Software details

MicroManager:

Used for hardware control. We couple our sCMOS Hamamatsu ORCA-Flash2.8 camera with MicroManager and perform fluorescence imaging. MicroManager has scripting option which gives user the power to further extend its capabilities. For purpose of closed-loop experiment, we have constructed a script for fast image acquisition and simultaneous communication between MicroManager and image analysis software (see CaImAn below).

CaImAn:

Toolbox for processing recordings obtained with calcium or voltage imaging. One of its algorithms, namely OnACID, performs powerful online analysis of streaming fluorescence imaging data. This feature is implemented in our protocol as extension to the MicroManager imaging script. OnACID extracts fluorescence trace from a detected neuron in a streaming fashion by analysing data frame-by-frame, during the ongoing acquisition. Ideally, it would output inferred fluorescence values as they are being acquired, however, we are awaiting for such update from its developers.

StdpC:

Dynamic clamp software used for modelling of artificial synaptic response. We use StdpC in all-optical setup to modulate optogenetic signal used for photostimulation. StdpC should take streaming datapoints computed by OnACID (see CaImAn above) as its input, model the synaptic conductance and use simulated synaptic response to affect light intensity used for optogenetic photostimulation.