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New file type into omero

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New file type into omero

Postby chriswood » Tue May 11, 2010 2:21 pm

I am interested in importing fluorescence correlation spectroscopy (fcs) files from a Zeiss confo-cor 3 into OMERO. The data in this case is generally a time series with one or two channels.

I am able to create a new “image” and put the raw bytes into pixels and also retrieve them from the server. What I would like to in addition to this is store the metadata and be able to view the time series and correlation curve in Insight.

So, is there standard that is used for developing import methods and metadata? And is there a good way to add functionality to Insight (like can be done with ImageJ).

If anyone has any documents for these questions I would appreciate it.

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Re: New file type into omero

Postby cxallan » Thu May 20, 2010 1:53 pm

There are a few standard ways to get data into OMERO. One is of course as you have already been doing using the OMERO API. Another, and probably the most useful, is to create a Bio-Formats reader. This library is what OMERO.importer uses.

Are you familiar at all with Bio-Formats?

As OMERO.insight is open source, like ImageJ, you're certainly welcome to hack directly on the source code itself. We're happy to accept patches! :D Alternatively if you'd like to write an entire agent, which is similar to an ImageJ plug-in, Jean-Marie can likely help you out.
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