Three excellent pieces of neuroscience software have been recently updated or freshly released. I have used two of them, Ephus and ScanImage, on a daily basis as primary data collection tools. The third, Neuroptikon, is quite useful for post-hoc illustration of neural circuits.
Ephus is a modular Matlab-based electrophysiology program that can control and record many channels of tools and data simultaneously. Under control of a sophisticated internal looper or external trigger, you can initiate an ephys recording, trigger camera frames, adjust galvo positions, open/close shutters, trigger optical stimulation, punishments, rewards, etc. It is a workhorse program for non-imaging related in vitro and in vivo electrophysiology experiments. Ephus is named for the fabled baseball pitch, and pronounced as “EFF-ess”. As with the pitch, it may trick you at first, but eventually you’re sure to hit a home run. Of course, the name also evokes electrophysiology, which is the fundamental orientation of the project, be it optical or electrical.
Ephus 2.1.0 is a major release, and the only official version at this time. The software is fully described in a publication in Frontiers in Neuroscience. New features include unlimited recording time, with disk streaming, for applications such as EEGs and long traces during in-vivo behavior. A number of additional scripts for in-the-loop control have been added. New configuration/start-up files have been created, with a template to help get up and running quickly. This release also includes a number of bug fixes.
ScanImage is another Matlab-related software program that is used for optical imaging and stimulation of neurons in vitro and in vivo. It finds much use a control platform for 2-photon imaging, glutamate uncaging and laser-scanning photostimulation. An early incarnation is described in this paper by Pologruto, et al. It provides a lot of power right out of the box (bidirectional scanning @ 0.5ms/line, etc) and is easily extensible via custom user function plugins.
Neuroptikon is a sophisticated network visualization tool. It can build Van Essen-like diagrams of any circuit you like, but it is so much more. The direction of communication is animated, and subsets of regions and connections can be brought into focus, which greatly eases the clarity of the network. The diagrams can be built in three-dimensions, to preserve relative topography, or functional grouping. There is simple GUI-based control, while more complex tasks can use a scripting interface. This is great software for anyone who needs to imagine information flow in a complex network.
All three tools are released for free use under the HHMI/Janelia Farm open source license.
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