Visualizing cortical waves and timing from data

Kay A. Robbins1 Mark Robinson2 David M. Senseman3

University of Texas at San Antonio University of Texas at San Antonio University of Texas at San Antonio
Cajal Neuroscience Research Center Cajal Neuroscience Research Center

Waves are a fundamental mechanism for conveying information in many physical problems. Direct visualization techniques are often used
to display wave fronts. However, the information derived from such visualizations may not be as central to an investigation as an
understanding of how the location, structure and time course of the wave change as key experimental parameters are varied. In
experimental data, these questions are confounded by noise and incomplete data. Recognition of waves in networks of neurons is
additionally complicated by the presence of long-range physical connections and recurrent excitation. This paper applies visual techniques
to analyze the structural details of waves in response data from the turtle visual cortex. We emphasize low-cost visualizations that allow
comparisons across neural data sets and variables to reconstruct the choreography for a complex response.
 CLIP 1: Response to diffuse flash (soma voltage)

Clip 1 shows snapshots from a 3D animation of the response of the excitatory neurons (lateral and medial) to a diffuse light flash. The
response has been low-pass filtered with a cut-off of 20 Hz and interpolated on a 32 × 32 grid. A hot color map displays response amplitude
with yellow-white representing maximum amplitude and dark red representing zero amplitude. The insets in the upper left of each frame
display a contour map of the response. The labels a, b, c and d correspond to labeled times in the space-time diagram of Fig. 4 and the
shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 4 Space-time diagram of soma voltage of Fig. 12 Snapshots of the soma voltage in response
the lateral pyramidal cells in response to a to a diffuse flash stimulus for selected times.
diffuse light flash.

a b c d
368
lateral neurons

124 ms 208 ms

1
0 time (ms) 800

475 ms 650 ms
 CLIP 2: Response to diffuse flash versus spot flash (soma voltage)

Clip 2 shows snapshots from a 3D animation comparing the response of the excitatory neurons (lateral and medial) to a diffuse light flash
with the response to a spot flash. The response has been low-pass filtered with a cut-off of 20 Hz and interpolated on a 32 × 32 grid. The
diffuse response is shown as in Clip 1 using a colored surface. A hot color map displays response amplitude with yellow-white representing
maximum amplitude and dark red representing zero amplitude. The response for the spot stimulus is represented by a wire mesh. The insets
in the upper left of each frame display a contour map of the response difference. A yellow inset color means the colored surface
representing the diffuse flash response is greater. A cyan color means the wire frame surface representing the spot flash response is greater.
The labels a, b, c and d correspond to labeled times in the space-time diagram of Fig. 5 and the shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 5 Space-time diagram of Fig. 4 overlaid Fig. 12 Snapshots of the soma voltage in response
with a contour map (in black) of the response to to a diffuse flash stimulus for selected times.
a spot stimulus.

a b c d
368
lateral neurons

124 ms 208 ms

1
0 time (ms) 800

475 ms 650 ms
 CLIP 3: Soma voltage versus excitatory AMPA current for diffuse flash

Clip 3 shows snapshots from a 3D animation comparing the soma voltage to the AMPA excitatory current for the excitatory neurons
(lateral and medial) in response to a diffuse light flash. The response has been low-pass filtered with a cut-off of 20 Hz and interpolated on
a 32 × 32 grid. The diffuse response voltage is shown as in Clip 1 using a colored surface. A hot color map displays response amplitude
with yellow-white representing maximum amplitude and dark red representing zero amplitude. The AMPA current is represented by a wire
mesh. Both surfaces have been scaled so that their resting level is zero and their maximum is 1.0. The insets in the upper left of each frame
display a contour map of the response difference. A yellow inset color means the colored surface representing the voltage response is
relatively greater. A cyan color means the wire frame surface representing the AMPA current response is relatively greater. The labels a, b,
c and d correspond to labeled times in the space-time diagram of Fig. 6 and the shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 6 Space-time diagram of Fig. 4 overlaid Fig. 12 Snapshots of the soma voltage in response to
with contour maps of AMPA (in black) and a diffuse flash stimulus for selected times.
NMDA (in blue) currents

a b c d
368
lateral neurons

124 ms 208 ms

1
0 time (ms) 800

475 ms 650 ms
 CLIP 4: Soma voltage versus excitatory NMDA current for diffuse flash

