Category Archives: Uncategorized

The unsolved problems of neuroscience

The neuroskeptic blog recently mentioned a viewpoint paper which includes a list of the solved and unsolved problems of neuroscience. I’m probably not yet as deep into neuroscience as is the author of the paper, but I find it tempting to sharpen my … Continue reading

Posted in Uncategorized | 3 Comments

Gain and photons per pixel

In 2010, Labrigger wrote about how to measure the gain of a imaging system. As mentioned there in the comments, this was discussed in more detail by James Pawley in the confocal microscopy mailing list quite recently (following a question I asked to the list), and I was … Continue reading

Posted in Uncategorized | Tagged , , | 1 Comment

Colormaps (without colorspace theory)

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

Posted in Uncategorized | Leave a comment

The excitation PSF in 2P point scanning

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

Posted in Uncategorized | Leave a comment

Odd opinions in neurobiology

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

Posted in Uncategorized | Leave a comment

Genetically encoded voltage sensors

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

Posted in Uncategorized | Leave a comment

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.

Posted in Uncategorized | Tagged , | Leave a comment

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

Posted in Uncategorized | 1 Comment

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

Posted in Uncategorized | Tagged , , , | Leave a comment

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

Posted in Uncategorized | Tagged , | Leave a comment