Ephys Link

Manipulator and probe in pinpoint moving in sync

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

uMp-4
uMp-3

New Scale

Pathfinder MPM Control v2.8+
M3-USB-3:1-EP

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

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.

Launch from Pinpoint (Recommended)

Pinpoint comes bundled with the correct version of Ephys Link. If you are using Pinpoint on the same computer your manipulators are connected to, you can launch the server from within Pinpoint. Follow the instructions in the Pinpoint documentation.

Install as Standalone Executable

Download the latest executable from the releases page.
Double-click the executable file to launch the configuration window.
1. Take note of the IP address and port. Copy this information into Pinpoint to connect.
Select the desired configuration and click “Launch Server”.

The configuration window will close and the server will launch. Your configurations will be saved for future use.

To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the same computer that Pinpoint is, use

Server: localhost
Port: 8081

If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup window instead of localhost.

Install as a Python package

pip install ephys-link

Import the modules you need and launch the server.

from ephys_link.server import Server

server = Server()
server.launch("sensapex", 8081)

Install for Development

Clone the repository.
Install Hatch
Install the latest Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11) via Visual Studio Build Tools Installer.
In a terminal, navigate to the repository’s root directory and run
```
hatch shell
```

This will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.

CLI Usage

Ephys Link can be launched from the command line directly without the configuration window. This is useful for computers or servers without graphical user interfaces.

With the standalone executable downloaded, invoking the executable from the command line:

EphysLink-vX.X.X.exe -b

Use the actual name of the executable you downloaded. The -b or --background flag will launch the server without the configuration window and read configuration from CLI arguments.

Run the following commands in a terminal to start the server for the desired manipulator platform without the startup window (replace EphysLink.exe with the actual name of the executable you downloaded):

Manipulator Platform	Command
Sensapex uMp-4	`EphysLink.exe -b`
Sensapex uMp-3	`EphysLink.exe -b -t ump3`
New Scale Pathfinder MPM Control v2.8.8+	`EphysLink.exe -b -t new_scale_pathfinder`
New Scale M3-USB-3:1-EP	`EphysLink.exe -b -t new_scale`

More options can be viewed by running EphysLink.exe -h.

“New Scale Pathfinder MPM Control” vs “New Scale M3-USB-3:1-EP”

New Scale manipulators have two methods of connection. The first method is through the Pathfinder MPM Control software (-t new_scale_pathfinder) and the second is via a direct hardware connection (-t new_scale). The first method is only available if Pathfinder is running on the same computer as Ephys Link. New Scale manipulators should be connected to the Pathfinder software first and the Pathfinder HTTP server should be running.