VollanMoserAlternating2025#

class brainsets.datasets.VollanMoserAlternating2025(root=None, recording_ids=None, transform=None, dirname='vollan_moser_alternating_2025', **kwargs)[source]#

Bases: SpikingDatasetMixin, Dataset

Neuropixels recordings from MEC and hippocampus in rats during spatial navigation and sleep.

Rats performed various navigation tasks (open field, linear track, M-maze, wagon wheel) while neural activity was recorded from medial entorhinal cortex (MEC) and/or hippocampus (HC) using Neuropixels probes. Sleep sessions with identified SWS and REM epochs are also included. The dataset contains grid cells, head direction cells, and other spatially tuned neurons.

Preprocessing

To download and prepare this dataset, run

brainsets prepare vollan_moser_alternating_2025

Tasks: Open Field, Linear Track, M-Maze, Wagon Wheel, Sleep

Brain Regions: MEC, Hippocampus

Dataset Statistics

  • Subjects: 19

  • Total Sessions: 51 (31 Open Field, 7 Linear Track, 2 Wagon Wheel, 1 M-Maze, 1 Novel Open Field, 9 Sleep)

  • Recording Tech: Neuropixels

Navigation sessions (42 sessions) contain:

rec.spikes

Spike timestamps and unit indices.

rec.units

Per-unit metadata: id, location (mec/hc), probe_id, shank_id, shank_pos, mean_rate, ks2_label, is_grid.

rec.samples

All variables on the shared 10 ms timebase (speed-filtered at 5 cm/s) in a single flat IrregularTimeSeries:

Observed tracking variables:

  • x – head x-position relative to arena centre (m)

  • y – head y-position relative to arena centre (m)

  • z – head z-position relative to floor (m)

  • hd – 2D head direction / azimuth (rad)

  • speed – horizontal head speed (m/s)

  • theta – instantaneous theta phase (rad)

  • id – decoded internal direction (rad, from the LMT model)

LMT decoded variables (for each population {pop} in mec, hc, mec_hc):

  • lmt_{pop}_theta – theta phase (fixed; largely duplicates theta)

  • lmt_{pop}_hd – head direction (fixed; largely duplicates hd)

  • lmt_{pop}_id – internal direction (latent)

  • lmt_{pop}_pos_x – decoded x-position (latent)

  • lmt_{pop}_pos_y – decoded y-position (latent)

Populations not present for a given animal are NaN-padded so all sessions share the same field schema.

rec.theta_chunks

Theta-cycle-binned timeseries (separate timebase, one sample per theta cycle): id, L (log-likelihood, n_cycles x 30), P (probability, n_cycles x 30).

rec.probe_channels

Probe channel geometry: probe_id, channel_index, x_um, y_um, shank_id, connected.

Sleep sessions (9 sessions) have a fundamentally different structure and should be treated independently. They contain only:

rec.spikes

Spike timestamps and unit indices within SWS/REM epochs.

rec.units

Minimal unit metadata (id only).

rec.domain

Union of SWS and REM epoch intervals.

None of the navigation fields (samples, theta_chunks, probe_channels) are present on sleep sessions.

References

Vollan, A. Z., Gardner, R. J., Moser, M.-B. & Moser, E. I. Left-right-alternating theta sweeps in the entorhinal-hippocampal spatial map. Dataset: EBRAINS.

Parameters:

  • root (str, optional) – Root directory for the dataset. Defaults to processed_dir from brainsets config.

  • recording_ids (list[str] or str, optional) –

    Recording IDs to load. Defaults to all sessions. Can be:

    • A list of individual recording IDs.

    • A string shorthand: "all" (default), "sleep", "navigation", "of", "lt", "mmaze", "ww", "of_novel".

    • A RECORDING_IDS sub-group for finer control:

      from brainsets.datasets.VollanMoserAlternating2025 import RECORDING_IDS
ds = VollanMoserAlternating2025(root, recording_ids=RECORDING_IDS.navigation.of)

  • transform (Callable, optional) – Data transformation to apply.

  • dirname (str, optional) – Subdirectory for the dataset. Defaults to “vollan_moser_alternating_2025”.