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Author Archives: P.T.R. Rupprecht
PhD at the FMI
In April, I started my PhD in neuroscience in the Friedrich lab at the FMI. Topic will be the investigation of brain areas for higher olfactory processing in the zebrafish, and I’ll be working with different physiological methods.
Beyond correlation analysis: Dynamic causal modeling (DCM)
I was surprised to find a method like DCM in Olav Stetter’s list (link) for neural network methods (even as a so-called ‘standard method’), because it differs from those I discussed before. I will now describe why I don’t think … Continue reading
Posted in Data analysis, Network analysis
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Beyond correlation analysis: Transfer entropy
When reading through the first informative web pages on transfer entropy, it turns out how closely its concept is related to mutual information, and even closer to incremental mutual information; and, although it’s based on a totally different approach, it tries to … Continue reading
Posted in Data analysis, Network analysis
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Beyond correlation analysis: Granger causality
Granger causality has been named after the econometrician Clive Granger and has been adapted in the last 10-15 years as time-series analysis tool for neuroscience. The best account for this topic that I have found, is on scholarpedia again (link). … Continue reading
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Some interesting 2-photon microscopy papers
In the last few months, I built a special kind of 2P-microsope. In the meantime, I encountered some papers on microscope techniques which I found interesting and worth a side-note. Using AODs instead of galvoscanners for point-scanning: High-speed in vivo … Continue reading
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Tagged Calcium Imaging, Microscopy, Scanning, Temporal Focusing
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Beyond correlation analysis: incremental mutual information
Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits is a 2010 paper by A. Singh and N. Lesica in PLoS Computational Biology that describes a method which can be used as an … Continue reading
Beyond correlation analysis: mutual information
Last time, I mentioned a website which gives an overview of methods to analyze neuronal (and other) networks. Let’s have a closer look. Here’s a list of the methods: Cross-correlation (the standard method) Mutual Information Incremental Mutual Information Granger Causality … Continue reading
Posted in Data analysis, Network analysis
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Beyond correlation analysis
There are many papers out that use calcium imaging of a lot (tens to thousands) of neurons in animal brains. When I first encountered these kind of publications (roughly a year ago), it took me some hours to become familiar … Continue reading
Posted in Calcium Imaging, Data analysis, Neuronal activity
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A blog about neurophysiology 