Category Archives: Calcium Imaging

How deconvolution of calcium data degrades with noise

Posted on August 22, 2017 by P.T.R. Rupprecht

How does the noisiness of the recorded calcium data affect the performance of spiking-inferring deconvolution algorithms? I cannot offer a rigorous treatment of this question (Update August 2020: Now I have treated this question rigorously.) , but some intuitive examples. … Continue reading →

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, machine learning, Neuronal activity | Tagged , , , , | 3 Comments

A convolutional network to deconvolve calcium traces, living in an embedding space of statistical properties

Posted on August 1, 2017 by P.T.R. Rupprecht

As mentioned before (here and here), the spikefinder competition was set up earlier this year to compare algorithms that infer spiking probabilities from calcium imaging data. Together with Stephan Gerhard, a PostDoc in our lab, I submitted an algorithm based on convolutional networks. Looking … Continue reading →

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, machine learning, Neuronal activity | Tagged , , , , | 2 Comments

Spike detection competition

Posted on December 11, 2016 by P.T.R. Rupprecht

The main drawback of functional calcium imaging is its slow dynamics. This is not only due to limited frame rates, but also due to calcium dynamics, which are a slow transient readout of fast spiking activity. A perfect algorithm would infer the … Continue reading →

Posted in Calcium Imaging, Data analysis, machine learning | Tagged , , | 2 Comments

Preamplifier bandwidth & two ways of counting photons

Posted on September 20, 2016 by P.T.R. Rupprecht

For two-photon point scanning microscopy, the excitation laser is typically pulsing at a repetition rate of 80 MHz, that is one pulse each 12.5 ns. To avoid aliasing, it was suggested to synchronize the sampling clock to laser pulses. For this, it is important … Continue reading →

Posted in Calcium Imaging, Imaging, Microscopy | Tagged , , , | 10 Comments

The larval zebrafish, and the adult zebrafish

Posted on July 17, 2016 by P.T.R. Rupprecht

Zebrafish are often used as a model organism for in vivo brain imaging, because they are transparent. Or at least that is what many people think who do not work with zebrafish. In reality, most people use zebrafish larvae for in vivo … Continue reading →

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

Large field of view microscopes for mouse brain imaging

Posted on June 30, 2016 by P.T.R. Rupprecht

For typical confocal or two-photon microscopes that maintain (sub)cellular resolution, a high-magnification objective is needed (typically 16x, 20x or 25x). This in turn limits the field of view (FOV) to ⌀ 1.0-1.5 mm. For imaging in the mouse brain cortex, which is … Continue reading →

Posted in Calcium Imaging, Imaging, Microscopy | Tagged , , | 7 Comments

Spatial visualization of temporal components for neuronal activity imaging

Posted on May 3, 2016 by P.T.R. Rupprecht

The standard analysis workflow for neuronal activity imaging based on calcium signals is to 1) draw ROIs around putative neurons, 2) extract the average fluorescence time trace of this ROI, 3) work with this timetrace for subsequent analysis (principal components, … Continue reading →

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Fast z-scanning using a voice coil motor

Posted on April 6, 2016 by P.T.R. Rupprecht

We just published a paper on fast remote z-scanning using a voice coil motor. For 2P calcium imaging. It’s a nice paper with some interesting technical details. The starting point was the remote z-scanning scheme used by Botcherby et al. (2012) from … Continue reading →

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

Modulating laser intensity on multiple timescales (x, y and z)

Posted on March 25, 2016 by P.T.R. Rupprecht

In point-scanning microscopy and especially when using resonant scanners, the intensity of the beam is typically modulated using a Pockels cell. For resonant scanning, the dwell time per micrometer is not constant along the scanned line, and one wants either to … Continue reading →

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

Undistort/unwarp images for resonant scanning microscopy

Posted on February 16, 2016 by P.T.R. Rupprecht

For image acquisition using a resonant scanning microscope, one of the image axes is scanned non-linearly, following the natural sinusoidal movements of the resonant scanner. This leads to a distortion of the acquired images, unless a online correction algorithm or … Continue reading →

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