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Category Archives: Imaging
Why your two-photon images are noisier than you expect
A gallery of calcium imaging recordings of neurons and astrocytes with single noisy frames on the left and averaged beautiful noise-free images on the right side. Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience, zebrafish
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning, zebrafish
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Improving the resonant scanner’s sync signal using a phase locked loop (PLL)
Calcium imaging with two-photon point scanning is the technique to chronically record from identified neurons in the living brain of animals. The central piece of two-photon point scanning microscopes is a scan engine. This can be a complex optical device … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Microscopy, photons, Scanning
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Interesting papers on recent neuroscience methods
Find below three interesting methods papers relevant for neuroscience. All three of them are, in my opinion, worth a quick read. Acoustic cameras to localize ultrasound vocalization of mice Sterling et al. (2023) from the lab of Bernhard Englitz addressed … Continue reading
Posted in Data analysis, Imaging, Microscopy, neuroscience, Reviews
Tagged Data analysis, Microscopy, photons
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Interesting papers on online motion correction for calcium imaging
In a living animal, the brain is moving up and down in the skull. This brain motion can be due to breathing, heartbeat, tongue movements, but also due to changes of posture or running. For each brain region and posture, … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, machine learning, Microscopy, Neuronal activity, neuroscience
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning
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“Laser Scanners” by William Benner
William Benner is a scanner enthusiast and the president of the company Pangolin. His company sells equipment mostly for laser shows but also for other applications. Some years ago, he wrote a book on “Laser Scanners”, which is available through … Continue reading
Self-supervised denoising of calcium imaging data
This blog post is about algorithms based on deep networks to denoise raw calcium imaging movies. More specifically, I will write about the difficulties to interprete their outputs, and on how to address these limitations in future work. I will … Continue reading
Video introduction to CASCADE
A video with tutorial on CASCADE, a supervised method to infer spike rates from calcium imaging data. Continue reading
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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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
5 Comments
A blog about neurophysiology 