Ephys Link

Code Organization

Ephys Link is a modular application structured in 3 layers to enable future extensibility:

1. The Server

2. The Manipulator Platforms

3. Specific Manipulator Instances

1. The Server

At its core, Ephys Link is a Python-based WebSocket server that is used to communicate between client applications and manipulator platforms. The server declares a standardized set of websocket events that clients can call to enact platform specific manipulator API calls. All events, their inputs, and return values are error checked on the server.

In code, the server is an asynchronous HTTP server with events declared with the @sio.event annotation. It is also responsible for handling CLI arguments, starting the serial connection to the emergency stop button, and launching the GUI.

2. The Manipulator Platforms

Each manipulator platform implements the set of events declared by the WebSocket server. Manipulator platforms are responsible for managing connected manipulator instances and API calls that affect all instances simultaneously (such as calibration and emergency stops).

In code, a platform is represented as a class that inherits the abstract class PlatformHandler. The PlatformHandler class defines the implementation of events and pre-implements standard error checking for input and output. Platform classes typically start with some call to initialize the platform’s specific API and manage the available/visible manipulators.

3. Specific Manipulator Instances

To help with manipulator management, each in vivo manipulator can be instantiated as a manipulator class specific to the platform. This class encapsulates details and implementations specific to an instance of a manipulator such as its ID, position, and movement queue. Certain API’s such as the Sensapex uMp API return a manipulator object which can be stored in the manipulator instance class.

Developing and Adding Manipulator Platforms to Ephys Link

Ephys Link primarily support Sensapex uMp Micromanipulators and New Scale manipulators. However, with the modular design defined in the Code Organization section, it is very easy to add custom platforms to Ephys Link.

Installing Ephys Link for development

1. Clone the repo

2. cd ephys-link and run pip install -r requirements.txt

3. python ephys_link/server.py launches the server

4. Unit tests are available to run under the tests/ directory

Docker can also be used for development

1. Install Docker in any way you like

2. Clone the repo

3. cd ephys-link

4. docker-compose up to build the container and run the server

5. docker attach <container-id> to view the server logs

6. You can edit the command line in docker-compose.yml to configure the server’s parameters

7. docker exec -it <container_id> /bin/bash if you need to enter the container

8. The package is located in the root directory as ephys_link

9. Unit tests are available to run under the tests/ directory

10. docker-compose stop to stop the container or docker-compose down to stop and remove the container

Adding a new platform

Before beginning to write a platform handler, ensure the target platform has some windows-compatible API and (ideally) some python library to interface with. Once an API connection can be established, the platform handler can be implemented in the following steps:

1. Create a new file in ephys_link/platforms/ with the name of the platform (e.g. my_platform.py)

2. Create a new class that inherits from PlatformHandler and implement the abstract methods

   1. Follow ephys_link/platforms/sensapex_handler.py as an example. Error checking is handled within the PlatformHandler class so only implement the necessary API calls to the platform.

3. Optionally, add a platform manipulator class in ephys_link/platforms. As described in the code organization section, a platform manipulator class definition can be used to help abstract code specific to instances of manipulators away from general platform management code.

   1. Follow ephys_link/platforms/sensapex_manipulator.py as an example.

4. Add the new platform to the launch command in ephys_link/server.py

   1. Add a new case for the platform in the match statement in the launch_server function. The case pattern will be the input string used in the CLI to select this platform with the -t/--type argument.

   2. Set the platform variable to the imported platform. Use importlib to do so (use the sensapex and new_scale cases as examples).

General code practices

• Type hinting is implemented where possible

• All functions and classes must have a Sphinx/reStructuredText formatted docstring

• Only one client can be connected to the server at a time

• For safety, ensure the stop function is implemented for all manipulators and that it is called when the server is stopped.

Deployment

Ephys Link is published to the Python Package Index (PyPI). To publish a new version:

1. Be a collaborator to the Ephys Link PyPI project

2. Update the version number in pyproject.toml

3. (Optional) Locally test the package by running pip install -e . in the root directory

4. Ensure build tools are installed: pip install build twine

5. Build the package: python -m build

6. Check the build integrity: twine check dist/*

7. Test upload to the test PyPI server: twine upload --repository testpypi dist/*

8. Upload to the PyPI server: twine upload dist/*

Developing a client application

Ephys Link can be interfaced with any WebSocket client or used directly as a python library. The following is information that can be helpful for developers looking to build client applications that utilize Ephys Link.

Importing Ephys Link as a Python library

For Python applications, Ephys Link can be imported as a library. To do so:

1. Follow the installation instructions

2. Use from ephys_link import server and call server.launch() to start the server

   1. Alternatively, use import ephys_link and call ephys_link.server.launch()

WebSocket application

As a WebSocket server, Ephys Link defines a standardized set of WebSocket events that can be used to interact with manipulator platforms. The following section describes the available events and how to use them.

