Tag Archives: photons

Dirigo: a future Python alternative to Scanimage?

Posted on November 14, 2025 by P.T.R. Rupprecht

Over the last 20 years, many microscopes that are capable of resonant scanning two-photon microscopy have converged on using ScanImage, a powerful software package with many strengths but also two downsides: First, it is no longer open-source, and second, it … Continue reading →

Posted in Calcium Imaging, Imaging, Microscopy, neuroscience | Tagged , , , , | Leave a comment

I never meant to study the brainstem

Posted on September 25, 2025 by P.T.R. Rupprecht

I was recently invited to contribute a guest post on Substack by Vijay Iyer – some years ago one of the main developers of ScanImage in the lab of Karel Svoboda, and more recently a strong advocate for ME/CFS awareness … Continue reading →

Posted in Astrocytes, Brain machine interface, Calcium Imaging, hippocampus, Locus coeruleus, Microscopy, writing | Tagged , , , , , , , | Leave a comment

Accurately computing noise levels for calcium imaging data

Posted on April 25, 2025 by P.T.R. Rupprecht

It is fascinating how much data quality can vary between different calcium imaging data sets. In this blog post, I will discuss a metric to quantify and compare data quality and in particular shot noise between calcium imaging datasets. This … Continue reading →

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

Protocols to check the performance of your multiphoton microscope

Posted on March 18, 2025 by P.T.R. Rupprecht

In an exceptionally useful paper, Lees et al. provide a set of protocols for checking the performance of your multiphoton microscope: Standardized measurements for monitoring and comparing multiphoton microscope systems (link to preprint). The paper covers the following procedures: Check … Continue reading →

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

Non-linearity of calcium indicators: history-dependence of spike reporting

Posted on March 14, 2025 by P.T.R. Rupprecht

Calcium indicators are used to report the calcium concentration inside single cells. In neurons, calcium imaging can be used as a readout of neuronal activity (action potentials). However, some calcium indicators like GCaMP transform the calcium concentration of a cell … Continue reading →

Posted in Calcium Imaging, Data analysis, Imaging, machine learning, Microscopy, neuroscience | Tagged , , , , , , | Leave a comment

A resource paper for building two-photon microscopes

Posted on September 28, 2024 by P.T.R. Rupprecht

The article discusses the challenges in learning to build microscopes, highlighting a manuscript by Schottdorf et al. that offers practical assembly instructions and rationale based on years of successful use. It emphasizes useful insights, such as design suggestions, performance compromises, and comprehensive documentation on GitHub, making it a valuable resource for researchers. Continue reading →

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

Why your two-photon images are noisier than you expect

Posted on April 24, 2024 by P.T.R. Rupprecht

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 , , , , , | 22 Comments

Improving the resonant scanner’s sync signal using a phase locked loop (PLL)

Posted on October 19, 2023 by P.T.R. Rupprecht

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 , , | 6 Comments

Interesting papers on recent neuroscience methods

Posted on September 12, 2023 by P.T.R. Rupprecht

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 , , | Leave a comment

Interesting papers on online motion correction for calcium imaging

Posted on September 4, 2023 by P.T.R. Rupprecht

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 , , , , | 4 Comments