For health and civic-holiday reasons, it was a very short day today. I took a look at some of the classic or leading papers on cryo-EM data reduction, provided to me by Marina Spivak (SCDA). Many of these talk about optimizing a marginalized likelihood, which was just about all the cleverness I had come up with myself, so I am not sure I have much to contribute to this literature! The idea is that you really do have a strong prior on the distribution of projection angles (isotropic!) and you really do think each molecular shadow is independent, so there really is a case for marginalizing the likelihood function. Magland showed me correlations (time correlations) among neuron firings in his spike-sorting output. There is lots of phenomenology to understand there!
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