Tag Archives: Calcium Imaging

Online spike rate inference with Cascade

To infer spike rates from calcium imaging data for a time point t, knowledge about the calcium signal both before and after time t is required. Our algorithm Cascade (Github) uses by default a window that is symmetric in time … Continue reading

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Temporal dispersion of spike rates from deconvolved calcium imaging data

On Twitter, Richie Hakim asked whether the toolbox Cascade for spike inference (preprint, Github) induces temporal dispersion of the predicted spiking activity compared to ground truth. This kind of temporal dispersion had been observed in a study from last year … Continue reading

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Simultaneous calcium imaging and extracellular recording from the same neuron

Calcium imaging is a powerful method to record from many neurons simultaneously. But what do the recorded signals really mean? This question can only be properly addressed by experiments which record both calcium signals and action potentials from the same … Continue reading

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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

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, Network analysis, Neuronal activity, Reviews | Tagged , | 1 Comment

How well do CNNs for spike detection generalize to unseen datasets?

Some time ago, Stephan Gerhard and I have used a convolutional neural network (CNN) to detect neuronal spikes from calcium imaging data. (I have mentioned this before, here, here, and on Github.) This method is covered by the spikefinder paper … Continue reading

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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

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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

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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

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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

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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

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