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docs/source/user/py/rdesigneur/rdes.rst
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...@@ -169,7 +169,7 @@ the plot. ...@@ -169,7 +169,7 @@ the plot.
The *rdes.display()* function causes the plots to be displayed. The *rdes.display()* function causes the plots to be displayed.
.. figure:: ./images/rdes2_passive_squid.png .. figure:: ../../../../images/rdes2_passive_squid.png
:alt: Plot for current input to passive compartment :alt: Plot for current input to passive compartment
Plot for current input to passive compartment Plot for current input to passive compartment
...@@ -213,14 +213,14 @@ seconds. The *plotList* now includes two entries, and will generate two plots. ...@@ -213,14 +213,14 @@ seconds. The *plotList* now includes two entries, and will generate two plots.
The first is for plotting the soma membrane potential, just to be sure that The first is for plotting the soma membrane potential, just to be sure that
the voltage clamp is doing its job. the voltage clamp is doing its job.
.. figure:: ./images/ex2.1_vclamp_a.png .. figure:: ../../../../images/ex2.1_vclamp_a.png
:alt: Plot for membrane potential in voltage clamp :alt: Plot for membrane potential in voltage clamp
Plot for membrane potential in voltage clamp Plot for membrane potential in voltage clamp
The second graph plots the holding current. Note the capacitive transients. The second graph plots the holding current. Note the capacitive transients.
.. figure:: ./images/ex2.1_vclamp_b.png .. figure:: ../../../../images/ex2.1_vclamp_b.png
:alt: Plot for holding current for voltage clamp :alt: Plot for holding current for voltage clamp
Plot for holding current for voltage clamp Plot for holding current for voltage clamp
...@@ -283,7 +283,7 @@ Here we introduce two new model specification lines: ...@@ -283,7 +283,7 @@ Here we introduce two new model specification lines:
As before we apply a somatic current pulse. Since we now have HH As before we apply a somatic current pulse. Since we now have HH
channels in the model, this generates action potentials. channels in the model, this generates action potentials.
.. figure:: ./images/rdes3_squid.png .. figure:: ../../../../images/rdes3_squid.png
:alt: Plot for HH squid simulation :alt: Plot for HH squid simulation
Plot for HH squid simulation Plot for HH squid simulation
...@@ -334,7 +334,7 @@ Here we see the classic HH current response, a downward brief deflection due to ...@@ -334,7 +334,7 @@ Here we see the classic HH current response, a downward brief deflection due to
the Na channel, and a slower upward sustained current due to the K delayed the Na channel, and a slower upward sustained current due to the K delayed
rectifier. rectifier.
.. figure:: ./images/ex3.1_squid_vclamp.png .. figure:: ../../../../images/ex3.1_squid_vclamp.png
:alt: Plot for HH squid voltage clamp pulse. :alt: Plot for HH squid voltage clamp pulse.
Plot for HH squid voltage clamp pulse. Plot for HH squid voltage clamp pulse.
...@@ -418,7 +418,7 @@ neuronal geometry. ...@@ -418,7 +418,7 @@ neuronal geometry.
rdes.displayMoogli( 0.00005, 0.05, 0.0 ) rdes.displayMoogli( 0.00005, 0.05, 0.0 )
.. figure:: ./images/ex3.2_axon_propagating_AP.png .. figure:: ../../../../images/ex3.2_axon_propagating_AP.png
:alt: Axon with propagating action potential :alt: Axon with propagating action potential
Axon with propagating action potential Axon with propagating action potential
...@@ -448,7 +448,7 @@ Watch how the AP is triggered bidirectionally from the stimulus point on the ...@@ -448,7 +448,7 @@ Watch how the AP is triggered bidirectionally from the stimulus point on the
100th segment of the axon, and observe what happens when two action potentials 100th segment of the axon, and observe what happens when two action potentials
bump into each other. bump into each other.
