AMF Tools
Collaborative Projects
Zapit: random-access optogenetics
Zapit is a scanner-based opto-stimulator system for head-fixed mouse behavioural tasks. The software will run on a variety of hardware designs and experimental paradigms. A user-friendly MATLAB GUI handles creation of stimulus sets, scanner calibration, and alignment of stereotaxic coordinates to the sample. The experiment itself is run via a MATLAB API: using a small number of simple commands the user can initiate and stop opto-stimulation, and handle trial logging to disk. There is a Python wrapper for the MATLAB API and support for presenting stimuli in other programming languages.
eLife GitHub
Monitor blanking for in-vivo multi-photon imaging
In systems neuroscience research it is common to present visual stimuli to animals whilst monitoring neural activity using functional calcium imaging. Neurons are typically imaged with a multi-photon microscope that uses highly sensitive photo-multiplier tubes (PMTs) to detect light emitted from the brain and allow an image to reconstructed on a computer. The PMT signal from the brain is easily drowned out by light from the screens presenting the visual stimuli, and in extreme conditions this can even damage the PMTs. One solution to this is to synchronise illumination of the screen to epochs when the PMT is not collecting light from the sample. The SWC FabLab and Mrsic-Flogel group collaborated with the AMF to make a custom electronics controller to modulate the monitor backlight with digital pulses. This allows experimenters to "blank" the monitor illumination during the so-called "turn-around" periods of the multi-photon microscope's scan pattern, effectively allowing simultaneous imaging and visual stimulation without interference.
GitHubSoftware Tools
Multiphoton Quality Control
This MATLAB package interacts with ScanImage to run many of the tests described in the methods paper "Standardized measurements for monitoring and comparing multiphoton microscope systems" by Lees, et al. The package is in active development and now includes code for generating longitudinal measurements, as well as a web dashboard for visualising them.
GitHub
2-Photon Cross-Section Plotter
This web app collates 2-photon excitation spectra from different publications into a single plot.
Launch
BakingTray: serial-section acquisition software
BakingTray is modular serial-section acquisition software for MATLAB. It can easily be modified to utilise any desired acquisition hardware (scanners, stages, etc). Images are acquired with ScanImage, but BakingTray can be extended to work with any acquisition system (e.g. a spinning-disk confocal or even your own scanning software).
GitHub
Example Data Acquisition Software
We produced a variety of microscopy-related example data acquisition tools to serve as tutorials for those new to the field. SimpleMScanner is MATLAB-based scanning software. SimplePyScanner is the Python equivalent. These are backed up by a host of NI DAQmx examples in MATLAB and Python.