# Connecting to Manipulators via Ephys Link
Pinpoint can be connected to electrophysiology manipulators
enabling experimenters to automate the placement of manipulators as well as
observe live where probes are placed inside the brain.
**In this tutorial you will learn how to:**
1. [Configure and launch Ephys Link](configure-and-launch-ephys-link)
2. [Mirror the positions of _in
vivo_ probes in Pinpoint](ephys-link-mirror-probes)
3. [Automate insertions with Ephys Copilot](ephys-copilot)
[//]: # (**If you would like to use beta version of)
[//]: # (Ephys Link with Pinpoint, please use Steam to install Pinpoint and [switch to)
[//]: # (the `ephys-link-beta`branch](https://partner.steamgames.com/doc/store/application/branches#:~:text=To%20switch%20to%20a%20custom,be%20the%20%22BETAS%22%20tab))
[//]: # (.**)
[//]: # (To enable this feature, an instance of an Ephys Link server must be running on)
[//]: # (the local network. Please see the)
[//]: # (instructions [here](https://virtualbrainlab.org/ephys_link/installation_and_use.html#installation))
[//]: # (on how to install and run a server.)
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[//]: # (
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[//]: # ( )
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(configure-and-launch-ephys-link)=
## 1. Configure and Launch Ephys Link
Ephys Link comes bundled with Pinpoint. Navigate to the "Ephys Link" tab in the
menu to configure and launch the server.
![Ephys Link configuration window](../../_static/images/tutorial/ephys_link/ephys_link_launch.png)
1. Press ESC to open the main menu.
2. Navigate to the "Ephys Link" tab.
3. Use the dropdown to select the manipulator platform that you are using.
4. Press the launch button to start the server. After a few seconds, you will
see the Ephys Link window open separately and Pinpoint will establish a
connection. Leave the Ephys Link window running in the background.
5. Your manipulators will appear here. You can configure them and link them to
probes in the scene.
6. To disconnect from the server, press the disconnect button. The Ephys Link
window will close as well. Ephys Link will disconnect and close automatically
when you close Pinpoint.
7. When you are finished, press ESC to close the
settings menu.
Below are more details on the configuration options for each manipulator type.
### Connecting to Sensapex Manipulators
Select the appropriate Sensapex model from the dropdown.
- "Sensapex uMp-4": 4-axis manipulators.
- "Sensapex uMp-3": 3-axis manipulators.
### Connecting to New Scale Manipulators via Pathfinder MPM Control
1. Open Pathfinder MPM.
2. Connect your manipulators.
3. Ensure
the [HTTP server is broadcasting](https://www.newscaletech.com/sending-commands-to-pathfinder-from-other-applications/).
4. In Pinpoint, select the "New Scale Pathfinder MPM Control v2.8.8+" option
from the dropdown.
5. A text box will appear to let you configure the port number of Pathfinder's
HTTP server. You only need to change this value if you changed the
broadcasting port in Pathfinder (the default of 8080 should work for most
users).
6. Press "Launch".
7. Pinpoint will connect to Pathfinder and generate dummy probes for
visualization in Pinpoint.
Pathfinder's configuration is automatic so there is no need to continue with the
rest of this tutorial. [See below for details](mpm-no-need-config).
### Connecting to New Scale Manipulators via M3-USB-3:1-EP
1. Select "New Scale M3-USB-3:1-EP" from the dropdown.
2. Press "Launch".
3. After the Ephys Link window opens, a second window will open to select the
serial port that the manipulators are connected to. Select the appropriate
port and press "OK".
### Connecting to an Existing Server Instance (Advanced)
This option is for users who have Ephys
Link [installed](https://virtualbrainlab.org/ephys_link/installation_and_use.html#installation)
and running on a separate machine than Pinpoint. This is useful for users who
have a dedicated computer for controlling manipulators or are using the hardware
stop button feature.