.. figure:: ./images/ex3.3_AP_collision.png .. figure:: ../../../../images/ex3.3_AP_collision.png
:alt: Colliding action potentials :alt: Colliding action potentials
Colliding action potentials Colliding action potentials
...@@ -545,7 +545,7 @@ When you run the example, keep an eye out for a few things: ...@@ -545,7 +545,7 @@ When you run the example, keep an eye out for a few things:
- **Speed:** Compare the propagation speed with the previous, - **Speed:** Compare the propagation speed with the previous,
unmyelinated axon. Note that the current model is larger! unmyelinated axon. Note that the current model is larger!
.. figure:: ./images/rdes3.2_myelinated_axon.png .. figure:: ../../../../images/rdes3.2_myelinated_axon.png
:alt: Myelinated axon with propagating action potential :alt: Myelinated axon with propagating action potential
Myelinated axon with propagating action potential Myelinated axon with propagating action potential
...@@ -598,7 +598,7 @@ Here the crucial line is the *cellProto* line. There are four arguments here: ...@@ -598,7 +598,7 @@ Here the crucial line is the *cellProto* line. There are four arguments here:
This is what the soma looks like: This is what the soma looks like:
.. figure:: ./images/ex4.0_scaledSoma.png .. figure:: ../../../../images/ex4.0_scaledSoma.png
:alt: Image of soma. :alt: Image of soma.
Image of soma. Image of soma.
...@@ -660,7 +660,7 @@ arguments are optional. ...@@ -660,7 +660,7 @@ arguments are optional.
This is what the ball-and-stick cell looks like: This is what the ball-and-stick cell looks like:
.. figure:: ./images/ex4.1_ballAndStick.png .. figure:: ../../../../images/ex4.1_ballAndStick.png
:alt: Image of ball and stick cell. :alt: Image of ball and stick cell.
Image of ball and stick cell. Image of ball and stick cell.
...@@ -722,7 +722,7 @@ very similar to the previous one, ex4.1: ...@@ -722,7 +722,7 @@ very similar to the previous one, ex4.1:
While the real point of this simulation is to check speed, it does illustrate While the real point of this simulation is to check speed, it does illustrate
how to deliver a stimulus shaped like a sine wave: how to deliver a stimulus shaped like a sine wave:
.. figure:: ./images/ex4.2_sine_stim.png .. figure:: ../../../../images/ex4.2_sine_stim.png
:alt: Sine-wave shaped stimulus. :alt: Sine-wave shaped stimulus.
Sine-wave shaped stimulus. Sine-wave shaped stimulus.
...@@ -730,7 +730,7 @@ how to deliver a stimulus shaped like a sine wave: ...@@ -730,7 +730,7 @@ how to deliver a stimulus shaped like a sine wave:
We can see that the cell has a peculiar response to this. Not surprising, as We can see that the cell has a peculiar response to this. Not surprising, as
the cell uses HH channels which are not good at rate coding. the cell uses HH channels which are not good at rate coding.
.. figure:: ./images/ex4.2_spiking.png .. figure:: ../../../../images/ex4.2_spiking.png
:alt: Spiking response to sine-wave shaped stimulus. :alt: Spiking response to sine-wave shaped stimulus.
Spiking response to sine-wave shaped stimulus. Spiking response to sine-wave shaped stimulus.
...@@ -790,7 +790,7 @@ Most of this is similar to previous stimLists. ...@@ -790,7 +790,7 @@ Most of this is similar to previous stimLists.
As the model has no voltage-gated channels, we do not see spiking. As the model has no voltage-gated channels, we do not see spiking.
.. figure:: ./images/ex5.0_random_syn_input.png .. figure:: ../../../../images/ex5.0_random_syn_input.png
:alt: Random synaptic input with a Poisson distribution. :alt: Random synaptic input with a Poisson distribution.
Random synaptic input with a Poisson distribution. Random synaptic input with a Poisson distribution.
...@@ -826,7 +826,7 @@ periodic. The one change is of an argument in the stimList to say ...@@ -826,7 +826,7 @@ periodic. The one change is of an argument in the stimList to say
As designed, we get periodically firing synaptic input. As designed, we get periodically firing synaptic input.
