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Author Archives: P.T.R. Rupprecht
Simple geometrical optics to understand and design point-scanning microscopes
Custom-built microscopes have become more and more sophisticated over the last years to provide a larger FOV, better resolution through some flavor of adaptive optics or simply more neurons simultaneously. Professional optical engineers are hired to design the ideal lens … Continue reading
Public peer review files
Peer-review is probably the most obscure part of the publication of scientific results. In this blog post, I would like to make the point that the best way to learn about it – except by being directly involved – is … Continue reading
Posted in Calcium Imaging, Imaging, machine learning, Microscopy, Neuronal activity, Review
Tagged deep learning, Microscopy, neuroscience, peer review
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Annual report of my intuition about the brain (2021)
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
Large-scale calcium imaging & noise levels
Calcium imaging based on two-photon scanning microscopy is a standard method to record the activity of neurons in the living brain. Due to the point-scanning approach, sampling speed is limited and the dwell time on a single neuron reduces with … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, Microscopy, Neuronal activity
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning
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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
A blog about neurophysiology 