allen_open_scope — Wavelet RF Mapping

Receptive field mapping pipeline applied to Allen Open Scope electrophysiology data. Zebra noise (pink noise video) stimuli are decomposed by a Gabor wavelet filter bank, and the resulting wavelet responses are cross-correlated with single-unit spike rates to estimate receptive field maps.

Setup

1. Install the environment

conda env create -f envs/waven_dandi.yml
conda activate waven_dandi

This installs the waven package directly from the develop branch of github.com/RaabeM/waven.

2. Configure paths

Open waven_settings.py and update the two path entries to point to your data:

"Movie Path": "/path/to/zebra_allen_screen_tscale_30_scale_10.mp4",
"Library Path": "/path/to/filter_libraries/",

• Movie Path: Path to Zebra stimulus, can be downloaded from Open-Scope-Repo Link
• Library Path: Path to where the wavelet library will be saved

Running the pipeline

Caution: Under the current settings loading the filter libraries takes 256 GB of RAM! I am working on making it more handy.

Wavelet RF mapping (main pipeline)

python compute_waven_pipeline.py ProbeB \***
    --nwb-path /data/sub-820454.nwb \
    --results-dir /results/waven/

• probe (positional, default ProbeB): probe to process
• --nwb-path: path to the NWB file
• --results-dir: root directory for output HDF5 files

Results are saved to <results-dir>/<probe>/lib_<hash>/ as one .h5 file per (delay, duration) combination.

Output format

Each result file is an HDF5 with the following structure:

/attrs:  sigmas, thetas, frequencies, delay, duration, session, probe
/unit_ids                — (n_units,) unit identifiers
/correlation_matrix      — (n_units, nx, ny, n_thetas, ns, n_freqs)  gzip-4
/best_gabor_params_idx   — (5, n_units)
/best_gabor_params_degree — (4, n_units)
/abs_max_value           — (n_units,)

Optimize parameters

After running the pipeline across the full delay × duration grid:

python optimize_waven_parameters.py /results/waven/ProbeB/lib_<hash>/ \
    --output /results/waven/ProbeB/lib_<hash>/best_params.h5

Output format

/unit_ids      — (n_units,) unit identifier strings
/rf_maps       — (n_units, nx, ny)  float32  gzip-4  spatial RF map at best params
/delay         — (n_units,)  optimal delay in seconds
/duration      — (n_units,)  optimal duration in seconds
/abs_max_value — (n_units,)  peak |Pearson r| across all (delay, duration, θ, σ, f)
/x_deg         — (n_units,)  RF centre azimuth in visual degrees
/y_deg         — (n_units,)  RF centre elevation in visual degrees
/theta_deg     — (n_units,)  orientation in Waven's degree convention
/theta_rad     — (n_units,)  orientation in radians
/sigma_deg     — (n_units,)  Gabor σ in visual degrees
/sigma         — (n_units,)  Gabor σ in pixels
/frequency     — (n_units,)  spatial frequency in cycles/pixel
/xi, /yi       — (n_units,)  grid indices of RF centre
/theta_idx, /sigma_idx, /frequency_idx  — (n_units,)  grid indices of best params
/lib_id        — (n_units,)  filter library hash string
/source_file   — (n_units,)  path to the per-(delay, duration) source .h5