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Category Archives: Network analysis
Discrepancies between calcium imaging and extracellular ephys recordings
To record the activity from a population of neurons, calcium imaging and extracellular recordings with small electrodes are the two most widely used methods that are still able to disentangle the contributions from single units. Here, I would like to … Continue reading
Annual report of my intuition about the brain (2019)
How does the brain work and how can we understand it? I want to make it a habit to report some of the thoughts about the brain that marked me most during the past twelve month at the end of … Continue reading
Precise synaptic balance of excitation and inhibition
The main paper of my PhD just got published: Rupprecht and Friedrich, Precise Synaptic Balance in the Zebrafish Homolog of Olfactory Cortex, Neuron (2018). (PDF) You might like it if you are also interested in Classical balanced networks Things you … Continue reading
Entanglement of temporal and spatial scales in the brain, but not in the mind
In physics, many problems can be solved by a separation of scales and thereby become tractable. For example, let’s have a look at surface waves on water: they are rather easy to understand when the water wave-length is much larger … Continue reading
Open access 3D electron microscopy datasets of brains
One of the coolest technical developments in neuroscience during the last decade has been driven by 3D electron microscopy (3D EM). This allowed to cut large junks of small brains (or small junks of big brains) into 8-50 nm thick … Continue reading
Posted in Data analysis, machine learning, Microscopy, Network analysis, zebrafish
Tagged Data analysis, Microscopy, Network analysis, zebrafish
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The basis of feature spaces in deep networks
In a new article on Distill, Olah et al. write up a very readable and useful summary of methods to look into the black box of deep networks by feature visualization. I had already spent some time with this topic … Continue reading
Posted in machine learning, Network analysis, Neuronal activity
Tagged CNN, deep learning, machine learning, Network analysis, Python
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Neuroscience on Youtube
Recently, I’ve been to the Basel ICON conference, where the recent Nobel laureate Eric Betzig gave an impressive talk on microscopy techniques (including lattice light sheet, SIM and expansion microscopy). Some days ago, I found a similar talk by Eric … Continue reading
Posted in Data analysis, Microscopy, Network analysis
Tagged Data analysis, theoretical neuroscience
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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: 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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A blog about neurophysiology 