diff --git a/doc/gs_single_cell.rst b/doc/gs_single_cell.rst
index 6c1a2e61e8495fd9bacbb84259f15fff3fa49940..ece7dc599d7343dd840b1dc9de612e72501ab1f8 100644
--- a/doc/gs_single_cell.rst
+++ b/doc/gs_single_cell.rst
@@ -22,7 +22,7 @@ Single compartment cell with HH dynamics
The most trivial representation of a cell in Arbor is to model the entire cell as a
cylinder. The following example shows the steps required to construct a model of a
cylindrical cell with radius 3 μm, Hodgkin–Huxley dynamics and a current clamp stimulus,
-then run the model for 100 ms.
+then run the model for 30 ms.
The first step is to construct the cell. In Arbor, the abstract representation used to
define a cell with branching "cable" morphology is a ``cable_cell``, which holds a
@@ -107,8 +107,8 @@ and provides an interface for recording potentials and running the simulation.
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
m.probe('voltage', '"center"', frequency=10000)
- # (6) Run simulation for 100 ms of simulated activity.
- m.run(tfinal=100)
+ # (6) Run simulation for 30 ms of simulated activity.
+ m.run(tfinal=30)
Step **(4)** instantiates the :class:`arbor.single_cell_model<arbor.single_cell_model>`
with our single-compartment cell.
@@ -118,7 +118,7 @@ is used to record variables from the model. Three pieces of information are
provided: the type of quantity we want probed (voltage), the location where we want to
probe ('center'), and the frequency at which we want to sample (10kHz).
-Finally, step **(6)** starts the actual simulation for a duration of 100 ms.
+Finally, step **(6)** starts the actual simulation for a duration of 30 ms.
Results
----------------------------------------------------
@@ -139,6 +139,7 @@ spike_detector and a voltage probe. Let's see what they have produced!
# (8) Plot the recorded voltages over time.
import pandas, seaborn # You may have to pip install these.
+ seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV").savefig('single_cell_model_result.svg')
diff --git a/doc/images/single_cell_model_result.svg b/doc/images/single_cell_model_result.svg
index 920a073097c256abab0e69b15f2560eb0312a329..fa86b8642c1623d1289185928e234907386b466d 100644
--- a/doc/images/single_cell_model_result.svg
+++ b/doc/images/single_cell_model_result.svg
@@ -2,7 +2,7 @@
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (https://matplotlib.org/) -->
-<svg height="366.07625pt" version="1.1" viewBox="0 0 366.432812 366.07625" width="366.432812pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg height="363.939687pt" version="1.1" viewBox="0 0 364.088906 363.939687" width="364.088906pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<defs>
<style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
@@ -10,33 +10,28 @@
</defs>
<g id="figure_1">
<g id="patch_1">
- <path d="M 0 366.07625
-L 366.432812 366.07625
-L 366.432812 0
+ <path d="M 0 363.939687
+L 364.088906 363.939687
+L 364.088906 0
L 0 0
z
" style="fill:#ffffff;"/>
</g>
<g id="axes_1">
<g id="patch_2">
- <path d="M 48.982813 328.52
-L 359.232812 328.52
-L 359.232812 7.2
-L 48.982813 7.2
+ <path d="M 55.528906 320.98
+L 356.888906 320.98
+L 356.888906 7.2
+L 55.528906 7.2
z
-" style="fill:#ffffff;"/>
+" style="fill:#eaeaf2;"/>
</g>
<g id="matplotlib.axis_1">
<g id="xtick_1">
<g id="line2d_1">
- <defs>
- <path d="M 0 0
-L 0 3.5
-" id="m49bb8fd34e" style="stroke:#000000;stroke-width:0.8;"/>
- </defs>
