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Getting a DOI looks like it would be a good idea. We're going to have a 3.0 tagged release soon-ish so I'll probably try to get a DOI for that. In the meantime if you have to you could cite this PLoS paper, which is the closest thing to an OpenMIMS publication.
How should I cite OpenMIMS in my thesis?
With Hyperspy (another piece of software directed at microscopy), we let people cite using a DOI reference: http://hyperspy.org/hyperspy-doc/current/citing.html
Are there papers published, perhaps?
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