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Author Archives: P.T.R. Rupprecht
The most interesting machine learning AMAs on Reddit
It is very clear that Reddit is part of the rather wild zone of the internet. But especially for practical questions, Reddit can be very useful, and even more so for anything connected to the internet or computer technology, like machine … Continue reading
Posted in Data analysis, machine learning
Tagged deep learning, machine learning, Python, theoretical neuroscience
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How deconvolution of calcium data degrades with noise
How does the noisiness of the recorded calcium data affect the performance of spiking-inferring deconvolution algorithms? I cannot offer a rigorous treatment of this question (Update August 2020: Now I have treated this question rigorously.) , but some intuitive examples. … Continue reading
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
A short report from a Cold Spring Harbor lab course
One of the best things of being a PhD student is that one is supposed to learn new things. As part of this mission, I attended a two-week laboratory course in the Cold Spring Harbor Laboratories on ‘Advanced Techniques in … 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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Whole-cell patch clamp, part 2: Line-frequency pick-up via the perfusion system
With the experience of more than one year of patching (although you might say that this is not a lot), I’m now used to problems that I can solve after some time, but without being able to tell what the problem has … Continue reading
The spikefinder dataset
Recently, I mentioned a public competition for spike detection – spikefinder.codeneuro.org. I decided to spend a day two days and have a closer look at the datasets, especially the training datasets that provide both simultaneously recorded calcium and spike trains for single neurons. In … Continue reading
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The crow as an animal model for neuroscience
Close to my apartment in the outskirts of Basel, green fields and some small woods lie basically in front of my house door. This is also where some flocks of crows gather around, partly searching the fields for food, partly … Continue reading
Posted in electrophysiology, Imaging, Neuronal activity, Uncategorized
Tagged consciousness, 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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Matlab code for control of a resonant scanning microscope
For control of resonant scanning 2P microscopes, my host lab uses a software that I have written in Matlab. Due to some coincidences, the software is based on Scanimage 4.2, a version developed few years ago for an interface with a Thorlabs scope and Thorlabs … Continue reading
A blog about neurophysiology 