Tag Archives: Calcium Imaging

The larval zebrafish, and the adult zebrafish

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

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Large field of view microscopes for mouse brain imaging

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

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Spatial visualization of temporal components for neuronal activity imaging

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

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

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

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

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Undistort/unwarp images for resonant scanning microscopy

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

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Point spread functions

One way to characterize the quality of one’s microscope is to measure the point spread function (PSF), that is the image that is created by a point source  (which can be a fluorescent bead smaller than the expected size of the … Continue reading

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EODs for kHz imaging

J. Schneider et al., and S. Hell recently published a paper on STED microscopy, using EODs (electro-optical deflectors) to scan 512 x 512 pixels at frame rates of 1000 Hz. Compared to AODs, EODs offer the costumer-friendly advantage of not dispersing … Continue reading

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Gain and photons per pixel

In 2010, Labrigger wrote about how to measure the gain of a imaging system. As mentioned there in the comments, this was discussed in more detail by James Pawley in the confocal microscopy mailing list quite recently (following a question I asked to the list), and I was … Continue reading

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Some interesting 2-photon microscopy papers

In the last few months, I built a special kind of 2P-microsope. In the meantime, I encountered some papers on microscope techniques which I found interesting and worth a side-note. Using AODs instead of galvoscanners for point-scanning: High-speed in vivo … Continue reading

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