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="63.085085" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 69.227088 320.98
+L 69.227088 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_1">
<!-- 0 -->
@@ -63,216 +58,196 @@ Q 19.53125 74.21875 31.78125 74.21875
z
" id="DejaVuSans-48"/>
</defs>
- <g transform="translate(59.903835 343.118437)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(65.727713 338.838281)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="xtick_2">
<g id="line2d_2">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="119.564776" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 115.040405 320.98
+L 115.040405 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_2">
- <!-- 20 -->
+ <!-- 5 -->
<defs>
- <path d="M 19.1875 8.296875
-L 53.609375 8.296875
-L 53.609375 0
-L 7.328125 0
-L 7.328125 8.296875
-Q 12.9375 14.109375 22.625 23.890625
-Q 32.328125 33.6875 34.8125 36.53125
-Q 39.546875 41.84375 41.421875 45.53125
-Q 43.3125 49.21875 43.3125 52.78125
-Q 43.3125 58.59375 39.234375 62.25
-Q 35.15625 65.921875 28.609375 65.921875
-Q 23.96875 65.921875 18.8125 64.3125
-Q 13.671875 62.703125 7.8125 59.421875
-L 7.8125 69.390625
-Q 13.765625 71.78125 18.9375 73
-Q 24.125 74.21875 28.421875 74.21875
-Q 39.75 74.21875 46.484375 68.546875
-Q 53.21875 62.890625 53.21875 53.421875
-Q 53.21875 48.921875 51.53125 44.890625
-Q 49.859375 40.875 45.40625 35.40625
-Q 44.1875 33.984375 37.640625 27.21875
-Q 31.109375 20.453125 19.1875 8.296875
+ <path d="M 10.796875 72.90625
+L 49.515625 72.90625
+L 49.515625 64.59375
+L 19.828125 64.59375
+L 19.828125 46.734375
+Q 21.96875 47.46875 24.109375 47.828125
+Q 26.265625 48.1875 28.421875 48.1875
+Q 40.625 48.1875 47.75 41.5
+Q 54.890625 34.8125 54.890625 23.390625
+Q 54.890625 11.625 47.5625 5.09375
+Q 40.234375 -1.421875 26.90625 -1.421875
+Q 22.3125 -1.421875 17.546875 -0.640625
+Q 12.796875 0.140625 7.71875 1.703125
+L 7.71875 11.625
+Q 12.109375 9.234375 16.796875 8.0625
+Q 21.484375 6.890625 26.703125 6.890625
+Q 35.15625 6.890625 40.078125 11.328125
+Q 45.015625 15.765625 45.015625 23.390625
+Q 45.015625 31 40.078125 35.4375
+Q 35.15625 39.890625 26.703125 39.890625
+Q 22.75 39.890625 18.8125 39.015625
+Q 14.890625 38.140625 10.796875 36.28125
z
-" id="DejaVuSans-50"/>
+" id="DejaVuSans-53"/>
</defs>
- <g transform="translate(113.202276 343.118437)scale(0.1 -0.1)">
- <use xlink:href="#DejaVuSans-50"/>
- <use x="63.623047" xlink:href="#DejaVuSans-48"/>
+ <g style="fill:#262626;" transform="translate(111.54103 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-53"/>
</g>
</g>
</g>
<g id="xtick_3">
<g id="line2d_3">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="176.044466" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 160.853722 320.98
+L 160.853722 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_3">
- <!-- 40 -->
+ <!-- 10 -->
<defs>
- <path d="M 37.796875 64.3125
-L 12.890625 25.390625
-L 37.796875 25.390625
-z
-M 35.203125 72.90625
-L 47.609375 72.90625
-L 47.609375 25.390625
-L 58.015625 25.390625
-L 58.015625 17.1875
-L 47.609375 17.1875
-L 47.609375 0
-L 37.796875 0
-L 37.796875 17.1875
-L 4.890625 17.1875
-L 4.890625 26.703125
+ <path d="M 12.40625 8.296875
+L 28.515625 8.296875
+L 28.515625 63.921875
+L 10.984375 60.40625
+L 10.984375 69.390625
+L 28.421875 72.90625
+L 38.28125 72.90625
+L 38.28125 8.296875
+L 54.390625 8.296875
+L 54.390625 0
+L 12.40625 0
z
-" id="DejaVuSans-52"/>
