Ephus is a modular Matlab-based electrophysiology program that can control and record many channels of tools and data simultaneously.
ScanImage is another Matlab-related software program that is used for optical imaging and stimulation of neurons in vitro and in vivo.
Neuroptikon is a sophisticated network visualization tool. It can build Van Essen-like diagrams of any circuit you like ...
A lot more details, and links to download, at the URL above so go there. Or if you are already well-versed, the three tools are released for free use under the HHMI/Janelia Farm open source license.
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