Tag Archives: Microscopy

Large-scale calcium imaging & noise levels

Posted on October 4, 2021 by P.T.R. Rupprecht

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 , , , , | 6 Comments

Fast scanning, triplet states and photon yield

Posted on July 22, 2021 by P.T.R. Rupprecht

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 , , , , | 1 Comment

Interview with Bruno Pichler

Posted on September 25, 2020 by P.T.R. Rupprecht

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 , , | 2 Comments

Alignment tools

Posted on August 19, 2020 by P.T.R. Rupprecht

This blog posts covers some tools and techniques that I’m typically using to align two-photon microscopes. If you’re an expert, you will probably find nothing new, but if you haven’t been doing this for years, this might offer you some … Continue reading →

Posted in Imaging, Microscopy | Tagged , , , , | 4 Comments

A practical guide for adaptive optics

Posted on November 21, 2019 by P.T.R. Rupprecht

There is no standard curriculum to learn practical procedures about microscopy: how to align a setup, how to identify misalignments, how to identify broken parts, where to buy components, how to check their performance, and much more. How to learn … Continue reading →

Posted in Imaging, Microscopy | Tagged , , | 1 Comment

Review: An artificial ground truth for calcium imaging

Posted on September 2, 2019 by P.T.R. Rupprecht

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 →

Posted in Calcium Imaging, Data analysis, Imaging, Microscopy, Neuronal activity, Reviews | Tagged , , , , | 2 Comments

The cell-attached soundtrack of calcium imaging

Posted on July 30, 2019 by P.T.R. Rupprecht

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 →

Posted in Calcium Imaging, electrophysiology, Imaging, Neuronal activity, zebrafish | Tagged , , , | Leave a comment

Photon yield and pulse dispersion

Posted on March 13, 2019 by P.T.R. Rupprecht

This case report describes how a two-photon microscope was found to come with a fluorescence yield that was lower than expected; how the underlying cause was found out in a systematic manner; and how the problem was solved. All approaches and solutions are specific for the microscope under question. However, I hope that this report (1) will inspire other people who are troubleshooting or optimizing their microscopes, (2) will help other people better understand two-photon microscopes and the relevance of technical details. Continue reading →

Posted in Calcium Imaging, Imaging, Microscopy | Tagged , , , | 3 Comments

The power of correlation functions

Posted on January 9, 2019 by P.T.R. Rupprecht

During my physics studies, I got to know several mathematical tools that turned out to be extremely useful to describe the world and to analyze data, for example vector calculus, fourier analysis or differential equations. Another tool that I find … Continue reading →

Posted in Calcium Imaging, Data analysis, electrophysiology | Tagged , , , , | 6 Comments

Whole-cell patch clamp, part 4: look and feel

Posted on October 27, 2018 by P.T.R. Rupprecht

In previous blog posts, I have been discussing some aspects of whole-cell patch clamp recordings ([1], [2], [3], [4]). Today, I will show some instructive videos that I recorded during experiments. I’m hoping that they will convey the look and feel … Continue reading →

Posted in Calcium Imaging, electrophysiology, Imaging, Microscopy, Neuronal activity, zebrafish | Tagged , , , | 3 Comments