Display of neural recording data

Data linked in the "Calcium Imaging File" field of the Bento Experiment Manager will be plotted in the "traces" panel of Bento, to the right of any linked movies. Several neural recording data formats are supported.

The traces panel, displaying DF/F activity of a population of neurons as an image.

Basic display options for neural data

Bento provides several options for adjusting the display of neural activity:

The trace display toolbar.

1. The Window box determines the time window (in seconds) around the current time that is displayed in plotted neural activity traces, and in all other panels with a time axis (including tracking features, the fine-annotation panel, and the audio spectrogram).

2. When multiple traces are being plotted as Lines or Areas (see below), the Trace zoom buttons will scale up/down the amplitude of all plotted traces.

3. Scaling menu: raw plots of neural activity traces are on the same scale, so that level of activity of two neurons can be directly compared. zscored plots normalize the activity of each neuron to have mean zero and standard deviation 1. When traces are scaled by trial, trace scaling or zscoring is performed just over the current trial; when scaled by session, scaling/zscoring is performed over all trials for a given session.

4. Values plotted: allows you to plot either

   • The original neural activity ("units")
   • A smoothed time derivative of activity ("d/dt"). This can make it easier to see event onsets in calcium imaging data.
   • The first N principal components ("PCs") of the plotted traces; if selected, Bento opens a second interface to determine how many PCs to compute, and which trials to compute them from.
   • The first N nonnegative factors ("NMF") of the plotted traces, computed with non-negative matrix factorization; opens similar interface to PCA to specify dimensions/data used. Note: this analysis can take several seconds to complete.

5. Display style: displays neural activity as either plotted lines, shaded areas (often only works when there are not many traces plotted, eg with PCs), or as an image in which color encodes level of activity.

Toggling neuron visibility

You can display only a subset of neurons by selecting Display → Select traces to show. This opens an interface of radio-buttons to toggle display of neurons on or off. If neurons have been reordered (see below), neuron numbers refer to the order in which traces are plotted, with neuron 1 at the top of the traces panel.

Sorting traces

Bento comes with two interfaces for sorting neurons according to their response properties, available in the Plugins menu.

• Kmeans clustering will group neurons into K clusters based on their activity, using the K-means clustering algorithm. Users must specify the value of K and which trials are used during clustering. You may also elect to perform clustering only on activity from certain portions of a trial, and may choose to cluster based on raw or z-scored data.
• Sort neurons by tuning will sort neurons based on the degree of difference in their activity under a pair of conditions, called their "Choice Probability" (CP) (Britten et al. 1995, see also ED Fig. 4 of Remedios, Kennedy et al. 2017.) For each neuron, this analysis computes a histogram of neural activity under condition A, and a second histogram of neural activity under condition B, and quantifies the degree of separation of the two histograms by plotting them against each other and taking the area under the curve.

Plotting 2D projections of neural data

under construction