[ome-devel] Micro-Manager with Matlab

[Balaji Ramalingam]

Dear Yuriy,

We are glad that the integration workshop was useful for you and your team.

All the codes required for your workflow are present on github,
https://gist.github.com/bramalingam/1d36f827add8f5342068

The work shop was basically a proof of concept, and the code on github is no where near to being a release candidate.
So any comments/feedback from the user community via either the mailing-lists or the forums, would be very valuable at our end.

*Sunil and Doug might have to play around a little to get things going.

A gist :

1) Omero matlab toolbox comes with a libs folder , which carries the required jars for omero. Please add the following jars to it as well,
- bioformats_package.jar
- ini4j.jar

2) You will have to overwrite the (static) matlab google-collect.jar (packaged with matlab) with the guava.jar from the toolbox.
http://stackoverflow.com/questions/16366059/best-way-to-override-matlabs-default-static-javaclasspath

I have attached an example file for your benefit.

3) Startup code : (To set up the class path)

4) The acquisition code : micromanager_matlab_OMERO.m

Hope that helps.

Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: <Alexandrov>, Yuriy <y.alexandrov at imperial.ac.uk<mailto:y.alexandrov at imperial.ac.uk>>
Date: Monday, 9 June 2014 16:16
To: Balaji Ramalingam <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
Cc: "Kelly, Douglas J" <douglas.kelly09 at imperial.ac.uk<mailto:douglas.kelly09 at imperial.ac.uk>>, "Kumar, Sunil" <sunil.kumar03 at imperial.ac.uk<mailto:sunil.kumar03 at imperial.ac.uk>>
Subject: Micro-Manager with Matlab

Dear Balaji,

Thanks for Your kind attention and patience during our discussion of the issue at OME User meeting in Paris.
Your demonstration was impressive and practical at the same time.

I would like to ask for any code examples or related software that You find possible to share, and helpful for us to drive our devices via Micro-Manager (e.g. Plate Readers) directly from Matlab, and save data on disk or directly to Omero.
My colleagues Doug Kelly and Sunil Kumar are involved in Plate Readers and OPT hardware design and data acquisition, so they might be interested.

Hope to hear from You soon & keep collaborating,
Best wishes,
Yuriy

The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20140611/a485db9f/attachment.html>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: javaclasspath.txt
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20140611/a485db9f/attachment.txt>