Clip 4 shows snapshots from a 3D animation comparing the soma voltage to the NMDA excitatory current for the excitatory neurons
(lateral and medial) in response to a diffuse light flash. The response has been low-pass filtered with a cut-off of 20 Hz and interpolated on
a 32 × 32 grid. The diffuse response voltage is shown as in Clip 1 using a colored surface. A hot color map displays response amplitude
with yellow-white representing maximum amplitude and dark red representing zero amplitude. The NMDA current is represented by a wire
mesh. Both surfaces have been scaled so that their resting level is zero and their maximum is 1.0. The insets in the upper left of each frame
display a contour map of the response difference. A yellow inset color means the colored surface representing the voltage response is
relatively greater. A cyan color means the wire frame surface representing the NMDA current response is relatively greater. The labels a, b,
c and d correspond to labeled times in the space-time diagram of Fig. 6 and the shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 6 Space-time diagram of Fig. 4 overlaid with Fig. 12 Snapshots of the soma voltage in response to
contour maps of AMPA (in black) and NMDA (in a diffuse flash stimulus for selected times.
blue) currents

a b c d
368
lateral neurons

124 ms 208 ms

1
0 time (ms) 800

475 ms 650 ms
 CLIP 5: Soma voltage versus inhibitory GABAA current for diffuse flash

Clip 5 shows snapshots from a 3D animation comparing the soma voltage to the GABAA inhibitory current for the excitatory neurons
(lateral and medial) in response to a diffuse light flash. The response has been low-pass filtered with a cut-off of 20 Hz and interpolated on
a 32 × 32 grid. The diffuse response voltage is shown as in Clip 1 using a colored surface. A hot color map displays response amplitude
with yellow-white representing maximum amplitude and dark red representing zero amplitude. The GABAA current is represented by a
wire mesh. Both surfaces have been scaled so that their resting level is zero and their maximum is 1.0. The insets in the upper left of each
frame display a contour map of the response difference. A yellow inset color means the colored surface representing the voltage response is
relatively greater. A cyan color means the wire frame surface representing the GABAA current response is relatively greater. The labels a,
b, c and d correspond to labeled times in the space-time diagram of Fig. 7 and the shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 12 Snapshots of the soma voltage in response to

Fig. 6 Space-time diagram of Fig. 4 overlaid a diffuse flash stimulus for selected times.
with contour maps of GABAA (in black) and
GABAB (in blue) currents.

a b c d
368
lateral neurons

124 ms 208 ms

1
0 time (ms) 800
475 ms 650 ms
 CLIP 6: Soma voltage versus 2D KL reconstruction for diffuse flash

Clip 6 shows snapshots from a 3D animation comparing the soma voltage to the 2D KL reconstruction of the soma voltage for the
excitatory neurons (lateral and medial) in response to a diffuse light flash. The response has been low-pass filtered with a cut-off of 20 Hz
and interpolated on a 32 × 32 grid. The diffuse response voltage is shown as in Clip 1 using a colored surface. A hot color map displays
response amplitude with yellow-white representing maximum amplitude and dark red representing zero amplitude. The KL reconstruction
is represented by a wire mesh. The insets in the upper left of each frame display a contour map of the response difference. A yellow inset
color means the colored surface representing the voltage response is relatively greater. A cyan color means the wire frame surface
representing the 2D KL reconstruction of the response is relatively greater. The labels a, b, c and d correspond to labeled times in the
space-time diagram of Fig. 4 and the shape snapshots of Fig. 12.

(a) (b)

(c) (d)

Fig. 11 Projections on 2 most energetic KL spatial Fig. 12 Snapshots of the soma voltage in response to
basis functions for diffuse stimulus shows a diffuse flash stimulus for selected times.
landmarks marked by vertical gray lines on earlier
space-time diagrams.

end linear growth (124 ms)

stimulus end (150 ms)

recurrent (186 ms)

124 ms 208 ms

stimulus onset (0 ms)

prototypical (208 ms)

end recurrent (475 ms)

end oscillations (650 ms) 475 ms 650 ms