Manual clustering

phy lets you classify, merge, split clusters manually if the output of the automatic spike sorting algorithms are not satisfactory.

Merging clusters

When multiple clusters seem to correspond to the same unit, select them and press G ("group") to merge them into a new cluster.


All spikes belonging to either of the selected clusters will be assigned to that new cluster.


Splitting clusters

You can create a new cluster by drawing a polygon around a set of spikes in the feature view, the amplitude view, the template amplitude view, or the spike attribute views (Control+click to add points to the polygon).


Then, press k ("kluster"). All spikes within the polygon are assigned to a new cluster.


Remaining clusters, i.e. spikes outside the polygon, are also assigned to new cluster ids. Remember that cluster ids are unique and are not reused when the clusters change.

Note: if not all spikes are displayed (there is a limit to the number of spikes displayed in each view), then all spikes are loaded before computing which spikes belong to the drawn polygon.


The wizard is a way to quickly get to pairs of clusters that might require merging.

You can move up and down in the cluster view with the Up and Down arrows. When using the wizard, the cluster selected in the cluster view is called the best cluster.

You can move up and down in the similarity view with the Space and Shift-space arrows. The cluster selected in the similarity view is called the similar cluster. The idea is to go through every "best cluster" in the cluster view, and review the "similar clusters" in the similarity view (sorted by decreasing similarity with the best cluster).

For each similar cluster, you can either:

  • Press space to do nothing and go to the next similar cluster.
  • Press g to merge the best and similar clusters, and go to the next similar cluster.
  • Press one of the keyboard shortcuts to move either the similar cluster, the best cluster, or both clusters, to either the good, mua, or noise group (there are nine keyboard shorcuts for nine possibilities, see below). The best and/or similar clusters change automatically afterwards.
  • Press backspace to unselect all similar clusters, and keep only best clusters (in the cluster view) selected.

Moving clusters to different groups

Depending on the quality of the clusters, you can move them to the good, mua, or noise groups.

- move                                     - (:move)
- move_all_to_good                         ctrl+alt+g
- move_all_to_mua                          ctrl+alt+m
- move_all_to_noise                        ctrl+alt+n
- move_all_to_unsorted                     ctrl+alt+u
- move_best_to_good                        alt+g
- move_best_to_mua                         alt+m
- move_best_to_noise                       alt+n
- move_best_to_unsorted                    alt+u
- move_similar_to_good                     ctrl+g
- move_similar_to_mua                      ctrl+m
- move_similar_to_noise                    ctrl+n
- move_similar_to_unsorted                 ctrl+u

Using cluster labels

phy supports custom cluster labels.

Cluster label files

Cluster labels are saved in TSV (tab-separated values) files:

  • Filename: cluster_somename.tsv
  • Header: cluster_id somename on the first line (there is a tab character between)
  • Rows: cluster_id value (for example, 47 good)

A new column is automatically added for every cluster label TSV file found in the directory.

Cluster groups are saved in the same file format (cluster_group.tsv).

Using labels in the GUI

You can also add cluster labels in the GUI. For example, to add a new label neurontype and assign the value interneuron to selected clusters:

  • Select one or several clusters
  • Press :l neurontype interneuron (this is the lowercase L snippet)
  • Press Enter
  • Save with Control+S


A column is automatically added, and a cluster_neurontype.tsv file is automatically created with the following contents:

cluster_id  neurontype
299 interneuron

Undo and redo

You can undo and redo clustering actions (merge, split, move, label) with the Control+Z and Control+Y keyboard shortcuts.