+" id="DejaVuSans-49"/>
</defs>
- <g transform="translate(169.681966 343.118437)scale(0.1 -0.1)">
- <use xlink:href="#DejaVuSans-52"/>
+ <g style="fill:#262626;" transform="translate(153.854972 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-49"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="xtick_4">
<g id="line2d_4">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="232.524157" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 206.667039 320.98
+L 206.667039 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_4">
- <!-- 60 -->
- <defs>
- <path d="M 33.015625 40.375
-Q 26.375 40.375 22.484375 35.828125
-Q 18.609375 31.296875 18.609375 23.390625
-Q 18.609375 15.53125 22.484375 10.953125
-Q 26.375 6.390625 33.015625 6.390625
-Q 39.65625 6.390625 43.53125 10.953125
-Q 47.40625 15.53125 47.40625 23.390625
-Q 47.40625 31.296875 43.53125 35.828125
-Q 39.65625 40.375 33.015625 40.375
-z
-M 52.59375 71.296875
-L 52.59375 62.3125
-Q 48.875 64.0625 45.09375 64.984375
-Q 41.3125 65.921875 37.59375 65.921875
-Q 27.828125 65.921875 22.671875 59.328125
-Q 17.53125 52.734375 16.796875 39.40625
-Q 19.671875 43.65625 24.015625 45.921875
-Q 28.375 48.1875 33.59375 48.1875
-Q 44.578125 48.1875 50.953125 41.515625
-Q 57.328125 34.859375 57.328125 23.390625
-Q 57.328125 12.15625 50.6875 5.359375
-Q 44.046875 -1.421875 33.015625 -1.421875
-Q 20.359375 -1.421875 13.671875 8.265625
-Q 6.984375 17.96875 6.984375 36.375
-Q 6.984375 53.65625 15.1875 63.9375
-Q 23.390625 74.21875 37.203125 74.21875
-Q 40.921875 74.21875 44.703125 73.484375
-Q 48.484375 72.75 52.59375 71.296875
-z
-" id="DejaVuSans-54"/>
- </defs>
- <g transform="translate(226.161657 343.118437)scale(0.1 -0.1)">
- <use xlink:href="#DejaVuSans-54"/>
- <use x="63.623047" xlink:href="#DejaVuSans-48"/>
+ <!-- 15 -->
+ <g style="fill:#262626;" transform="translate(199.668289 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-49"/>
+ <use x="63.623047" xlink:href="#DejaVuSans-53"/>
</g>
</g>
</g>
<g id="xtick_5">
<g id="line2d_5">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="289.003847" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 252.480357 320.98
+L 252.480357 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_5">
- <!-- 80 -->
+ <!-- 20 -->
<defs>
- <path d="M 31.78125 34.625
-Q 24.75 34.625 20.71875 30.859375
-Q 16.703125 27.09375 16.703125 20.515625
-Q 16.703125 13.921875 20.71875 10.15625
-Q 24.75 6.390625 31.78125 6.390625
-Q 38.8125 6.390625 42.859375 10.171875
-Q 46.921875 13.96875 46.921875 20.515625
-Q 46.921875 27.09375 42.890625 30.859375
-Q 38.875 34.625 31.78125 34.625
-z
-M 21.921875 38.8125
-Q 15.578125 40.375 12.03125 44.71875
-Q 8.5 49.078125 8.5 55.328125
-Q 8.5 64.0625 14.71875 69.140625
-Q 20.953125 74.21875 31.78125 74.21875
-Q 42.671875 74.21875 48.875 69.140625
-Q 55.078125 64.0625 55.078125 55.328125
-Q 55.078125 49.078125 51.53125 44.71875
-Q 48 40.375 41.703125 38.8125
-Q 48.828125 37.15625 52.796875 32.3125
-Q 56.78125 27.484375 56.78125 20.515625
-Q 56.78125 9.90625 50.3125 4.234375
-Q 43.84375 -1.421875 31.78125 -1.421875
-Q 19.734375 -1.421875 13.25 4.234375
-Q 6.78125 9.90625 6.78125 20.515625
-Q 6.78125 27.484375 10.78125 32.3125
-Q 14.796875 37.15625 21.921875 38.8125
-z
-M 18.3125 54.390625
-Q 18.3125 48.734375 21.84375 45.5625
-Q 25.390625 42.390625 31.78125 42.390625
-Q 38.140625 42.390625 41.71875 45.5625
-Q 45.3125 48.734375 45.3125 54.390625
