Database of Computer-generated Animations
Contents
This database of mpeg and avi movies and other files allows one to visualize the models and experimental data described in the articles. The movies are complementary as they describe important aspects of the dynamical behavior not apparent in static figures; they are most of the time directly related to figures of the published papers. In some cases, demo packages for simulations are also available and reproduce figures of the corresponding papers. Please refer to the database of publications for all biological details.
These animations can be used by anyone interested – the only condition we ask is to give appropriate citation to the original paper(s).
COMPUTER-GENERATED ANIMATIONS
These computer-generated animations should be playable on any recent LINUX distribution, or Windows (in principle, they do not require any nonstandard codec or other application to be played).
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Forward-propagating dendritic spikes with and without background activity in neocortical pyramidal cells
These simulations are based on the following papers:
Michael Rudolph and Alain Destexhe. A fast conducting, stochastic integrative mode for neocortical neurons in vivo. Journal of Neuroscience 23: 2466-2476, 2003.
Alain Destexhe, Michael Rudolph and Denis Paré. The high-conductance state of neocortical neurons in vivo. Nature Reviews Neuroscience 4: 739-751, 2003.
Alain Destexhe. High-Conductance State. Scholarpedia 2(11): 1341 (2007).
These movie files illustrate the effect of synaptic noise on the propagation of dendritic spikes in a simulated neocortical layer VI pyramidal neuron. They are an excellent complement to the figures of the above papers. The somatodendritic distribution of membrane potential is shown by colors in two cases of dendritic action potential generation.
Forward-propagating action potential in a simulated neocortical layer VI pyramidal neuron. The color codes for the membrane potential, from deep blue (-90 mv) to yellow (-40 mV). Sodium and potassium currents were distributed with low density in soma and dendrites, and higher density in the axon. This simulation shows a dendritic action potential elicited by an excitatory synaptic stimulus in the distal dendrite. The action potential propagated forward, but failed to reach the soma. See Fig. 1C (Quiescent) of J. Neurosci. 23: 2466-2476, 2003..
Forward-propagating action potential in a simulated neocortical layer VI pyramidal neuron. Same simulation as above, but in the presence of synaptic background activity (high-conductance state). In this case, the action potential propagated forward and succeeds to reach the soma. See Fig. 1C (In Vivo-Like) of J. Neurosci. 23: 2466-2476, 2003..
Higher resolution movie showing the background activity only in the same layer VI pyramidal neuron as above. This animations shows well the “traffic” of forward- and back-propagating action potentials in dendrites under in vivo-like conditions. See J. Neurosci. 23: 2466-2476, 2003.
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Backpropagating action potentials in neocortical pyramidal cells
These simulations are based on the papers:
Paré D, Lang E and Destexhe A. Inhibitory control of somatic and dendritic sodium spikes in neocortical pyramidal neurons in vivo: an intracellular and computational study Neuroscience 84: 377-402, 1998.
Destexhe A, Lang E and Paré D. Somato-dendritic interactions underlying action potential generation in neocortical pyramidal cells in vivo. In: Computational Neuroscience. Trends in Research (edited by J. Bower), Plenum Press, New York, 1998, pp. 233-238.
These movie files illustrate the dynamics of membrane potential in soma and dendrites in a simulated neocortical layer V pyramidal neuron. They are an excellent complement to the figures of the paper. The somatodendritic distribution of membrane potential is shown by colors in three cases of action potential generation
Backpropagating action potential in a simulated neocortical layer V pyramidal neuron. The color codes for the membrane potential, from deep blue (-90 mv) to yellow (-40 mV). Sodium and potassium currents were distributed with low density in doma and dendrites, and high density in the axon. This simulation shows an action potential elicited by current injection in the soma. The action potential propagated retrogradely into the dendrites. See Fig. 9 of Neuroscience 84: 377-402, 1998 .
Action potential elicited by stimulation of synapses in the distal dendrites. The action potential initiated distally and propagated towards the soma. See Fig. 14 of Neuroscience 84: 377-402, 1998 .
Action potential elicited by stimulation of synapses in soma and proximal dendrites. The action potential initiated proximally but did not back-propagate in more distal dendrites. The amplitude of the action potential, as seen from the soma, was reduced in amplitude and duration. See Fig. 14 of Neuroscience 84: 377-402, 1998 .
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Dendritic calcium currents in thalamic reticular neurons
These simulations are based on the paper:
Destexhe, A., Contreras, D., Steriade, M., Sejnowski, T.J. and Huguenard, J.R. In vivo, in vitro and computational analysis of dendritic calcium currents in thalamic reticular neurons. Journal of Neuroscience 16: 169-185, 1996
These movie files illustrate the dynamics of membrane potential in soma and dendrites of thalamic reticular neurons. They are an excellent complement to the figures of the paper. The somatodendritic distribution of membrane potential is shown by colors during a burst of action potentials. In particular, see how distal dendrites are maintained at a depolarized level, “feeding” the soma with current during the burst.