.. figure:: ./images/ex5.1_periodic_syn_input.png .. figure:: ../../../../images/ex5.1_periodic_syn_input.png
:alt: Periodic synaptic input :alt: Periodic synaptic input
Periodic synaptic input Periodic synaptic input
...@@ -901,7 +901,7 @@ concentration of the molecular pool *b*. Note its full path within ...@@ -901,7 +901,7 @@ concentration of the molecular pool *b*. Note its full path within
MOOSE: */model/chem/dend/b*. It is scaled up 5x to give rise to slowly MOOSE: */model/chem/dend/b*. It is scaled up 5x to give rise to slowly
decaying oscillations. decaying oscillations.
.. figure:: ./images/rdes4_osc.png .. figure:: ../../../../images/rdes4_osc.png
:alt: Plot for single-compartment reaction simulation :alt: Plot for single-compartment reaction simulation
Plot for single-compartment reaction simulation Plot for single-compartment reaction simulation
...@@ -1000,7 +1000,7 @@ reaction-diffusion system making its way inward from the two ends. After ...@@ -1000,7 +1000,7 @@ reaction-diffusion system making its way inward from the two ends. After
the simulation ends the plots for all compartments for the whole run the simulation ends the plots for all compartments for the whole run
come up. come up.
.. figure:: ./images/rdes5_reacdiff.png .. figure:: ../../../../images/rdes5_reacdiff.png
:alt: Display for oscillatory reaction-diffusion simulation :alt: Display for oscillatory reaction-diffusion simulation
Display for oscillatory reaction-diffusion simulation Display for oscillatory reaction-diffusion simulation
...@@ -1008,7 +1008,7 @@ come up. ...@@ -1008,7 +1008,7 @@ come up.
For those who would rather use the much simpler matplotlib 3-D display option, For those who would rather use the much simpler matplotlib 3-D display option,
this is what the same simulation looks like: this is what the same simulation looks like:
.. figure:: ./images/ex7.0_spatial_chem_osc.png .. figure:: ../../../../images/ex7.0_spatial_chem_osc.png
:alt: Display for oscillatory reac-diff simulation using matplotlib :alt: Display for oscillatory reac-diff simulation using matplotlib
Display for oscillatory reac-diff simulation using matplotlib Display for oscillatory reac-diff simulation using matplotlib
...@@ -1103,7 +1103,7 @@ taking snapshots of the spatial profile of this pool. ...@@ -1103,7 +1103,7 @@ taking snapshots of the spatial profile of this pool.
Here are the snapshots, overlaid in a single plot: Here are the snapshots, overlaid in a single plot:
.. figure:: ./images/ex7.1_diffusive_gradient.png .. figure:: ../../../../images/ex7.1_diffusive_gradient.png
:alt: Display of how a molecule A spreads through the inter :alt: Display of how a molecule A spreads through the inter
Display for simple time-series of spread of a diffusing molecule Display for simple time-series of spread of a diffusing molecule
...@@ -1172,14 +1172,14 @@ Note how the dendritic calcium is displayed both as a time-series plot and ...@@ -1172,14 +1172,14 @@ Note how the dendritic calcium is displayed both as a time-series plot and
as a wave plot, which presents the time-evolution of the calcium as a function as a wave plot, which presents the time-evolution of the calcium as a function
of position in successive image frames. of position in successive image frames.
.. figure:: ./images/ex7.2_CICR_static.png .. figure:: ../../../../images/ex7.2_CICR_static.png
:alt: Time-series plot of dendritic calcium. Different colors represent :alt: Time-series plot of dendritic calcium. Different colors represent
different voxels in the dendrite. different voxels in the dendrite.
Time-series plot of dendritic calcium. Different colors represent Time-series plot of dendritic calcium. Different colors represent
different voxels in the dendrite. different voxels in the dendrite.
