Category Archives: Calcium Imaging

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

Beyond correlation analysis

Posted on February 8, 2014 by P.T.R. Rupprecht

There are many papers out that use calcium imaging of a lot (tens to thousands) of neurons in animal brains. When I first encountered these kind of publications (roughly a year ago), it took me some hours to become familiar … Continue reading →

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