attempt 
to write your own modules+chains.

src/xml/OME/Tests/MatlabTest.ome (Module, ST definitions)
src/mxl/OME/MatlabTestChain.ome (Chain Definition)

src/matlab/Tests/MatlabTestInput.m
src/matlab/Tests/MatlabTestOutput.m

All the best,

Tom

On Mar 22, 2005, at 3:51 PM, Anh Vu wrote:

> Hi! I want to develop an application to analyze images stored in the
> OME database but I don't know how to make this application available
> as an option for analysis within OME. The server I run OME on has
> matlab installed and the user has license to run matlab. Let say I use
> the example matlab script described on the website that takes in an
> image and rotate it 90 degree, how would I add it as a standalone
> image analysis module? I believe I would have to put the matlab file
> into /OME/matlab, but I'm pretty confused on what I would have to do
> next. If anyone has any suggestion, please help.
>
> -Anh
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