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Category Archives: Data analysis
A convolutional network to deconvolve calcium traces, living in an embedding space of statistical properties
As mentioned before (here and here), the spikefinder competition was set up earlier this year to compare algorithms that infer spiking probabilities from calcium imaging data. Together with Stephan Gerhard, a PostDoc in our lab, I submitted an algorithm based on convolutional networks. Looking … Continue reading
Whole-cell patch clamp, part 3: Limitations of quantitative whole-cell voltage clamp
Before I first dived into experimental neuroscience, I imagined whole-cell voltage clamp recordings to be the holy grail of precision. Directly listening to the currents that take place inside of a living neuron! How beautiful and precise, compared to poor-resolution techniques like fMRI or … Continue reading
Posted in Data analysis, electrophysiology, Neuronal activity, zebrafish
Tagged Data analysis, electrophysiology, zebrafish
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Spike detection competition
The main drawback of functional calcium imaging is its slow dynamics. This is not only due to limited frame rates, but also due to calcium dynamics, which are a slow transient readout of fast spiking activity. A perfect algorithm would infer the … Continue reading
Posted in Calcium Imaging, Data analysis, machine learning
Tagged Data analysis, machine learning, Matlab
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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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Spatial visualization of temporal components for neuronal activity imaging
The standard analysis workflow for neuronal activity imaging based on calcium signals is to 1) draw ROIs around putative neurons, 2) extract the average fluorescence time trace of this ROI, 3) work with this timetrace for subsequent analysis (principal components, … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, Neuronal activity
Tagged Calcium Imaging, zebrafish
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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
6 Comments
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 