-Q 45.3125 60.0625 41.71875 63.234375
-Q 38.140625 66.40625 31.78125 66.40625
-Q 25.390625 66.40625 21.84375 63.234375
-Q 18.3125 60.0625 18.3125 54.390625
+ <path d="M 19.1875 8.296875
+L 53.609375 8.296875
+L 53.609375 0
+L 7.328125 0
+L 7.328125 8.296875
+Q 12.9375 14.109375 22.625 23.890625
+Q 32.328125 33.6875 34.8125 36.53125
+Q 39.546875 41.84375 41.421875 45.53125
+Q 43.3125 49.21875 43.3125 52.78125
+Q 43.3125 58.59375 39.234375 62.25
+Q 35.15625 65.921875 28.609375 65.921875
+Q 23.96875 65.921875 18.8125 64.3125
+Q 13.671875 62.703125 7.8125 59.421875
+L 7.8125 69.390625
+Q 13.765625 71.78125 18.9375 73
+Q 24.125 74.21875 28.421875 74.21875
+Q 39.75 74.21875 46.484375 68.546875
+Q 53.21875 62.890625 53.21875 53.421875
+Q 53.21875 48.921875 51.53125 44.890625
+Q 49.859375 40.875 45.40625 35.40625
+Q 44.1875 33.984375 37.640625 27.21875
+Q 31.109375 20.453125 19.1875 8.296875
z
-" id="DejaVuSans-56"/>
+" id="DejaVuSans-50"/>
</defs>
- <g transform="translate(282.641347 343.118437)scale(0.1 -0.1)">
- <use xlink:href="#DejaVuSans-56"/>
+ <g style="fill:#262626;" transform="translate(245.481607 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-50"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="xtick_6">
<g id="line2d_6">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="345.483538" xlink:href="#m49bb8fd34e" y="328.52"/>
- </g>
+ <path clip-path="url(#p44c0473347)" d="M 298.293674 320.98
+L 298.293674 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
<g id="text_6">
- <!-- 100 -->
+ <!-- 25 -->
+ <g style="fill:#262626;" transform="translate(291.294924 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-50"/>
+ <use x="63.623047" xlink:href="#DejaVuSans-53"/>
+ </g>
+ </g>
+ </g>
+ <g id="xtick_7">
+ <g id="line2d_7">
+ <path clip-path="url(#p44c0473347)" d="M 344.106991 320.98
+L 344.106991 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
+ </g>
+ <g id="text_7">
+ <!-- 30 -->
<defs>
- <path d="M 12.40625 8.296875
-L 28.515625 8.296875
-L 28.515625 63.921875
-L 10.984375 60.40625
-L 10.984375 69.390625
-L 28.421875 72.90625
-L 38.28125 72.90625
-L 38.28125 8.296875
-L 54.390625 8.296875
-L 54.390625 0
-L 12.40625 0
+ <path d="M 40.578125 39.3125
+Q 47.65625 37.796875 51.625 33
+Q 55.609375 28.21875 55.609375 21.1875
+Q 55.609375 10.40625 48.1875 4.484375
+Q 40.765625 -1.421875 27.09375 -1.421875
+Q 22.515625 -1.421875 17.65625 -0.515625
+Q 12.796875 0.390625 7.625 2.203125
+L 7.625 11.71875
+Q 11.71875 9.328125 16.59375 8.109375
+Q 21.484375 6.890625 26.8125 6.890625
+Q 36.078125 6.890625 40.9375 10.546875
+Q 45.796875 14.203125 45.796875 21.1875
+Q 45.796875 27.640625 41.28125 31.265625
+Q 36.765625 34.90625 28.71875 34.90625
+L 20.21875 34.90625
+L 20.21875 43.015625
+L 29.109375 43.015625
+Q 36.375 43.015625 40.234375 45.921875
+Q 44.09375 48.828125 44.09375 54.296875
+Q 44.09375 59.90625 40.109375 62.90625
+Q 36.140625 65.921875 28.71875 65.921875
+Q 24.65625 65.921875 20.015625 65.03125
+Q 15.375 64.15625 9.8125 62.3125
+L 9.8125 71.09375
+Q 15.4375 72.65625 20.34375 73.4375
+Q 25.25 74.21875 29.59375 74.21875
+Q 40.828125 74.21875 47.359375 69.109375
+Q 53.90625 64.015625 53.90625 55.328125
+Q 53.90625 49.265625 50.4375 45.09375
+Q 46.96875 40.921875 40.578125 39.3125
z
-" id="DejaVuSans-49"/>
+" id="DejaVuSans-51"/>
</defs>
- <g transform="translate(335.939788 343.118437)scale(0.1 -0.1)">
- <use xlink:href="#DejaVuSans-49"/>
