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Tag Archives: laser scanning microscopy
Alignment tools
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 Alignment, laser scanning microscopy, Microscopy, Optics, Two-photon
4 Comments
Matlab code for control of a resonant scanning microscope
For control of resonant scanning 2P microscopes, my host lab uses a software that I have written in Matlab. Due to some coincidences, the software is based on Scanimage 4.2, a version developed few years ago for an interface with a Thorlabs scope and Thorlabs … Continue reading
Preamplifier bandwidth & two ways of counting photons
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 Calcium Imaging, laser scanning microscopy, Microscopy, Scanning
9 Comments
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
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy
7 Comments
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
Posted in Calcium Imaging, Imaging, Microscopy, Neuronal activity
Tagged Calcium Imaging, laser scanning microscopy, Microscopy, Scanning
3 Comments
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
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy, Scanning
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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
Posted in Calcium Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy, Scanning, zebrafish
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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
A blog about neurophysiology 