Metadata-Version: 2.1
Name: ephys-link
Version: 1.2.0
Summary: A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.
Project-URL: Documentation, https://virtualbrainlab.org/ephys_link/installation_and_use.html
Project-URL: Issues, https://github.com/VirtualBrainLab/ephys-link/issues
Project-URL: Source, https://github.com/VirtualBrainLab/ephys-link
Author-email: Kenneth Yang <kjy5@uw.edu>
Maintainer-email: Kenneth Yang <kjy5@uw.edu>
License-Expression: GPL-3.0-only
License-File: LICENSE
Keywords: electrophysiology,ephys,manipulator,neuroscience,neurotech,new-scale,sensapex,socket-io,virtualbrainlab
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: <3.13,>=3.8
Requires-Dist: aiohttp==3.9.1
Requires-Dist: platformdirs==4.1.0
Requires-Dist: pyserial==3.5
Requires-Dist: python-socketio==5.11.0
Requires-Dist: pythonnet==3.0.3
Requires-Dist: sensapex==1.400.0
Requires-Dist: wheel==0.42.0
Description-Content-Type: text/markdown

# Electrophysiology Manipulator Link

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<img width="100%" src="https://github.com/VirtualBrainLab/ephys-link/assets/82800265/0c7c60b1-0926-4697-a461-221554f82de1" alt="Manipulator and probe in pinpoint moving in sync">

The [Electrophysiology Manipulator Link](https://github.com/VirtualBrainLab/ephys-link)
(or Ephys Link for short) is a Python [Socket.IO](https://socket.io/docs/v4/#what-socketio-is) server that allows any
Socket.IO-compliant application (such
as [Pinpoint](https://github.com/VirtualBrainLab/Pinpoint))
to communicate with manipulators used in electrophysiology experiments.

**Supported Manipulators:**

| Manufacturer | Model                                                                     |
|--------------|---------------------------------------------------------------------------|
| Sensapex     | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul>                                  |
| New Scale    | <ul> <li>Pathfinder MPM Control v2.8.8+</li> <li>M3-USB-3:1-EP</li> </ul> |

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](https://virtualbrainlab.org/ephys_link/development.html).

For detailed descriptions of the server's API, see
the [API reference](https://virtualbrainlab.org/api_reference_ephys_link.html).

# Installation

## Prerequisites

1. An **x86 Windows PC is required** to run the server.
2. 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.
3. To use the emergency stop feature, ensure an Arduino with
   the [StopSignal](https://github.com/VirtualBrainLab/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.

## Install as Standalone Executable

1. Download the latest executable from
   the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
2. 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**.
3. 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 for Development

1. Clone the repository.
2. Install [Hatch](https://hatch.pypa.io/latest/install/)
3. Install the latest Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11)
   via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
4. In a terminal, navigate to the repository's root directory and run

   ```bash
   hatch shell
   ```

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

## Install as a Python package

```bash
pip install ephys-link
```

Import the modules you need and launch the server.

```python
from ephys_link.server import Server

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

# 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:

```bash
ephys_link-vX.X.X-Windows-x86_64.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 `ephys_link.exe` with the actual name of the executable you downloaded):

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

More options can be viewed by running `ephys_link.exe -h`.

# Documentation and More Information

Complete documentation including API usage and development installation can be
found on the [Virtual Brain Lab Documentation page][docs] for Ephys Link.

# Citing

If this project is used as part of a research project you should cite
the [Pinpoint repository][Pinpoint]. Please email
Dan ([dbirman@uw.edu](mailto:dbirman@uw.edu)) if you have questions.

Please reach out to Kenneth ([kjy5@uw.edu](mailto:kjy5@uw.edu)) for questions
about the Electrophysiology Manipulator Link server. Bugs may be reported
through the issues tab.

[Pinpoint]: https://github.com/VirtualBrainLab/Pinpoint

[StopSignal]: https://github.com/VirtualBrainLab/StopSignal

[docs]: https://virtualbrainlab.org/ephys_link/installation_and_use.html