+ <g style="fill:#262626;" transform="translate(337.108241 338.838281)scale(0.11 -0.11)">
+ <use xlink:href="#DejaVuSans-51"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
- <use x="127.246094" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
- <g id="text_7">
+ <g id="text_8">
<!-- t/ms -->
<defs>
<path d="M 18.3125 70.21875
@@ -363,7 +338,7 @@ Q 40.578125 54.546875 44.28125 53.078125
z
" id="DejaVuSans-115"/>
</defs>
- <g transform="translate(192.988281 356.796562)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(192.865469 354.244062)scale(0.12 -0.12)">
<use xlink:href="#DejaVuSans-116"/>
<use x="39.208984" xlink:href="#DejaVuSans-47"/>
<use x="72.900391" xlink:href="#DejaVuSans-109"/>
@@ -373,17 +348,12 @@ z
</g>
<g id="matplotlib.axis_2">
<g id="ytick_1">
- <g id="line2d_7">
- <defs>
- <path d="M 0 0
-L -3.5 0
-" id="m52d6302f9e" style="stroke:#000000;stroke-width:0.8;"/>
- </defs>
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="321.183759"/>
- </g>
+ <g id="line2d_8">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 313.815883
+L 356.888906 313.815883
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_8">
+ <g id="text_9">
<!-- −80 -->
<defs>
<path d="M 10.59375 35.5
@@ -392,8 +362,47 @@ L 73.1875 27.203125
L 10.59375 27.203125
z
" id="DejaVuSans-8722"/>
+ <path d="M 31.78125 34.625
+Q 24.75 34.625 20.71875 30.859375
+Q 16.703125 27.09375 16.703125 20.515625
+Q 16.703125 13.921875 20.71875 10.15625
+Q 24.75 6.390625 31.78125 6.390625
+Q 38.8125 6.390625 42.859375 10.171875
+Q 46.921875 13.96875 46.921875 20.515625
+Q 46.921875 27.09375 42.890625 30.859375
+Q 38.875 34.625 31.78125 34.625
+z
+M 21.921875 38.8125
+Q 15.578125 40.375 12.03125 44.71875
+Q 8.5 49.078125 8.5 55.328125
+Q 8.5 64.0625 14.71875 69.140625
+Q 20.953125 74.21875 31.78125 74.21875
+Q 42.671875 74.21875 48.875 69.140625
+Q 55.078125 64.0625 55.078125 55.328125
+Q 55.078125 49.078125 51.53125 44.71875
+Q 48 40.375 41.703125 38.8125
+Q 48.828125 37.15625 52.796875 32.3125
+Q 56.78125 27.484375 56.78125 20.515625
+Q 56.78125 9.90625 50.3125 4.234375
+Q 43.84375 -1.421875 31.78125 -1.421875
+Q 19.734375 -1.421875 13.25 4.234375
+Q 6.78125 9.90625 6.78125 20.515625
+Q 6.78125 27.484375 10.78125 32.3125
+Q 14.796875 37.15625 21.921875 38.8125
+z
+M 18.3125 54.390625
+Q 18.3125 48.734375 21.84375 45.5625
+Q 25.390625 42.390625 31.78125 42.390625
+Q 38.140625 42.390625 41.71875 45.5625
+Q 45.3125 48.734375 45.3125 54.390625
+Q 45.3125 60.0625 41.71875 63.234375
+Q 38.140625 66.40625 31.78125 66.40625
+Q 25.390625 66.40625 21.84375 63.234375
+Q 18.3125 60.0625 18.3125 54.390625
+z
+" id="DejaVuSans-56"/>
</defs>
- <g transform="translate(20.878125 324.982978)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(22.81375 317.995024)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-8722"/>
<use x="83.789062" xlink:href="#DejaVuSans-56"/>
<use x="147.412109" xlink:href="#DejaVuSans-48"/>
@@ -401,14 +410,46 @@ z
</g>
</g>
<g id="ytick_2">
- <g id="line2d_8">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="280.896601"/>
- </g>
+ <g id="line2d_9">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 274.474106
+L 356.888906 274.474106
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_9">
+ <g id="text_10">
<!-- −60 -->
- <g transform="translate(20.878125 284.695819)scale(0.1 -0.1)">
+ <defs>
+ <path d="M 33.015625 40.375
+Q 26.375 40.375 22.484375 35.828125