.. figure:: ./images/ex7.2_CICR_wave_lastFrame.png .. figure:: ../../../../images/ex7.2_CICR_wave_lastFrame.png
Place holder for time-evolving movie of dendritic calcium as a function of Place holder for time-evolving movie of dendritic calcium as a function of
position along the dendrite. position along the dendrite.
...@@ -1331,7 +1331,7 @@ There is a handy new line to specify cellular passive properties: ...@@ -1331,7 +1331,7 @@ There is a handy new line to specify cellular passive properties:
With these in place, the model behavior is rather neat. It starts out silent, With these in place, the model behavior is rather neat. It starts out silent,
then we apply 2 seconds of +ve current injection. then we apply 2 seconds of +ve current injection.
.. figure:: ./images/ex8.0_multiscale_currInj.png .. figure:: ../../../../images/ex8.0_multiscale_currInj.png
:alt: Current injection stimuli for multiscale model. :alt: Current injection stimuli for multiscale model.
Current injection stimuli for multiscale model. Current injection stimuli for multiscale model.
...@@ -1339,14 +1339,14 @@ then we apply 2 seconds of +ve current injection. ...@@ -1339,14 +1339,14 @@ then we apply 2 seconds of +ve current injection.
The cell fires briskly, and keeps firing even when the current injection The cell fires briskly, and keeps firing even when the current injection
drops to zero. drops to zero.
.. figure:: ./images/ex8.0_multiscale_cell_spiking.png .. figure:: ../../../../images/ex8.0_multiscale_cell_spiking.png
:alt: Firing responses of cell with multiscale signaling. :alt: Firing responses of cell with multiscale signaling.
Firing responses of cell with multiscale signaling. Firing responses of cell with multiscale signaling.
The firing of the neuron leads to Ca influx. The firing of the neuron leads to Ca influx.
.. figure:: ./images/ex8.0_multiscale_Ca.png .. figure:: ../../../../images/ex8.0_multiscale_Ca.png
:alt: Calcium buildup in cell due to firing. :alt: Calcium buildup in cell due to firing.
Calcium buildup in cell due to firing. Calcium buildup in cell due to firing.
...@@ -1355,7 +1355,7 @@ The chemical reactions downstream of Ca lead to phosphorylation of the K_A ...@@ -1355,7 +1355,7 @@ The chemical reactions downstream of Ca lead to phosphorylation of the K_A
channel. Only the unphosphorylated K_A channel is active, so the net effect channel. Only the unphosphorylated K_A channel is active, so the net effect
is to reduce K_A conductance while the Ca influx persists. is to reduce K_A conductance while the Ca influx persists.
.. figure:: ./images/ex8.0_multiscale_KA_conc.png .. figure:: ../../../../images/ex8.0_multiscale_KA_conc.png
:alt: Removal of KA channel due to phosphorylation. :alt: Removal of KA channel due to phosphorylation.
Removal of KA channel due to phosphorylation. Removal of KA channel due to phosphorylation.
...@@ -1467,7 +1467,7 @@ When we run this model, we trigger a propagating Ca wave from about voxel ...@@ -1467,7 +1467,7 @@ When we run this model, we trigger a propagating Ca wave from about voxel
number 16 of 40. It spreads in both directions, and comes to a halt at voxels number 16 of 40. It spreads in both directions, and comes to a halt at voxels
10 and 30, which mark the limits of the IP3 elevation zone. 10 and 30, which mark the limits of the IP3 elevation zone.
.. figure:: ./images/ex8.1_dend_Ca.png .. figure:: ../../../../images/ex8.1_dend_Ca.png
:alt: Calcium wave propagation along the dendrite :alt: Calcium wave propagation along the dendrite
Calcium wave propagation along the dendrite Calcium wave propagation along the dendrite
...@@ -1479,7 +1479,7 @@ diffusion in the dendrite and the action of pumps to within the ER, and ...@@ -1479,7 +1479,7 @@ diffusion in the dendrite and the action of pumps to within the ER, and
out of the cell. Note also that the gradient within the ER is actually quite out of the cell. Note also that the gradient within the ER is actually quite
small, being about a 12% deviation from the resting calcium. small, being about a 12% deviation from the resting calcium.
