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
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
on how to install and run a server.
Connecting to a server
Press [ESC] to open the settings menu
Switch to the “Ephys Link” tab
Fill in the server’s IP address
And the port number
Click “Connect”. Upon success, the connect button will read “Disconnect”
Panels for each manipulator will appear here. These panels allow for the
configuration of manipulators and linking them to probes in the scene.
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
Spawn the corresponding probe in the planner scene.
Press [ESC] to open the settings menu.
Switch to the “Ephys Link” tab.
Scroll down to the panel that represents the in vivo manipulator.
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
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.
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.
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.
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.
Press [ESC] again to close the settings menu.
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
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.