Optional dependencies

This page lists the optional extras and what each one enables. The base install runs the GUI on data on your own disk. Some features need extra packages, installed as extras:

pip install -e ".[ibl]"
pip install -e ".[ephysatlas]"

Extra	Installs	Needed for
ibl	ibllib	Converting kilosort output with extract_data; the alignment-gui-ibl command
ephysatlas	ibleatools, which also installs ibllib, torch and xgboost	The channel prediction models

Installing ephysatlas therefore also gives everything the ibl extra provides.

What changes without them

Without ibl

alignment-gui-ibl exits with a message saying how to install the extra. ibl_alignment_gui.convertors.extract_ephys cannot be imported. Everything in alignment-gui works.

Without ephysatlas

The Channel Prediction entry of Plugins, and the Feature Plots and Prediction Plots menus, are not shown.

Without torch

Only relevant if ibleatools was installed without its dependencies. The Plugins → Channel Prediction menu and the Prediction Plots menu then have no entries for the ProbeTransformer and alignment models; the XGBoost decoder still works.