1. Select "Connect to Existing Server" from the dropdown.
2. Text boxes will appear to let you configure the IP address and port number of
the server. Fill in the appropriate values and press "Connect".
(ephys-link-mirror-probes)=
## 2. Mirror the Positions of _in vivo_ Probes in Pinpoint
This step is not required for New Scale Pathfinder MPM connections. [See below
for details](mpm-no-need-config).
![Spawn probes in the planner scene](../../_static/images/tutorial/ephys_link/ephys_link_spawn.png)
1. Spawn the corresponding probes in the planner scene.
2. Ensure the orientation of the probe in the scene matches the orientation
of your _in vivo_ probe. Use the "Yaw", "Pitch", and "Roll" text boxes to
configure. A value of 0, 0, 0 by default means the probe is parallel to
the ground, pointing anteriorly, and probe's circuitry is facing
dorsally.
1. For Sensapex uMp-4 use a table protractor to identify these angles, for
Sensapex uMp-3 and New Scale manipulators, use the angles from your rigs.
![Connect a probe to a manipulator](../../_static/images/tutorial/ephys_link/ephys_link_connect_probe.png)
1. Press ESC to open the settings menu.
2. Switch to the "Ephys Link" tab.
3. Scroll down to the panel that represents the _in vivo_ manipulator.
4. Use the dropdown to configure the manipulator's handedness. As of March 2024,
handedness configuration is necessary for Sensapex uMp manipulators only.
Configuration is hidden for New Scale
manipulators. [See the section below for
more information.](sensapex-handedness)
5. Use the dropdown to select a probe to link to this manipulator. Probes are
identified by their unique ID (UUID) and their color in the scene.
6. Upon connection, the probe's stereotaxic position will be used as the zero
coordinate that all movements will be relative to. This zero coordinate can
be edited manually through the text boxes or by clicking the home button
(label 6.1) to re-read the manipulator's position and reset the probe in
Pinpoint.
1. For Sensapex manipulator users, you may zero out the manipulator's
position on the touch screen controller. The values there will not affect
Pinpoint.
7. The probe's offset from the brain surface and which direction it is
calculated can be adjusted here. The offset is the distance from the probe
tip to the brain surface. This offset can be determined as the distance from
the tip to the brain surface along the DV axis or the probe's depth axis.
8. Manual control of the manipulators can be enabled here. This allows
manipulators to be controlled with
the [same keyboard shortcuts](https://virtualbrainlab.org/pinpoint/tutorials/tutorial_basics.html#keyboard)
used to move probes in the planner around. Manipulators can also be driven
back to their zero coordinate.
9. Press ESC again to close the settings menu.
At this point, the _in vivo_ probe positions should be mirrored in Pinpoint in
real time.
(sensapex-handedness)=
### Sensapex Handedness
Handedness determines the orientation of the manipulator and which
direction it moves. Handedness is classified by which side of the
manipulator the probe will be mounted on. Ephys Link will use this to correctly
orient the manipulator's direction.
Below is a diagram of the handedness of Sensapex manipulators. Use this to
determine the handedness of your manipulator.
![Sensapex handedness](../../_static/images/tutorial/ephys_link/sensapex_manipulators.png)
(mpm-no-need-config)=
### New Scale Pathfinder MPM connections do not require configuration
Launching Ephys Link requires specifying the type of manipulator that is being
used. Configuration in Pinpoint will differ depending on the type of
manipulator. **New Scale Pathfinder connections do not require any
configuration** in Pinpoint as all manipulators are configured in Pathfinder.
Pinpoint will automatically create probes (colored in magenta) for
each manipulator from Pathfinder and automatically echo their positions,
angles, and shank count.
(ephys-copilot)=
## 3. Automate insertions with Ephys Copilot
Automation is currently a beta feature that is still in development.
Please [contact](https://virtualbrainlab.org/about/overview.html) Dan or Kenneth
if you would like to try it out.