+Q 18.609375 31.296875 18.609375 23.390625
+Q 18.609375 15.53125 22.484375 10.953125
+Q 26.375 6.390625 33.015625 6.390625
+Q 39.65625 6.390625 43.53125 10.953125
+Q 47.40625 15.53125 47.40625 23.390625
+Q 47.40625 31.296875 43.53125 35.828125
+Q 39.65625 40.375 33.015625 40.375
+z
+M 52.59375 71.296875
+L 52.59375 62.3125
+Q 48.875 64.0625 45.09375 64.984375
+Q 41.3125 65.921875 37.59375 65.921875
+Q 27.828125 65.921875 22.671875 59.328125
+Q 17.53125 52.734375 16.796875 39.40625
+Q 19.671875 43.65625 24.015625 45.921875
+Q 28.375 48.1875 33.59375 48.1875
+Q 44.578125 48.1875 50.953125 41.515625
+Q 57.328125 34.859375 57.328125 23.390625
+Q 57.328125 12.15625 50.6875 5.359375
+Q 44.046875 -1.421875 33.015625 -1.421875
+Q 20.359375 -1.421875 13.671875 8.265625
+Q 6.984375 17.96875 6.984375 36.375
+Q 6.984375 53.65625 15.1875 63.9375
+Q 23.390625 74.21875 37.203125 74.21875
+Q 40.921875 74.21875 44.703125 73.484375
+Q 48.484375 72.75 52.59375 71.296875
+z
+" id="DejaVuSans-54"/>
+ </defs>
+ <g style="fill:#262626;" transform="translate(22.81375 278.653246)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-8722"/>
<use x="83.789062" xlink:href="#DejaVuSans-54"/>
<use x="147.412109" xlink:href="#DejaVuSans-48"/>
@@ -416,14 +457,33 @@ z
</g>
</g>
<g id="ytick_3">
- <g id="line2d_9">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="240.609442"/>
- </g>
+ <g id="line2d_10">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 235.132328
+L 356.888906 235.132328
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_10">
+ <g id="text_11">
<!-- −40 -->
- <g transform="translate(20.878125 244.408661)scale(0.1 -0.1)">
+ <defs>
+ <path d="M 37.796875 64.3125
+L 12.890625 25.390625
+L 37.796875 25.390625
+z
+M 35.203125 72.90625
+L 47.609375 72.90625
+L 47.609375 25.390625
+L 58.015625 25.390625
+L 58.015625 17.1875
+L 47.609375 17.1875
+L 47.609375 0
+L 37.796875 0
+L 37.796875 17.1875
+L 4.890625 17.1875
+L 4.890625 26.703125
+z
+" id="DejaVuSans-52"/>
+ </defs>
+ <g style="fill:#262626;" transform="translate(22.81375 239.311469)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-8722"/>
<use x="83.789062" xlink:href="#DejaVuSans-52"/>
<use x="147.412109" xlink:href="#DejaVuSans-48"/>
@@ -431,14 +491,14 @@ z
</g>
</g>
<g id="ytick_4">
- <g id="line2d_10">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="200.322284"/>
- </g>
+ <g id="line2d_11">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 195.790551
+L 356.888906 195.790551
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_11">
+ <g id="text_12">
<!-- −20 -->
- <g transform="translate(20.878125 204.121503)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(22.81375 199.969691)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-8722"/>
<use x="83.789062" xlink:href="#DejaVuSans-50"/>
<use x="147.412109" xlink:href="#DejaVuSans-48"/>
@@ -446,61 +506,61 @@ z
</g>
</g>
<g id="ytick_5">
- <g id="line2d_11">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="160.035126"/>
- </g>
+ <g id="line2d_12">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 156.448773
+L 356.888906 156.448773
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_12">
+ <g id="text_13">
<!-- 0 -->
- <g transform="translate(35.620312 163.834345)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(39.030156 160.627914)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="ytick_6">
- <g id="line2d_12">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="119.747968"/>
