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Author Archives: P.T.R. Rupprecht
5 reasons why to use Cascade for spike inference
Our paper on A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging is out now in Nature Neuroscience. It consists of a large and diverse ground truth database with simultaneous calcium imaging and juxtacellular recordings … Continue reading
Fast scanning, triplet states and photon yield
In point-scanning microscopy like two-photon or confocal microscopy, a focused laser beam is scanned across the field of view and thereby sequentially recovers an image of the object. In this blog post, I will discuss the idea that scanning faster … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, Neuronal activity
Tagged Calcium Imaging, Microscopy, photons, Scanning, zebrafish
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Research and Intuition
So far I was very fortunate with my scientific long-term mentors and supervisors: both of them are kind, open, creative and stunningly intelligent. I could not wish for more. However, when asked about a role model, I would mention a … Continue reading
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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
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
Posted in Calcium Imaging, Imaging, Microscopy
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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
Annual report of my intuition about the brain (2020)
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
Posted in Data analysis, machine learning, Network analysis, Neuronal activity, Reviews
Tagged complexity, deep learning, evolution, self-organization
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Hodgkin-Huxley model in current clamp and voltage clamp
As a short modeling session for an electrophysiology course at the University of Zurich, I made a tutorial for students to play around with the Hodgkin-Huxley equations in a Colab Notebook / Python, which does not require them to install … Continue reading
Posted in electrophysiology, Neuronal activity
Tagged action potential, electrophysiology, Python
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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
Posted in Calcium Imaging, Data analysis, Imaging, Microscopy
Tagged interview, Microscopy, Two-photon
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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
