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Author Archives: P.T.R. Rupprecht
Weblogs on circuit and cellular neuroscience
A couple of days ago, I discovered a list of neuroblog feeds managed by Neurocritic, covering almost 200 blogs in total. Out of those, I picked the blogs most relevant for circuit and cellular neuroscience. This excludes most blogs on cognitive neuroscience and … Continue reading
Deep learning, part IV (2): Compressing the dynamic range in raw audio signals
In a recent blog post about deep learning based on raw audio waveforms, I showed what effect a naive linear dynamic range compression from 16 bit (65536 possible values) to 8 bit (256 possible values) has on audio quality: Overall perceived quality … Continue reading
Preamplifier bandwidth & two ways of counting photons
For two-photon point scanning microscopy, the excitation laser is typically pulsing at a repetition rate of 80 MHz, that is one pulse each 12.5 ns. To avoid aliasing, it was suggested to synchronize the sampling clock to laser pulses. For this, it is important … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy, Scanning
10 Comments
Deep learning, part IV: Deep dreams of music, based on dilated causal convolutions
As many neuroscientists, I’m also interested in artificial neural networks and am curious about deep learning networks. I want to dedicate some blog posts to this topic, in order to 1) approach deep learning from the stupid neuroscientist’s perspective and 2) to get a feeling … Continue reading
Posted in machine learning
Tagged deep learning, machine learning, recurrent networks, theoretical neuroscience
8 Comments
Whole-cell patch clamp, part 1: introductory reading
Ever since I my interested in neuroscience become more serious, I was fascinated by the patch clamp technique, especially applied for the whole cell. Calcium imaging or multi-channel electrophysiology (recent review) is the way to go in order to get an idea what … Continue reading
Posted in electrophysiology, Microscopy, zebrafish
Tagged Calcium Imaging, electrophysiology, patch clamp, zebrafish
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The larval zebrafish, and the adult zebrafish
Zebrafish are often used as a model organism for in vivo brain imaging, because they are transparent. Or at least that is what many people think who do not work with zebrafish. In reality, most people use zebrafish larvae for in vivo … Continue reading
Posted in Calcium Imaging, Neuronal activity, zebrafish
Tagged Calcium Imaging, zebrafish
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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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Large field of view microscopes for mouse brain imaging
For typical confocal or two-photon microscopes that maintain (sub)cellular resolution, a high-magnification objective is needed (typically 16x, 20x or 25x). This in turn limits the field of view (FOV) to ⌀ 1.0-1.5 mm. For imaging in the mouse brain cortex, which is … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy
7 Comments
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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Reglo ICC serial port control via Matlab
For my experiments with zebrafish, I typically generate dynamic odor landscapes for the fish / fish brain explant by varying the speed of the wheels of an Ismatec peristaltic pump, thereby changing the concentration of the applied stimuli over time. Recently, I bought one of their digital … Continue reading
Posted in Uncategorized
Tagged Cole-Parmer, Ismatec, Matlab, Reglo ICC, serial port, USB
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A blog about neurophysiology 