Manipulator interfacing
Interfacing with New Scale MPM requires the "Pathfinder" software running the HTTP server (see documentation from New Scale). This is functional both in simulation mode and with physical manipulators.
To connect with Pathfinder, click Manipulator > New Scale MPM.
In the dialog box that appears, enter the IP address and port for the Pathfinder HTTP server. If the same computer, IP is localhost, and the default port is 8080 (find this on Pathfinder by: Coordinate Sys > ... > Http server > Port)
Once connected, the probe positions in the trajectory explorer will synchronize with Pathfinder, and the text will turn from red to black when completed.
A new "Probe at brain surface" button will appear at the bottom of the "Probe areas" plot, used to set a DV offset to the probe:
How to use this button: when the probe is touching the brain, press this button to zero the DV coordinate at the brain surface. This calibrates the Pathfinder coordinate relative to skull thickness, since otherwise the uncalibrated coordinates may have the probe over or under the brain when it is actually on the surface.
Note on scaling: based on the bregma-lambda distance in Pathfinder, the atlas automatically scales to the size of the individual mouse assuming an template average distance of 4.1mm
- Open Pathfinder (ensuring HTTP server is runnning) and Neuropixels Trajectory Explorer
- Connect Neuropixels Trajectory Explorer to Pathfinder (Manipulator > New Scale MPM)
- In Pathfinder: calibrate bregma then lambda with probe A, calibrate bregma on all other probes
- For each probe
- Move to desired AP/ML position, adjust if necessary based on displayed trajectory to target region
- Lower in DV until just touching brain
- Press "Probe at brain surface" button to set DV offset
- Move probe into brain along the Z (direction of probe) axis, then insert to desired depth