WebSocket Events and API

This is a list of available WebSocket events. The code shown is pseudo-WebSocket code that can be used to interact with the server. The exact implementation will depend on the platform and WebSocket interface used.

In general:

• Each event will take in an input and call a callback function with a response dictionary/object as the argument

• Before a manipulator can be used, it must be registered and calibrated

  • Before a manipulator can be moved (including being calibrated), it must have its movement enabled

  • A manipulator’s position can be read before its movement is enabled, though

• The server will log unknown events, but will not return callback arguments or emit any messages

Table of Contents

• Getting available manipulators

• Registering a manipulator

• Unregistering a manipulator

• Calibrating a manipulator

  • Bypassing calibration

• Get a manipulator’s position

• Set position of a manipulator

• Drive manipulator to depth

• Set “inside brain” state of a manipulator

• Enable movement

• Emergency Stop

Getting available manipulators

Many implementations may want to first find out what manipulators are available. This can be done by simply sending this event which takes no arguments. A callback will return a list of the available manipulators.

Event: get_manipulators

Expected Arguments: None

Callback Responses Format: (manipulators: list[int], error: string)

Error message (error: string)	Description
''	No errors, the list of all discoverable/available manipulators is returned
Error getting manipulators	An unknown error has occurred getting discoverable/available manipulators

• manipulators will be an empty list on error, however, it is possible that there truly are no discoverable/available/compatible manipulators

Example

# Get available manipulators
ws.emit('get_manipulators', callback=my_callback_func)

Registering a manipulator

Some platforms require manipulators to be “registered” before use. Sensapex is one such platform.

Event: register_manipulator

Expected Arguments:

• Manipulator ID: int

Callback Responses Format: string

Error message (string)	Description
''	No errors, registered manipulator with ID manipulator_id
Manipulator already registered	Manipulator is already registered, no action taken
Manipulator not found	The manipulator is not discoverable by the API and may be disconnected or offline
Error registering manipulator	An unknown error has occurred while registering

Example

# Register manipulator with ID 1
ws.emit('register_manipulator', 1, callback=my_callback_func)

Unregistering a manipulator

Any registered manipulator can be easily disconnected from control by simply unregistering it.

Event: unregister_manipulator

Expected Arguments:

• Manipulator ID: int

Callback Responses Format: string

Error message (string)	Description
''	No errors, unregistered manipulator with ID manipulator_id
Manipulator not registered	The manipulator is not registered and therefore cannot be unregistered
Error unregistering manipulator	An unknown error has occurred while unregistering

Example

# Unregister manipulator with ID 1
ws.emit('unregister_manipulator', 1, callback=my_callback_func)

Calibrating a manipulator

To ensure all manipulators are working properly before applying autonomous control, all manipulators must have their movement checked and calibrated. This is done by invoking the calibrate API call on the manipulator. If the platform does not support a calibration call, use the bypass calibration event.

Event: calibrate

Expected Arguments:

• Manipulator ID: int

Callback Responses Format: string

Error message (string)	Description
''	No errors, calibrated manipulator with ID manipulator_id
Manipulator not registered	Manipulator is not registered yet
Error calibrating manipulator	An unknown error has occurred while calibrating
Cannot write to manipulator	The manipulator does not have write/movement privileges or it needs to be enabled

Example

# Calibrate manipulator 1
ws.emit('calibrate', 1, callback=my_callback_func)

Bypassing calibration

The calibration requirement may be bypassed by sending this event.

Event: bypass_calibration

Expected Arguments:

• Manipulator ID: int

Callback Responses Format: string:

Error message (string)	Description
''	No errors, bypassed calibration for manipulator with ID manipulator_id
Manipulator not registered	Manipulator is not registered yet
Error bypassing calibration	An unknown error has occurred while bypassing calibration

Example

# Bypass calibration for manipulator 1
ws.emit('bypass_calibration', 1, callback=my_callback_func)

Enable movement

To prevent accidental movement commands, a manipulator must have its movement feature enabled. A manipulator may have its movement enabled for a set period or enabled indefinitely. Relevant information is passed through the event. Once a write lease has expired, an event is emitted back to the server with the ID of the manipulator which can no longer write as the payload.

Event: set_can_write

Expected Arguments (dictionary/object with the following format):

• manipulator_id: int

• can_write: bool

• hours: float

Callback Responses Format: (state: bool, error: string)

Error message (error: string)	Description
''	No errors, set state is returned
Invalid data format	Invalid/unexpected argument format
Error in set_can_write	An unknown error occurred while starting this function
Manipulator not registered	Manipulator is not registered yet
Error setting can_write	An unknown error has occurred enabling movement

• state: Will be False if one was not provided properly in the request or if an error occurred

Response Event: write_disabled (sent when the write lease has expired)

Payload: manipulator_id: int

Example

# Enable movement for manipulator 1 indefinitely (0 = indefinite hours)
ws.emit('set_can_write', {
    'manipulator_id': 1,
    'can_write': True,
    'hours': 0
})

Get a manipulator’s position

Receive the position of a specified manipulator as X, Y, Z, W (depth) in mm from the origin.

