Phy interface

Exporting to Phy format

• After clustering in IronClust, you can export to Phy format to manually cluster the data.
• Phy version supported: Phy2

Command

• irc export-phy myparam.prm
  • This creates a new folder called phy where myparam.prm is stored
• irc export-phy myparam.prm output_dir
  • This creates a new folder in the specified path (e.g. output_dir)

Output

• amplitudes.npy
• spike_times.npy
• spike_sites.npy
• channel_map.npy
• channel_positions.npy
• spike_templates.npy
• similar_templates.npy
• template_ind.npy
• whitening_mat.npy
• whitening_mat_inv.npy

Phy data format

• https://github.com/kwikteam/phy-contrib/blob/master/docs/template-gui.md
• https://phy.readthedocs.io/en/latest/visualization/