Input datasets

This page lists the files the GUI reads, grouped by the folder each group is read from. The folders are given in the session YAML under the key shown for each group (see Session YAML). When a single data folder is opened instead of a YAML file, every dataset is read from that one folder.

To produce these files from your own recordings, see Prepare data. The files the GUI writes are described in Output files.

Datasets	YAML key	Contents
spikes.*, clusters.*, channels.*	spike_sorting	Spike sorting output
_iblqc_ephysTimeRms*, _iblqc_ephysSpectralDensityLF.*	processed_ephys	RMS and power spectra computed from the raw data
*.ap.meta, *.ap.bin, *.lf.bin	raw_ephys	Raw SpikeGLX recordings and their metadata
Histology volumes	histology	Histology images registered to the Allen CCF
*xyz_picks*.json	picks	Traced probe trajectory
Per-channel features (.pqt)	features	Electrophysiology features for the region prediction models

Spike sorting

Read from the spike_sorting folder. spikes.amps, spikes.clusters, spikes.depths and spikes.times are all needed: if any of them is missing, the spike sorting is treated as absent and a warning names the missing files. Kilosort output that has not been converted (with spikes.samples but no spikes.times) is in this case.

spikes.amps

Units V · Type double · Dimensions [number of spikes] · Format npy

Amplitude of each spike.

spikes.clusters

Units index · Type int · Dimensions [number of spikes] · Format npy

Cluster assignment of each spike, counting from 0. Can be used to index the clusters.* attributes directly.

spikes.depths

Units µm · Type double · Dimensions [number of spikes] · Format npy

Depth along the probe of each spike, computed from the waveform centre of mass. 0 is the probe tip, positive upwards.

spikes.times

Units s · Type float64 · Dimensions [number of spikes] · Format npy

Time of each spike, relative to the start of the experiment.

clusters.channels

Units index · Type int · Dimensions [number of clusters] · Format npy

The channel each cluster is assigned to, used to place the clusters along the probe.

clusters.metrics

Format csv or pqt · Dimensions [number of clusters]

Cluster-level quality metrics. No field is required, but two of them enable the unit filters: ks2_label enables the KS good and KS mua filters, and label enables the IBL good filter. If the field a filter needs is missing, the GUI logs a warning and shows all units.

clusters.peakToTrough

Units ms · Type double · Dimensions [number of clusters] · Format npy

Duration of the template waveform, from peak to trough (peak_sample - trough_sample). Negative if the peak comes first.

clusters.waveforms

Units V · Type single · Dimensions [number of clusters, number of time samples, number of selected channels] · Format npy

Template waveforms, stored only for the channels closest to the peak channel.

channels.localCoordinates

Units µm · Type float · Dimensions [number of channels, 2] · Format npy

Position of each channel in the probe coordinate system. The first column is across the width of the probe, the second is depth, with 0 at the deepest site and positive above it. Used for the probe geometry (see Probe geometry).

channels.rawInd

Units index · Type int · Dimensions [number of channels] · Format npy

Index of each channel in the raw recording file, counting from 0. Can be used to index the raw AP and LF binary files directly.

Processed electrophysiology

Read from the processed_ephys folder. If no processed_ephys path is given, it is read from the raw_ephys folder, or from the spike_sorting folder if there is no raw_ephys.

The channels of each object are the columns of its arrays. Column i is taken to hold channel i of the raw recording file, unless the object has a rawInd attribute giving the raw channel of each column (see Probe geometry for the channel order).

_iblqc_ephysSpectralDensityLF.power

Units V²/Hz · Type float32 · Dimensions [number of frequencies, number of channels] · Format npy

Power spectral density of the LF band of every channel, averaged over the time windows.

_iblqc_ephysSpectralDensityLF.freqs

Units Hz · Type float32 · Dimensions [number of frequencies] · Format npy

Frequencies of the power spectral density.