- </g>
+ <g id="line2d_13">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 117.106996
+L 356.888906 117.106996
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_13">
+ <g id="text_14">
<!-- 20 -->
- <g transform="translate(29.257812 123.547187)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(32.031406 121.286136)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-50"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="ytick_7">
- <g id="line2d_13">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="79.46081"/>
- </g>
+ <g id="line2d_14">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 77.765218
+L 356.888906 77.765218
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_14">
+ <g id="text_15">
<!-- 40 -->
- <g transform="translate(29.257812 83.260028)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(32.031406 81.944359)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-52"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
<g id="ytick_8">
- <g id="line2d_14">
- <g>
- <use style="stroke:#000000;stroke-width:0.8;" x="48.982813" xlink:href="#m52d6302f9e" y="39.173651"/>
- </g>
+ <g id="line2d_15">
+ <path clip-path="url(#p44c0473347)" d="M 55.528906 38.423441
+L 356.888906 38.423441
+" style="fill:none;stroke:#ffffff;stroke-linecap:round;"/>
</g>
- <g id="text_15">
+ <g id="text_16">
<!-- 60 -->
- <g transform="translate(29.257812 42.97287)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(32.031406 42.602581)scale(0.11 -0.11)">
<use xlink:href="#DejaVuSans-54"/>
<use x="63.623047" xlink:href="#DejaVuSans-48"/>
</g>
</g>
</g>
- <g id="text_16">
+ <g id="text_17">
<!-- U/mV -->
<defs>
<path d="M 8.6875 72.90625
@@ -529,7 +589,7 @@ L 39.796875 0
z
" id="DejaVuSans-86"/>
</defs>
- <g transform="translate(14.798438 181.494375)rotate(-90)scale(0.1 -0.1)">
+ <g style="fill:#262626;" transform="translate(16.318125 180.45125)rotate(-90)scale(0.12 -0.12)">
<use xlink:href="#DejaVuSans-85"/>
<use x="73.193359" xlink:href="#DejaVuSans-47"/>
<use x="106.884766" xlink:href="#DejaVuSans-109"/>
@@ -537,78 +597,83 @@ z
</g>
</g>
</g>
- <g id="line2d_15">
- <path clip-path="url(#pea632d05c8)" d="M 63.085085 240.609442
-L 63.367484 268.853158
-L 63.932281 295.739397
-L 64.426478 306.580671
-L 64.708876 309.451131
-L 64.991275 310.992518
-L 65.273673 311.794635
-L 65.556072 312.195492
-L 65.83847 312.376785
-L 66.473867 312.412842
-L 67.60346 312.053077
-L 69.58025 311.098473
-L 71.839437 309.759731
-L 74.381023 307.999988
-L 77.699205 305.415768
-L 86.171159 298.667669
-L 89.277542 296.531845
-L 91.254331 295.321216
-L 92.101526 21.805455
-L 92.383925 37.118805
-L 96.337503 156.820674
-L 96.9023 169.789614
-L 97.184698 217.926161
-L 97.749495 250.100895
-L 98.879089 303.501927
-L 99.161488 309.920879
-L 99.443886 312.611457
-L 99.726284 313.556795
-L 100.008683 313.849482
-L 100.57348 313.899438
-L 101.985472 313.588824
-L 104.24466 312.889842
-L 106.503847 311.968071
-L 108.763035 310.807197
-L 111.304621 309.2223
-L 114.128606 307.170475
-L 118.152783 303.929575
-L 124.083151 299.173071
-L 127.471932 296.762489
-L 130.295917 295.004761
-L 133.119901 293.497215
-L 135.943886 292.248918
-L 138.485472 291.351521
-L 141.027058 290.670668
-L 143.568644 290.205351
-L 146.392629 289.929787
-L 149.216613 289.878824
-L 152.605395 290.040577
-L 168.13731 291.106575
-L 174.632474 291.099525
-L 197.789147 290.878751
-L 249.468064 290.915211
