Two open-source trajectory planning tools – Pinpoint (left) and Neuropixels Trajectory Explorer (right) – interface with New Scale’s Pathfinder software for neural probe positioning.
The developers of the Neuropixels Trajectory Explorer and the Pinpoint trajectory planning tools have been collaborating with each other and with New Scale Technologies, continuing to refine their interfaces with our Pathfinder software for the Multi-Probe Micromanipulator (MPM) System. For in vivo neural recording, The MPM System provides probe positioning, and the open-source trajectory planning tools allow researchers to view the probe position in the Allen CCF atlas – both during trajectory planning and during live insertion.
Andrew Peters (Peters Lab, University of Oxford), developer of the Neuropixels Trajectory Explorer; Dan Birman (Steinmetz Lab, University of Washington), leader of the Virtual Brain Lab project and developer of the Pinpoint trajectory planner tool; and Kenneth Yang (Steinmetz Lab, University of Washington) have been working together to ensure that they are scaling and orienting the Allen CCF atlas in the same way. The result is a common framework for all tools.
We have demonstrated that Neuropixels Trajectory Explorer and Pinpoint agree when running a Pathfinder simulation, as seen by viewing the tools in separate windows simultaneously.
First, we used Neuropixels Trajectory Explorer to plan the VISp to LGN trajectory. We determined the Polar Angle (Azimuth) and Pitch Angle (complement of Elevation) and entered these values into Pathfinder. Then we calibrated Pathfinder to set up our stereotactic coordinates, using the Neuropixels Trajectory Explorer Top and Tip coordinates as our Insertion Start and Stop points. We Set Tip Position at the Start Point.
Next, we connected both Neuropixels Trajectory Explorer and Pinpoint to Pathfinder. When we did this, the probe in both systems moved to the start Position in the Atlas.
We then simulated the automatic insertion, and watched the probe movement in the atlas view of both systems. Both resulted in hitting the graphical target.
Bill Karsh (Tim Harris Lab at HHMI/Janelia Research Campus) and Josh Siegle (Allen Institute) announced that their SpikeGLX and Open Ephys GUI Data Acquisition systems now accept atlas location information from both Neuropixels Trajectory Explorer and Pinpoint.
We welcome inquiries from current MPM System users to beta test MPM System and Pathfinder Software with Pinpoint software, as well as the connections of Neuropixels Trajectory Explorer or Pinpoint to SpikeGLX or Open Ephys GUI. Contact us if you are interested.