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SpikeInterface's export_to_phy exports sparse templates by default (since v0.101.0), with templates.npy shape (n_templates, n_samples, max_sparse_channels) instead of the full (n_templates, n_samples, n_channels) format from native Kilosort. The companion file templates_ind.npy maps (template_idx, sparse_channel_idx) to actual channel indices, with -1 indicating padding. This fix updates get_best_channel() and extract_spike_depths() to: - Check if templates_ind exists (indicates SI-exported sparse format) - Use templates_ind to map sparse indices to actual channel indices - Fall back to original behavior for native Kilosort (dense) format Without this fix, spike_sites and best_channel values are incorrect when reading SI-exported Phy curations, as argmax returns indices into the sparse representation rather than actual channel indices. Related: dj-sciops/nei_nienborg#111 (Issue #2) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fix sparse template handling in kilosort reader for SI-exported Phy data
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