-L 345.13054 290.916218
-L 345.13054 290.916218
-" style="fill:none;stroke:#1f77b4;stroke-linecap:square;stroke-width:1.5;"/>
+ <g id="line2d_16">
+ <path clip-path="url(#p44c0473347)" d="M 69.227088 235.132328
+L 70.143354 262.713205
+L 71.059621 278.343474
+L 71.975887 288.96866
+L 72.663087 294.610628
+L 73.579353 299.555466
+L 74.49562 302.358507
+L 75.411886 303.863745
+L 76.328152 304.647116
+L 77.244419 305.038508
+L 78.160685 305.21549
+L 80.222284 305.250747
+L 83.88735 304.899435
+L 90.301214 303.967222
+L 97.631345 302.660027
+L 105.877742 300.941413
+L 115.727605 298.640724
+L 144.131862 291.828172
+L 153.294525 289.920866
+L 160.624656 288.560221
+L 161.540922 187.364307
+L 162.457188 59.752206
+L 163.373455 21.462727
+L 164.289721 36.416786
+L 165.205987 44.934375
+L 167.03852 59.028719
+L 168.871053 76.093999
+L 173.452385 122.289103
+L 175.284917 138.7316
+L 177.11745 153.309743
+L 178.949983 165.97436
+L 179.866249 212.981385
+L 180.782515 231.901548
+L 182.615048 257.252228
+L 184.447581 285.413153
+L 185.363847 296.548945
+L 186.280113 302.817378
+L 187.19638 305.444683
+L 188.112646 306.36786
+L 189.028912 306.65373
+L 190.861445 306.702401
+L 195.442777 306.399218
+L 202.772907 305.71657
+L 210.103038 304.81647
+L 217.433169 303.682728
+L 224.7633 302.320362
+L 233.009697 300.551758
+L 243.317693 298.09974
+L 268.056884 292.114569
+L 278.135814 289.967592
+L 287.298478 288.251161
+L 296.461141 286.778969
+L 304.707538 285.670289
+L 312.953935 284.770563
+L 321.200332 284.082269
+L 329.446729 283.604744
+L 338.609393 283.311685
+L 343.190724 283.251399
+L 343.190724 283.251399
+" style="fill:none;stroke:#4c72b0;stroke-linecap:round;stroke-width:1.5;"/>
</g>
<g id="patch_3">
- <path d="M 48.982813 328.52
-L 48.982813 7.2
-" style="fill:none;stroke:#000000;stroke-linecap:square;stroke-linejoin:miter;stroke-width:0.8;"/>
+ <path d="M 55.528906 320.98
+L 55.528906 7.2
+" style="fill:none;stroke:#ffffff;stroke-linecap:square;stroke-linejoin:miter;stroke-width:1.25;"/>
</g>
<g id="patch_4">
- <path d="M 48.982813 328.52
-L 359.232812 328.52
-" style="fill:none;stroke:#000000;stroke-linecap:square;stroke-linejoin:miter;stroke-width:0.8;"/>
+ <path d="M 55.528906 320.98
+L 356.888906 320.98
+" style="fill:none;stroke:#ffffff;stroke-linecap:square;stroke-linejoin:miter;stroke-width:1.25;"/>
</g>
</g>
</g>
<defs>
- <clipPath id="pea632d05c8">
- <rect height="321.32" width="310.25" x="48.982813" y="7.2"/>
+ <clipPath id="p44c0473347">
+ <rect height="313.78" width="301.36" x="55.528906" y="7.2"/>
</clipPath>
</defs>
</svg>
diff --git a/python/example/single_cell_model.py b/python/example/single_cell_model.py
index f2159bad00d39e119e5549bc269561c34c0697ca..5ef30b3ac4eabbad8568234889d13918a7c125d7 100644
--- a/python/example/single_cell_model.py
+++ b/python/example/single_cell_model.py
@@ -21,8 +21,8 @@ m = arbor.single_cell_model(cell)
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
m.probe('voltage', '"center"', frequency=10000)
-# (6) Run simulation for 100 ms of simulated activity.
-m.run(tfinal=100)
+# (6) Run simulation for 30 ms of simulated activity.
+m.run(tfinal=30)
# (7) Print spike times, if any.
if len(m.spikes)>0:
@@ -34,6 +34,7 @@ else:
# (8) Plot the recorded voltages over time.
import pandas, seaborn # You may have to pip install these.
+seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV").savefig('single_cell_model_result.svg')