Category 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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Heating up the objective for two-photon imaging

To image neurons in vivo with a large field of view, a large objective is necessary. This big piece of metal and glass is in indirect contact with the brain surface, with only water and maybe a cover slip in … 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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Interview with Bruno Pichler

Bruno Pichler studied medicine, obtained a PhD in neuroscience, worked in the labs of Arthur Konnerth, Tom Mrsic-Flogel and Troy Margrie, and was R&D manager at Scientifica, before founding his own company, INSS, “to provide the international neuroscience community with … 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

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Annual report of my intuition about the brain (2019)

How does the brain work and how can we understand it? I want to make it a habit to report some of the thoughts about the brain that marked me most during the past twelve month at the end of … Continue reading

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Review: An artificial ground truth for calcium imaging

Selected paper: Charles, Song, Tank et al., Neural Anatomy and Optical Microscopy Simulation (NAOMi) for evaluating calcium imaging methods, bioRxiv (2019). What is the paper about? Calcium imaging is a central method to observe neuronal activity in the brain of … Continue reading

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The cell-attached soundtrack of calcium imaging

Old-school electrophysiologists like to listen to the ephys signals during experiments. For example, this allows to precisely hear when the patch pipette approaches a target neuron. The technique is discussed in the Axon Guide: “Audio Monitor: Friend or Foe?”. The … Continue reading

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Post-publication review: Somato-dendritic coupling of L5 neurons in V1

It requires more than a quick look at the abstract and the figures to fully understand a research paper and its limitations. One way to get there is to write a summary or critical review of a paper. In a contribution to … Continue reading

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