Open Microscopy Environment

I want to create an analysis chain in OMERO using existing Matlab code. Can I use the latest schema release (July 2012) for that purpose? It will also be very helpful if people can share their experience in implementing a Matlab analysis chain. I have not done this before and any help will be much appreciated.

Thanks in advance.

Hello nandyk,

AnalysisChain and MLI were last part of the the schema in September 2009, but they were legacy at that point. They were last worked on seriously pre 2007.

For the current state of the schemas see:
http://www.openmicroscopy.org/Schemas/
For a change history see:
https://www.openmicroscopy.org/site/sup ... s/versions

They have never been part of OMERO. They were used by the original OME server (developed from June 2004 to October 2007).

You can use OMERO with Matlab, but not via AnalysisChain.

Let us know what it is you are trying to do and we can suggest the current way of achieving what you want.

Hope this helps,

Andrew

Hi Andrew,

Thanks for the information. I have a MATLAB analysis software which is modular and I want to tool-chain them using OMERO. I am currently using a file to store the analysis process description(information such as script location, inputs and outputs) which I use to run the analysis. However, given the infrastructure provided by OMERO, I was thinking of using it for the same.

It will be very helpful if you could suggest a good way of tool-chaining the modules using OMERO. Thanks,

Kaustav Nandy

Hi,

The way you choose to store any data in OMERO really depends on the nature of the data and how you might want to retrieve or query it.

You probably want to use annotations of some type, either plain text (comment) or xml (if that's the current form of your analysis files) or even a File annotation.

You could link a single annotation to all of the images in the chain, possibly including image IDs in the text/xml itself, to indicate which steps apply to which images. OR you could split the analysis file into smaller pieces that describe a single analysis step each, and link each one to the relevant image that was generated from that step.

In a very simple 'analysis chain' I have previously used the description field for the new image to record the ID of the source image and a number of parameters for how it was processed (see the end of http://cvs.openmicroscopy.org.uk/snapsh ... pting4.mov). If you add "Image ID: 123" to an image description, OMERO.insight client will actually give you a link to that image (we haven't yet done Image-Image links 'properly' in OMERO).

I guess you may not have an image in OMERO for every step in the chain, in which case the first idea might be better.

You can use your own namespace on the annotation to identify them as coming from your analysis chain (helps with querying etc).

Hope that helps,

Will.