Electrophysiology Manipulator Link Server
The Electrophysiology Manipulator Link ( or Ephys Link for short) is a Python WebSocket server that allows any WebSocket-compliant application (such as [Pinpoint (electrophysiology planning tool)][Pinpoint]) to communicate with manipulators used in electrophysiology experiments.
Currently, Ephys Link only supports Sensapex uMp Micromanipulators. However, this platform is designed to be extensible to other manipulators and more may be added in the future.
Table of Contents
For more information regarding the server’s implementation and how the code is organized, see the package’s API reference
Installation
Prerequisites
An x86 Windows PC is recommended to run this server.
The server has been verified to work well with Sensapex devices on Windows. This is unverified for Linux and macOS. However, developing the server is possible on a Linux operating system (macOS users should virtualize Linux).
For Sensapex devices, the controller unit must be connected to the PC via an ethernet cable. A USB-to-ethernet adapter is acceptable as well.
To use the emergency stop feature, ensure an Arduino with the [StopSignal][StopSignal] sketch is connected to the computer. Follow the instructions on that repo for how to set up the Arduino.
Installation
Ensure Python 3.8+ and pip are installed
pip install ephys-linkRun
python -m ephys_linkto start the serverTo view available command-line arguments, run
python -m ephys_link --helpNote: all arguments are optional and none are needed to use the server normally
For usage like a library
Ensure Python 3.8+ and pip are installed
pip install ephys-linkUse
from ephys_link import serverand callserver.launch()to start the serverAlternatively, use
import ephys_linkand callephys_link.server.launch()
To develop this package with a local install
Ensure Python 3.8+ and pip are installed
Clone the repo
cd ephys-linkand runpip install -r requirements.txtpython ephys_link/server.pylaunches the serverUnit tests are available to run under the
tests/directory
To develop this package with Docker
Install Docker in any way you like
Clone the repo
cd ephys-linkdocker-compose upto build the container and run the serverdocker attach <container-id>to view the server logsYou can edit the
commandline indocker-compose.ymlto configure the server’s parametersdocker exec -it <container_id> /bin/bashif you need to enter the containerThe package is located in the root directory as
ephys_linkUnit tests are available to run under the
tests/directorydocker-compose stopto stop the container ordocker-compose downto stop and remove the container
Usage
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
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 (up to 50 of them).
Event: get_manipulators
Expected Arguments: None
Callback Responses Format: (manipulators: list[int], error: string)
Error message ( |
Description |
|---|---|
|
No errors, the list of all discoverable/available manipulators is returned |
|
An unknown error has occurred getting discoverable/available manipulators |
manipulatorswill be an empty list on error, however, it is possible that there truly are no discoverable/available/compatible manipulators
Example
# Register manipulator with ID 1
ws.emit('get_manipulators', callback=my_callback_func)
Registering a manipulator
Every manipulator in a Sensapex setup must be registered to the server before being used.
Event: register_manipulator
Expected Arguments:
Manipulator ID:
int
Callback Responses Format: (error: string)
Error message ( |
Description |
|---|---|
|
No errors, registered manipulator with ID |
|
Manipulator is already registered, no action taken |
|
The manipulator is not discoverable by the API and may be disconnected or offline |
|
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: (error: string)
Error message ( |
Description |
|---|---|
|
No errors, unregistered manipulator with ID |
|
The manipulator is not registered and therefore cannot be unregistered |
|
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 moving all four axes through their full range of motion while also invoking the calibrate functionality.
Event: calibrate
Expected Arguments:
Manipulator ID:
int
Callback Responses Format: (error: string)
Error message ( |
Description |
|---|---|
|
No errors, calibrated manipulator with ID |
|
Manipulator is not registered yet |
|
A Sensapex SDK error has occurred while calibrating |
|
An unknown error has occurred while calibrating |
Example
# Calibrate manipulator 1
ws.emit('calibrate', 1, callback=my_callback_func)
Bypassing calibration
FOR TESTING PURPOSES ONLY!! Do not use it in production code.
The calibration requirement may be bypassed by sending this event.
Event: bypass_calibration
Expected Arguments:
Manipulator ID:
int
Callback Responses Format: (error: string):
Error message ( |
Description |
|---|---|
|
No errors, bypassed calibration for manipulator with ID |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
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:intcan_write:boolhours:float
Callback Responses Format: (state: bool, error: string)
Error message ( |
Description |
|---|---|
|
No errors, set state is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred enabling movement |
state: Will beFalseif 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 ( |
Description |
|---|---|
|
No errors, position is returned |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
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 µm.
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:intpos:float[4](in x, y, z, w as µm from the origin)speed:int(in µm/s)
Callback Responses Format: (position: array, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Emergency stop was used and manipulator movements have been canceled |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
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 µm. 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:intdepth:float(in µm from the origin)speed:int(in µm/s)
Callback Responses (depth: float, error: string)
| Error message (error: string) | Description |
——————————- |
|---|
|
|
|
this function |
|
movements have been canceled |
|
|
|
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:intinside:bool
Callback Responses (state: bool, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
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: state: bool
true: No errors, all movement stoppedfalse: An unknown error has occurred while stopping all movement
Example
# Stop all movement
ws.emit('stop')
General code practices (for developers looking to contribute)
Type hinting is implemented where possible
All functions and classes must have a Sphinx/reStructuredText formated docstring
Only one client can be connected to the server at a time