Multi-Shank Data

The IBL Alignment GUI supports probes with multiple shanks. The GUI supports two methods for organizing multi-shank probe data.

Method 1: All Shanks in a Single Directory

In this format, spike sorting is run on the full probe, and the output contains results from all shanks together. The extracted raw features also include data from all shanks.

The GUI automatically detects the number of shanks from the channel metadata and displays them accordingly.

Requirements

You must provide one probe tracing (xyz picks) file per shank in the picks directory.

For example, for a four-shank probe, the picks directory should contain:

xyz_picks_shank_1.json
xyz_picks_shank_2.json
xyz_picks_shank_3.json
xyz_picks_shank_4.json

Each file corresponds to the trajectory of a single shank.

Output

The output results will be saved in the output directory with a suffix indicating the shank number:

channel_locations_shank_1.json
channel_locations_shank_2.json
channel_locations_shank_3.json
channel_locations_shank_4.json

Method 2: Each Shank in a Separate Directory

In this format, spike sorting is run independently for each shank, and the extracted raw features contain data from only that shank.

To load this type of data, use the multi-probe configuration described in the Usage section. Each shank should be treated as a separate probe and specified as its own entry in the YAML configuration file.

This allows all shanks to be displayed simultaneously within the same GUI window, while still handling them as independent probes internally.

Example YAML configuration:

probes:
  path: /path/to/session_data
  shank_0:
    datasets:
      spike_sorting:
        path: shank_0/spike_sorting
      processed_ephys:
        path: shank_0/processed_ephys
      raw_ephys:
        path: shank_0/raw_ephys
      picks:
        path: shank_0/picks
      output:
        path: shank_0/output

  shank_1:
    datasets:
      spike_sorting:
        path: shank_1/spike_sorting
      processed_ephys:
        path: shank_1/processed_ephys
      raw_ephys:
        path: shank_1/raw_ephys
      picks:
        path: shank_1/picks
      output:
        path: shank_1/output

   shank_2:
    datasets:
      spike_sorting:
        path: shank_2/spike_sorting
      processed_ephys:
        path: shank_2/processed_ephys
      raw_ephys:
        path: shank_2/raw_ephys
      picks:
        path: shank_2/picks
      output:
        path: shank_2/output

  shank_3:
    datasets:
      spike_sorting:
        path: shank_3/spike_sorting
      processed_ephys:
        path: shank_3/processed_ephys
      raw_ephys:
        path: shank_3/raw_ephys
      picks:
        path: shank_3/picks
      output:
        path: shank_3/output

Launch command:

alignment-gui -y path/to/multi_shank_config.yaml

See Usage for more multi-probe configuration examples.

Working with Multi-Shank Data

Regardless of which method you use, the following features are available when working with multi-shank data:

Display Modes

Two display modes are available:

Display Mode	Description
Tabbed view	Each shank displayed under its own tab
Non-tabbed view	All shanks displayed simultaneously

Toggle between display modes:

Shortcut	Action
Click Tabbed View in Display menu	Toggle view mode
Shift+T	Toggle view mode

Navigation

Navigate between shanks:

Shortcut	Action
Click shank tabs	Switch between shanks
Left / Right	Switch between shanks

The active shank is highlighted in red in the title bar of each figure.

Alignment

• Alignment is always performed independently per shank, regardless of how the data are organized on disk

• The Fit figure shows fit lines for all shanks simultaneously

• Up to four shanks can be visualized at once