phy lets you classify, merge, split clusters manually if the output of the automatic spike sorting algorithms are not satisfactory.
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.
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).
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
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
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:
spaceto do nothing and go to the next similar cluster.
gto 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
noisegroup (there are nine keyboard shorcuts for nine possibilities, see below). The best and/or similar clusters change automatically afterwards.
Moving clusters to different groups
Depending on the quality of the clusters, you can move them to the
- 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:
cluster_id somenameon the first line (there is a tab character between)
cluster_id value(for example,
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 (
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
:l neurontype interneuron(this is the lowercase L snippet)
- 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.