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 mouse brain.

We currently (July 2023) support Sensapex uMp-4 and New Scale 3-axis manipulators.

These features are only available on the Windows Desktop build of Pinpoint they will not run in the web browser.

To enable this feature, an instance of an Ephys Link server must be running on the local network. Please see the instructions here on how to install and run a server.

Connecting to a server

1. Press [ESC] to open the settings menu

2. Switch to the “Ephys Link” tab

3. Fill in the server’s IP address

4. And the port number

5. Click “Connect”. Upon success, the connect button will read “Disconnect”

6. Panels for each manipulator will appear here. These panels allow for the configuration of manipulators and linking them to probes in the scene.

7. Press [ESC] again to close the settings menu

Linking a probe in the planner to a manipulator in vivo

This step is not required for New Scale Pathfinder connections. See below for details.

1. Spawn the corresponding probe in the planner scene.

2. Press [ESC] to open the settings menu.

3. Switch to the “Ephys Link” tab.

4. Scroll down to the panel that represents the in vivo manipulator.

5. Use the dropdown to configure the manipulator’s handedness. Currently (July 2023), configuration is necessary for Sensapex uMp manipulators only. Configuration is hidden for New Scale manipulators. See the section below for more information.

6. 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.

7. 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 to reset the position to the current probe position.

8. 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.

9. Manual control of the manipulators can be enabled here. This allows manipulators to be controlled with the same keyboard shortcuts used to move probes in the planner around. Manipulators can also be driven back to their zero coordinate.

10. Press [ESC] again to close the settings menu.

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.

New Scale Pathfinder 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 and angles.

Enabling experiment automation (Ephys Copilot)

Automation is currently a beta feature that is still in development. Please contact Dan or Kenneth if you would like to try it out.