.. figure:: ./images/ex8.1_ER_Ca.png .. figure:: ../../../../images/ex8.1_ER_Ca.png
:alt: Calcium depletion and buildup in the ER due to CICR wave. :alt: Calcium depletion and buildup in the ER due to CICR wave.
Calcium depletion and buildup in the ER due to CICR wave. Calcium depletion and buildup in the ER due to CICR wave.
...@@ -1569,7 +1569,7 @@ The spines get synaptic input onto NMDARs and gluRs. There is a baseline ...@@ -1569,7 +1569,7 @@ The spines get synaptic input onto NMDARs and gluRs. There is a baseline
input rate of 1 Hz thoughout, and there is a burst at 40 Hz for 1 second at input rate of 1 Hz thoughout, and there is a burst at 40 Hz for 1 second at
t = 10s. t = 10s.
.. figure:: ./images/ex8.2_Vm.png .. figure:: ../../../../images/ex8.2_Vm.png
:alt: Membrane potential responses of cell with synaptic input and multiscale signaling :alt: Membrane potential responses of cell with synaptic input and multiscale signaling
Membrane potential responses of cell with synaptic input and multiscale signaling Membrane potential responses of cell with synaptic input and multiscale signaling
...@@ -1578,7 +1578,7 @@ t = 10s. ...@@ -1578,7 +1578,7 @@ t = 10s.
At baseline, we just have small EPSPs and little Ca influx. A burst of At baseline, we just have small EPSPs and little Ca influx. A burst of
strong synaptic input causes Ca entry into the spine via NMDAR. strong synaptic input causes Ca entry into the spine via NMDAR.
.. figure:: ./images/ex8.2_Ca_spine.png .. figure:: ../../../../images/ex8.2_Ca_spine.png
:alt: Calcium influx into spine. :alt: Calcium influx into spine.
Calcium influx into spine. Calcium influx into spine.
...@@ -1586,7 +1586,7 @@ strong synaptic input causes Ca entry into the spine via NMDAR. ...@@ -1586,7 +1586,7 @@ strong synaptic input causes Ca entry into the spine via NMDAR.
Ca diffuses from the spine into the dendrite and spreads. In the graph below Ca diffuses from the spine into the dendrite and spreads. In the graph below
we see how Calcium goes into the 50-odd voxels of the dendrite. we see how Calcium goes into the 50-odd voxels of the dendrite.
.. figure:: ./images/ex8.2_Ca_dend.png .. figure:: ../../../../images/ex8.2_Ca_dend.png
:alt: Calcium influx and diffusion in dendrite. :alt: Calcium influx and diffusion in dendrite.
Calcium influx and diffusion in dendrite. Calcium influx and diffusion in dendrite.
...@@ -1597,7 +1597,7 @@ triggers activation of CaMKII and its translocation to the PSD, where ...@@ -1597,7 +1597,7 @@ triggers activation of CaMKII and its translocation to the PSD, where
it phosphorylates and increases the conductance of gluR. We have two spines it phosphorylates and increases the conductance of gluR. We have two spines
with slightly different geometry, so the CaMKII activity differs slightly. with slightly different geometry, so the CaMKII activity differs slightly.
.. figure:: ./images/ex8.2_active_CaMKII.png .. figure:: ../../../../images/ex8.2_active_CaMKII.png
:alt: Activation of CaMKII and translocation to PSD :alt: Activation of CaMKII and translocation to PSD
Activation of CaMKII and translocation to PSD Activation of CaMKII and translocation to PSD
...@@ -1726,7 +1726,7 @@ First, just the spiking activity of the cell. Here the burst of activity is ...@@ -1726,7 +1726,7 @@ First, just the spiking activity of the cell. Here the burst of activity is
followed by a few seconds of enhanced synaptic weight, followed by subthreshold followed by a few seconds of enhanced synaptic weight, followed by subthreshold
EPSPs: EPSPs:
.. figure:: ./images/ex8.3_Vm.png .. figure:: ../../../../images/ex8.3_Vm.png
:alt: Membrane potential and spiking. :alt: Membrane potential and spiking.
