Mrsic-Flogel Lab

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FocusStack & StimServer

FocusStack is a new, open-source, Matlab-based two-photon analysis toolchain designed to process large two-photon imaging stacks with only a small memory footprint. This makes analysis possible on comparatively cheap consumer hardware. FocusStack is designed to integrate with StimServer, a new open-source Matlab-based server for visual stimulus generation and presentation which can be controlled remotely over TCP or UDP network links. Project webpage.

Optics Course

The Mrsic-Flogel lab ran an optics course for the Department in 2016. The course was modeled on the optics module from TENSS. The bench optics GitHub repo contains the Latex source code for the handouts on basic optics, beam alignment, and construction of a transmission scanning microscope on a rail. The latest compiled versions of the PDFs are here. Lectures are here: Intro to light, Lenses, Scanning microscopy, 2-photon imaging, Limitation of 2-photon, Detectors and noise.


You can find code and resources produced by the Mrsic-Flogel lab on our GitHub page and also on the SWC GitHub page. Code related to serial-section imaging is covered on our Open Serial Sectioning resource site.

You can also find code on the personal GitHub pages of current and past lab members: Dylan Muir, Petr Znamenskiy, Rob Campbell.