A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.
Project description
Electrophysiology Manipulator Link
The Electrophysiology Manipulator Link (or Ephys Link for short) is a Python Socket.IO server that allows any Socket.IO-compliant application (such as Pinpoint) to communicate with manipulators used in electrophysiology experiments.
Supported Manipulators:
Manufacturer | Model |
---|---|
Sensapex |
|
New Scale |
|
Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
For more information regarding the server's implementation and how the code is organized, see the package's development documentation.
For detailed descriptions of the server's API, see the API reference.
Installation
Prerequisites
- Python ≥ 3.8, < 3.13
- Python 3.12+ requires the latest version of Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11) to be installed. They can be acquired through the Visual Studio Build Tools Installer.
- An x86 Windows PC is required to run the server.
- For Sensapex devices, the controller unit must be connected via an ethernet cable and powered. A USB-to-ethernet adapter is acceptable. For New Scale manipulators, the controller unit must be connected via USB and be powered by a 6V power supply.
- To use the emergency stop feature, ensure an Arduino with the StopSignal sketch is connected to the computer. Follow the instructions on that repo for how to set up the Arduino.
NOTE: Ephys Link is an HTTP server without cross-origin support. The server is currently designed to interface with local/desktop instances of Pinpoint. It will not work with the web browser versions of Pinpoint at this time.
Using a Python virtual environment is encouraged.
Create a virtual environment by running python -m venv ephys_link
Activate the environment by running .\ephys_link\scripts\activate
A virtual environment helps to isolate installed packages from other packages on your computer and ensures a clean installation of Ephys Link
Install for use
Run the following command to install the server:
pip install ephys-link
Update the server like any other Python package:
pip install --upgrade ephys-link
Install for development
-
Clone the repository.
-
Install Hatch
-
In a terminal, navigate to the repository's root directory and run
hatch shell
This will create a virtual environment and install the package in editable mode.
Usage
Run the following commands in a terminal to start the server for the desired manipulator platform:
Manipulator Platform | Command |
---|---|
Sensapex uMp-4 | ephys-link |
Sensapex uMp-3 | ephys-link -t ump3 |
New Scale | ephys-link -t new_scale |
New Scale via Pathfinder HTTP server | ephys-link -t new_scale_pathfinder |
There are a couple additional aliases for the Ephys Link executable: ephys_link
and el
.
By default, the server will broadcast with its local IP address on port 8081. Copy this information into Pinpoint to connect.
For example, if the server is running on the same computer that Pinpoint is, use
- Server:
localhost
- Port:
8081
Documentation and More Information
Complete documentation including API usage and development installation can be found on the Virtual Brain Lab Documentation page for Ephys Link.
Citing
If this project is used as part of a research project you should cite the Pinpoint repository. Please email Dan (dbirman@uw.edu) if you have questions.
Please reach out to Kenneth (kjy5@uw.edu) for questions about the Electrophysiology Manipulator Link server. Bugs may be reported through the issues tab.
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