Membrane potential and spiking. Membrane potential and spiking.
...@@ -1734,7 +1734,7 @@ EPSPs: ...@@ -1734,7 +1734,7 @@ EPSPs:
Then, we fast-forward to the amount of *chan_p* which is the molecule that Then, we fast-forward to the amount of *chan_p* which is the molecule that
controls spine size scaling: controls spine size scaling:
.. figure:: ./images/ex8.3_chan_p.png .. figure:: ../../../../images/ex8.3_chan_p.png
:alt: Molecule that controles spine size :alt: Molecule that controles spine size
Molecule that controles spine size Molecule that controles spine size
...@@ -1743,7 +1743,7 @@ This causes some obvious outcomes. One of them is to increase the synaptic ...@@ -1743,7 +1743,7 @@ This causes some obvious outcomes. One of them is to increase the synaptic
conductance of the glutamate receptor. The system assumes that the conductance conductance of the glutamate receptor. The system assumes that the conductance
of all channels in the PSD scales linearly with the psdArea. of all channels in the PSD scales linearly with the psdArea.
.. figure:: ./images/ex8.3_gluR.png .. figure:: ../../../../images/ex8.3_gluR.png
:alt: Conductance of glutamate receptor :alt: Conductance of glutamate receptor
Conductance of glutamate receptor Conductance of glutamate receptor
...@@ -1756,7 +1756,7 @@ size and the time taken for diffusion and further reactions to replenish ...@@ -1756,7 +1756,7 @@ size and the time taken for diffusion and further reactions to replenish
CaMKII. In the current model we don't have a diffusive coupling of CaMKII to CaMKII. In the current model we don't have a diffusive coupling of CaMKII to
the dendrite, so this replenishment doesn't happen. the dendrite, so this replenishment doesn't happen.
.. figure:: ./images/ex8.3_CaMKII_spine.png .. figure:: ../../../../images/ex8.3_CaMKII_spine.png
:alt: Concentration of CaMKII in the spine :alt: Concentration of CaMKII in the spine
Concentration of CaMKII in the spine Concentration of CaMKII in the spine
...@@ -1848,7 +1848,7 @@ Here we have: ...@@ -1848,7 +1848,7 @@ Here we have:
Vm : Field to display Vm : Field to display
Soma potential : Title for display. Soma potential : Title for display.
.. figure:: ./images/ex9.0_passive_cell_morpho.png .. figure:: ../../../../images/ex9.0_passive_cell_morpho.png
:alt: 3-D display for passive neuron :alt: 3-D display for passive neuron
3-D display for passive neuron 3-D display for passive neuron
...@@ -1988,7 +1988,7 @@ Also note the two Moogli displays. The first is the calcium ...@@ -1988,7 +1988,7 @@ Also note the two Moogli displays. The first is the calcium
concentration. The second is the membrane potential in each compartment. concentration. The second is the membrane potential in each compartment.
Easy! Easy!
.. figure:: ./images/rdes8_active.png .. figure:: ../../../../images/rdes8_active.png
:alt: 3-D display for active neuron :alt: 3-D display for active neuron
3-D display for active neuron 3-D display for active neuron
...@@ -2138,7 +2138,7 @@ Only the first two arguments are mandatory. ...@@ -2138,7 +2138,7 @@ Only the first two arguments are mandatory.
angle. Defaults to 2 PI radians, so the spines come out in any angle. Defaults to 2 PI radians, so the spines come out in any
direction. direction.
.. figure:: ./images/rdes9_spiny_active.png .. figure:: ../../../../images/rdes9_spiny_active.png
:alt: 3-D display for spiny active neuron :alt: 3-D display for spiny active neuron
3-D display for spiny active neuron 3-D display for spiny active neuron
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