Author Archives: P.T.R. Rupprecht

Colormaps (without colorspace theory)

Posted on January 27, 2015 by P.T.R. Rupprecht

The labrigger blog keeps posting links to all kind of colormaps, so I tried out some of them. Being partially colorblind, I do not like the default colormaps e.g. of Matlab. Here are some noisy data, with two different scalings … Continue reading →

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The excitation PSF in 2P point scanning

Posted on January 27, 2015 by P.T.R. Rupprecht

For quite some time, I was unsure about the reasons why images degrade when going to deeper layers with 2P point scanning. This also has remained largely unclear to me until the present point, after having done the estimates presented … Continue reading →

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Odd opinions in neurobiology

Posted on November 10, 2014 by P.T.R. Rupprecht

I have the impression that neurobiology is the single field in biology where many people with sometimes rather selective knowledge of the field have strong opinions about how it should work (i.e. how the brain should work). I don’t want to … Continue reading →

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Genetically encoded voltage sensors

Posted on August 16, 2014 by P.T.R. Rupprecht

Genetically encoded calcium indicators (GECIs) are nowadays commonly used to report activity of many cells in transgenic animals; similarly, injected dyes like Rhod-2 can act as optical calcium reporters. The main shortcoming of this method is that it measures neuronal … Continue reading →

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Neuroengineering blogs

Posted on May 4, 2014 by P.T.R. Rupprecht

Some neuroscience blogs that do not focus on biological questions (here’s a list on circuit neuroscience blogs), but rather on technical hurdles of lab work and how to overcome them. Here, I’d like to point out some blogs that are to … Continue reading →

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PhD at the FMI

Posted on April 17, 2014 by P.T.R. Rupprecht

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.

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Beyond correlation analysis: Dynamic causal modeling (DCM)

Posted on March 25, 2014 by P.T.R. Rupprecht

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 →

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Beyond correlation analysis: Transfer entropy

Posted on March 19, 2014 by P.T.R. Rupprecht

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 →

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Beyond correlation analysis: Granger causality

Posted on March 15, 2014 by P.T.R. Rupprecht

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

Posted on March 13, 2014 by P.T.R. Rupprecht

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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