Tag Archives: Microscopy

Simple geometrical optics to understand and design point-scanning microscopes

Posted on May 28, 2022 by P.T.R. Rupprecht

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 →

Posted in Calcium Imaging, Imaging, Microscopy | Tagged , , | 2 Comments

Public peer review files

Posted on February 11, 2022 by P.T.R. Rupprecht

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 , , , | Leave a comment

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 , , , , | 4 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 , , , , | Leave a 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 , , | 1 Comment

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