Event: get_pos

Expected Arguments:

• Manipulator ID: int

Callback Responses Format: (position: array, error: string)

Error message (error: string)	Description
''	No errors, position is returned
Manipulator not registered	Manipulator is not registered yet
Manipulator not calibrated	Manipulator is not calibrated yet
Error getting position	An unknown error has occurred while getting position

• position: Will be an empty array if one was not provided properly in the request or if an error occurred

# Gets the position of manipulator 1
ws.emit('get_pos', 1, callback=my_callback_func)

Set the position of a manipulator

Instructs a manipulator to go to a position relative to the origin in mm.

Manipulators move asynchronously from each other. This means large batches of movement events can be sent to the server for several manipulators and each manipulator will move through the events assigned to them independently.

When a manipulator is set to be “inside” the brain, it will have all axes except the depth axis locked. This is to prevent accidental lateral movement while inside brain tissue. This state is set by set_inside_brain . One may also explicitly specify movement in only the depth axis using drive_to_depth

Event: goto_pos

Expected Arguments (dictionary/object with the following format):

• manipulator_id: int

• pos: float[4] (in x, y, z, w as mm from the origin)

• speed: int (in µm/s)

Callback Responses Format: (position: array, error: string)

Error message (error: string)	Description
''	No errors, position is returned
Invalid data format	Invalid/unexpected argument format
Error in goto_pos	An unknown error occurred while starting this function
Manipulator movement canceled	Emergency stop was used and manipulator movements have been canceled
Manipulator not registered	Manipulator is not registered yet
Manipulator not calibrated	Manipulator is not calibrated yet
Error moving manipulator	An unknown error has occurred while moving to position

• position: Will be an empty array if one was not provided properly in the request or if an error occurred

# Set manipulator 1 to position 0, 0, 0, 0 at 2000 µm/s
ws.emit('goto_pos', {
    'manipulator_id': 1,
    'pos': [0, 0, 0, 0],
    'speed': 2000
})

Drive to depth

Instructs a manipulator to go to a specific depth in mm. This is equivalent to setting the position of the manipulator to the same position but with a different depth. This function helps to explicitly make sure no other axis except the depth axis is moving during a movement call.

Event: drive_to_depth

Expected Arguments (dictionary/object with the following format):

• manipulator_id: int

• depth: float (in mm from the origin)

• speed: int (in µm/s)

Callback Responses (depth: float, error: string)

Error message (error: string)	Description
''	No errors, position is returned
Invalid data format	Invalid/unexpected argument format
Error in drive_to_depth	An unknown error occurred while starting this function
Manipulator movement canceled	Emergency stop was used and manipulator movements have been canceled
Manipulator not registered	Manipulator is not registered yet
Manipulator not calibrated	Manipulator is not calibrated yet
Error moving manipulator	An unknown error has occurred while driving to depth

Example

# Drive manipulator 1 to a depth of 1000 µm at 2000 µm/s
ws.emit('drive_to_depth', {
    'manipulator_id': 1,
    'depth': 1000,
    'speed': 2000
})

Set “inside brain” state

Sets the “inside brain” state of a manipulator. When a manipulator is inside the brain, it will have all axes except the depth axis locked. This is to prevent accidental lateral movement while inside brain tissue.

Event: set_inside_brain

Expected Arguments (dictionary/object with the following format):

• manipulator_id: int

• inside: bool

Callback Responses (state: bool, error: string)

Error message (error: string)	Description
''	No errors, position is returned
Invalid data format	Invalid/unexpected argument format
Error in set_inside_brain	An unknown error occurred while starting this function
Manipulator not registered	Manipulator is not registered yet
Manipulator not calibrated	Manipulator is not calibrated yet
Error moving manipulator	An unknown error has occurred while setting inside brain

Example

# Set manipulator 1 to be inside the brain
ws.emit('inside_brain', {
    'manipulator_id': 1,
    'inside': True
})

Emergency Stop

There are two ways an emergency stop can be triggered: through this event or the hardware/serial attached button. The server will connect to the first serial device it finds which names itself “USB Serial Device” (which is what an Arduino would appear as) and listen for any serial input from this source (at a baud rate of 9600). The system will poll the serial port every 50 ms to check. The Arduino is running this sketch which will continuously send 1 (followed by a new line symbol) through serial whenever the stop button is pressed.

Both the WebSocket event and the serial method will stop all movement, remove all movement in the queue, and set all manipulators to be unwritable. Therefore, one must re-enable movement on the manipulators again before continuing.

Event: stop

Expected Arguments (dictionary/object with the following format):

• None

Callback Responses Format: bool

• true: No errors, all movement stopped

• false: An unknown error has occurred while stopping all movement

Example

# Stop all movement
ws.emit('stop')