Prepare data
These guides show you how to convert your electrophysiology and histology data into files the GUI can read. The full list of files the GUI understands, and where each one goes, is in Input datasets.
To run the GUI you need three things:
- Electrophysiology data
Spike sorting output (
spikes.*,clusters.*,channels.*), processed electrophysiology (the RMS and power spectrum files,_iblqc_*), or both.- The position of each channel on the probe
So that the GUI can place the electrophysiology along the probe’s depth. This comes from the channel positions in the spike sorting output (
channels.localCoordinates) or from the SpikeGLX metadata file (.ap.meta). See Probe geometry.- The traced probe track
The trajectory (3D coordinates) of the probe traced in your histology, in IBL coordinates, as
xyz_picks.json.
Anything more gives you more plots and makes landmarks easier to find: raw data adds snippets of the raw signal, and your own histology images can be shown in the Slice figure. The features used by the channel prediction models can also be computed from the raw data alone (see How to compute the features for a probe).
- How to convert SpikeGLX and kilosort output
- How to convert data with SpikeInterface
- How to export a track from brainreg-segment
- How to export a track from Lasagna
- How to convert between CCF and IBL coordinates
- How to show your own histology in the Slice figure
- How to open a session that has not been spike sorted
Tracing tools
The trajectory can come from any tool that traces the probe track in histology registered to the Allen atlas, such as brainreg-segment, Lasagna, SHARP-Track or HERBS. If your tool is not covered by a guide above, export the traced points in Allen CCF coordinates and follow How to convert between CCF and IBL coordinates.