Category Archives: Calcium Imaging

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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All-optical entirely passive laser scanning with MHz rates

Is it possible to let a laser beam scan over an angle without moving any mechanical parts to deflect the beam? It is. One strategy is to use a very short-pulsed laser beam: A short pulse width means a finite … Continue reading

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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, but some intuitive examples. The short answer: If a calcium transient is not visible at … Continue reading

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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

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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

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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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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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