Category Archives: Microscopy

“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

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Ambizione fellowship and an open PhD position

I’m glad to share that I am going to start my own junior research group at the University of Zurich in March 2023! As an Ambizione fellow, I will receive funding for my own salary, some equipment, consumables and a … Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, machine learning, Microscopy, Neuronal activity | Tagged , , , , , , , | Leave a comment

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

Posted in Calcium Imaging, Data analysis, Imaging, machine learning, Microscopy, Neuronal activity, Review, zebrafish | Tagged , , , , | Leave a comment

Video introduction to CASCADE

A video with tutorial on CASCADE, a supervised method to infer spike rates from calcium imaging data. Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, machine learning, Microscopy, Neuronal activity | Tagged , , , , | Leave a comment

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

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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

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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

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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

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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

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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

Posted in Calcium Imaging, Imaging, Microscopy | 2 Comments