How-to guides

These guides are here for when you have something specific to get done with your own data. Each one starts from a goal, such as “convert my kilosort output” or “open a probe whose shanks were sorted separately”, and takes you straight to the steps that get you there.

They assume you are already familiar with the GUI and how it works. If this is your first time, we’d recommend starting with the Tutorials: they’ll give you a feel for how everything fits together, and these guides will make much more sense afterwards.

The guides are grouped by what you’re trying to do:

Install

Add the optional packages for converting kilosort output, the IBL online mode and the Channel Prediction plugin.

Prepare data

Turn your spike sorting, raw data and histology into the files the GUI reads.

Configure sessions

Tell the GUI where your data lives, from a single folder to multi-shank probes and side-by-side configurations.

Align

Pick up earlier work, recover a lost alignment, and adjust what the plots show while you align.

Channel prediction

Run the channel prediction models on your own recordings.

IBL online mode

Align IBL probe insertions directly from the Alyx database.

Extend the GUI

Add your own plots and unit filters with a plugin.

Can’t find what you’re looking for? The Reference lists every setting, file and shortcut, and the Explanation pages explain why the GUI works the way it does.

All guides