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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
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
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
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
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
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
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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
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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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
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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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