Simultaneous recordings from hundreds of grid cells in rats, combined with topological data analysis, show that network activity in grid cells resides on a toroidal manifold that is invariant across environments and brain states.
. After surgery, the rats were left to recover for approximately 3 h before beginning recording. Postoperative analgesia was administered during the surgical recovery period.The details of the Neuropixels hardware system and the procedures for freely moving recordings have been described previously. In brief, electrophysiological signals were amplified with a gain of 500 or 80 , low-pass-filtered at 300 Hz or 0.5 Hz , high-pass-filtered at 10 kHz, and then digitized at 30 kHz .
Three-dimensional motion capture was used to track the rat’s head position and orientation, by attaching a set of five retroreflective markers to implant during recordings. The 3D marker positions were projected onto the horizontal plane to yield the rat’s 2D position and head direction. An Arduino microcontroller was used to generate digital pulses, which were sent to the Neuropixels acquisition system and the OptiTrack system , to permit precise temporal alignment of the recorded data streams.
Single units were discarded if more than 1% of their interspike interval distribution consisted of intervals less than 2 ms. In additions, units were excluded if they had a mean spike rate of less than 0.05 Hz or greater than 10 Hz .During spike sorting, Kilosort assigned each unit with a 2 ms spike waveform template on each recording channel.
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