_iblqc_ephysTimeRmsAP.rms

Units V · Type float32 · Dimensions [number of time windows, number of channels] · Format npy

RMS amplitude of the AP band over time. extract_ephys destripes the AP band first: high-pass at 300 Hz, as Neuropixels 2.0 probes record it with the LFP, ADC sample shift correction and the median of each shank subtracted.

_iblqc_ephysTimeRmsAP.timestamps

Units s · Type float32 · Dimensions [number of time windows] · Format npy

Times of the AP RMS windows, relative to the raw binary file.

_iblqc_ephysTimeRmsLF.rms

Units V · Type float32 · Dimensions [number of time windows, number of channels] · Format npy

RMS amplitude of the LF band over time. For Neuropixels 2.0 probes without an LF file, extract_ephys computes the LF band from the AP band, decimated to 2.5 kHz.

_iblqc_ephysTimeRmsLF.timestamps

Units s · Type float32 · Dimensions [number of time windows] · Format npy

Times of the LF RMS windows, relative to the raw binary file.

_iblqc_ephysTimeRmsAP.rawInd, _iblqc_ephysTimeRmsLF.rawInd, _iblqc_ephysSpectralDensityLF.rawInd : Units index · Type int32 · Dimensions [1, number of channels] · Format npy

Optional. Index in the raw recording file of the channel in each column, counting from 0. Written by extract_ephys. Without it the columns are taken to be in file order; a local file without it is reported when the raw file does not store the channels in shank and depth order, as it may then show the wrong channels (see How to convert SpikeGLX and kilosort output).

Raw electrophysiology

Read from the raw_ephys folder. These files are optional, but without them the raw data plots are not available.

*.ap.meta

Format SpikeGLX metadata

Metadata of the AP band. Used for the probe geometry, and the only source of it when there is no spike sorting (see Probe geometry).

*.ap.bin, *.lf.bin

Format SpikeGLX binary

Raw AP and LF recordings. Short snippets are read to display the raw data plots, each shank showing its own channels. The snippets are cached in the same folder, in alignment_gui_raw_data_snippets.npy; caches made by older versions are rebuilt.

Histology

Read from the histology folder. Optional: without histology images, the alignment is done against the Allen atlas template and annotation, which are always available.

The folder is searched for NRRD files first, then TIFF files.

NRRD

Dimensions [AP, DV, ML] voxels · registered to the 25 µm Allen CCF

A file with RD in its name is loaded as the red channel, and one with GR in its name as the green channel.

TIFF (.tif or .tiff)

Dimensions [ML, DV, AP] voxels · registered to the 25 µm Allen CCF

A file with RD or C1 in its name is loaded as the red channel, and one with GR or C0 in its name as the green channel. C0 and C1 can be used when the channels are not named by colour.

Each histology volume found adds an entry to the Slice Plots menu. Only one red and one green volume are loaded. The colour sets the volume’s name in the menu.

Probe trajectory

Read from the picks folder. If no picks path is given, it is read from the spike_sorting folder.

xyz_picks

Units µm · Type double · Dimensions [number of points, 3] · Format json

Points along the traced probe track, as ML, AP, DV coordinates relative to bregma (see Coordinate systems). The file is matched as *xyz_picks.json, so a prefix may be added. For a probe with more than one shank there is one file per shank, matched as *xyz_picks_shank<N>.json, counting from 1.

{"xyz_picks": [[-2863, -3999, -643], [-2813, -3975, -842], [-2788, -4025, -1193]]}

Electrophysiology features

The path to a single file, given by the features key. When a data folder is opened instead of a YAML file, the one parquet file in the folder with features in its name is used. Optional, and only used by the channel prediction models (see Channel prediction plugin).

features

Format parquet · Rows one per channel

Per-channel electrophysiology features computed with ibleatools. A channel column holds the raw-data channel index. For a probe with more than one shank, one file can hold every shank’s channels: the rows are split per shank by matching channel against channels.rawInd.