config.json

{
  "seed": 0,
  "project": "ibl_neuropixel_brainwide_01_2026_W41",
  "vintage": "2026_W41",
  "channel_model": "int-brain-lab/ea-encoder-channel",
  "force_reprepare_data": false,
  "prepare_data_if_missing": true,
  "use_acg": true,
  "use_stpc": true,
  "modality_latent_dim": 20,
  "waveform_shape": [
    20,
    128
  ],
  "acg_shape": [
    10,
    201
  ],
  "stpc_shape": [
    161
  ],
  "ae_batch_size": 512,
  "eval_batch_size": 1024,
  "ae_epochs": 60,
  "ae_learning_rate": 0.0002,
  "ae_weight_decay": 0.0001,
  "ae_patience": 8,
  "ae_min_delta": 1e-05,
  "grad_clip": 5.0,
  "num_workers": 0,
  "latent_std_target": 0.5,
  "lambda_latent_variance": 0.05,
  "lambda_latent_covariance": 0.002,
  "feature_fidelity": false,
  "feature_fidelity_hidden_dim": 128,
  "lambda_feature_continuous": 0.25,
  "lambda_feature_polarity": 0.1,
  "gmm_components": 25,
  "gmm_covariance_type": "full",
  "gmm_reg_covar": 0.0001,
  "gmm_n_init": 10,
  "gmm_max_iter": 500,
  "gmm_min_component_fraction": 0.001,
  "n_cell_pcs": 50,
  "n_gene_pcs": 50,
  "context_atlas_subdir": "context_atlas",
  "context_hidden_dim": 128,
  "context_layers": 2,
  "context_dropout": 0.1,
  "context_weight_epochs": 80,
  "context_weight_batch_size": 2048,
  "context_weight_lr": 0.0003,
  "context_weight_decay": 0.0001,
  "context_weight_patience": 10,
  "rare_component_power": 0.5,
  "rare_component_weight_cap": 10.0,
  "knn_decoder_k": 20,
  "readout_key_dim": 3,
  "readout_key_alphas": [
    100.0,
    1000.0,
    10000.0,
    30000.0,
    100000.0
  ],
  "readout_neighbours": 4096,
  "readout_shrinkage": 10.0,
  "readout_off_data_quantile": 0.99,
  "mirror_x_to_single_hemisphere": true,
  "mirror_x_sign": -1.0,
  "region_gaussian_variance_floor": 0.001,
  "kde_neighbors": 128,
  "kde_spatial_bandwidth_um": 350.0,
  "kde_latent_bandwidth": 0.55,
  "kde_chunk_size": 256,
  "waveform_sampling_rate_hz": 30000.0,
  "diagnostic_examples": 16,
  "diagnostic_hist_bins": 40,
  "diagnostic_samples_per_region": 3000,
  "diagnostic_slice_quantiles": [
    0.2,
    0.5,
    0.8
  ],
  "diagnostic_spatial_pcs": 3,
  "diagnostic_voxel_size_um": 100.0,
  "diagnostic_slice_cmap": "seismic",
  "diagnostic_feature_slice_cmap": "seismic",
  "diagnostic_save_voxel_predictions": false,
  "max_regions_in_distribution_plot": 16,
  "feature_slice_count": 5,
  "feature_slice_seed": 20260831,
  "feature_slice_reference_max_units": 20000,
  "feature_slice_component_mc_samples": 128,
  "feature_slice_regional_mc_samples": 128,
  "feature_slice_display_quantiles": [
    0.02,
    0.98
  ],
  "feature_slice_display_padding_fraction": 0.03,
  "feature_slice_center": "median",
  "feature_nll_samples_per_test_unit": 4,
  "feature_nll_min_bandwidth_fraction": 0.02,
  "feature_categorical_alpha": 1.0,
  "latent_fidelity_test_units": 8000,
  "latent_fidelity_sliced_wasserstein_projections": 128,
  "merfish_correlation_voxel_um": 200,
  "merfish_correlation_cmap": "inferno",
  "merfish_correlation_vmin": 0.0,
  "merfish_correlation_vmax": 0.5
}