Dendritically-generated burst in a simulated thalamic reticular neuron. The color codes for the membrane potential, from deep blue (-90 mv) to yellow (-40 mV). Distal dendrites contain high densities of T-current and generate most of the calcium spike, “feeding” the soma with depolarizing current during the burst. The soma contained sodium/potassium currents responsible for action potentials and lower densities of T-current. The genesis of the burst by dendrites accounts for many electrophysiological properties of these neurons. (large size movie, also contains a plot of the membrane potential at the soma) See Fig. 8 of J. Neurosci. 16: 169-185, 1996 .
(medium size movie)
(small size movie)
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Propagating synchronized oscillations in thalamic networks:
These simulations are based on the paper: Destexhe, A., Bal, T., McCormick, D.A. and Sejnowski, T.J. Ionic mechanisms underlying synchronized oscillations and propagating waves in a model of ferret thalamic slices. Journal ofNeurophysiology 76: 2049-2070, 1996
9-11 Hz spindle oscillation in a 1-dim network of 50 TC and 50 RE cells with intact connectivity. Extent of axonal projections: 11 cells; 2000 frames with 2ms between frames; 8pixel/frame; t=28 sec to 32 sec. Color scale: -90 (blue) to -40 mV and over (yellow). See Fig. 12 of J. Neurophysiol. 76: 2049-2070, 1996 .
3-4 Hz bicuculline-induced oscillation in a 1-dim network of 50 TC and 50 RE cells following block of GABA(A) receptors. Extent of axonal projections: 11 cells; 2200 frames with 2ms between frames; 8pixel/frame; t=28.6 sec to 33 sec. Color scale: -90 (blue) to -40 mV and over (yellow). See Fig. 13 of J. Neurophysiol. 76: 2049-2070, 1996. These mpeg movies show experimental data from the paper: Contreras, D., Destexhe, A., Sejnowski, T.J. and Steriade, M. Control of spatiotemporal coherence of a thalamic oscillation by corticothalamic feedback. Science 274: 771-774, 1996
Spatiotemporal maps of the distribution of electrical activity across the thalamus during spindle oscillations recorded by eight equidistant tungsten electrodes in cats during barbiturate anesthesia. These animations are animated versions of Fig. 2 of the paper. The spatiotemporal maps were constructed as follows: a color was assigned to the value of the local field potential (LFP) at each electrode; the color scale ranged in 10 steps from the baseline (blue) to -100 microvolts (yellow); the LFPs from anterior to posterior are shown from left to right; time was divided in frames each representing a snapshot of 4ms of thalamic activity and arranged in a column from top to bottom. The whole frame is shifted downwards as time evolves (similar to a chart recorder), for better visualization of the spread of activity. In this type of representation, synchronized oscillations appear as vertical stripes. This animation corresponds to multisite recordings in the thalamus with intact cortex and shows the large-scale synchrony of oscillations.
Same animation at a slower time scale.
Same representation of multisite recordings of thalamic oscillations, after removal of the cortex (decorticate). The electrodes were placed in approximately the same locations. Although each site individually oscillated at the same frequency as with intact cortex, the large-scale synchrony of the oscillations was disrupted following removal of the cortex.
Same animation at a slower time scale.
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Simulations of the thalamic reticular nucleus:
These simulations are based on the paper:
Destexhe, A., Contreras, D., Sejnowski, T.J. and Steriade, M. A model of spindle rhythmicity in the isolated thalamic reticular nucleus. Journal of Neurophysiology 72:803-818, 1994
N=100, 3rd neighb, 2ms between frames, 10pixel/frame 1000 frames, from t=5 sec to 6 sec; -90 (white) to -60 mV (black) See Fig. 9 in J. Neurophysiol. 72: 803-818,1994 .
N=400, 3rd neighb, 2ms between frames, 5pixel/frame 1000 frames, from t=4 sec to 5 sec; -90 (white) to -60 mV (black)
N=400, 1st neighb, 2ms between frames, 5pixel/frame 1000 frames, from t=4 sec to 5 sec; -90 (white) to -60 mV (black) See Fig. 10 in J. Neurophysiol. 72: 803-818, 1994 .
N=1600, 3rd neighb, 2ms between frames, 5pixel/frame 1000 frames, from t=4 sec to 5 sec; -90 (white) to -60 mV (black)
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Spatiotemporal patterns in networks of excitatory and inhibitorycells:
These simulations are based on the paper: Oscillations, complex spatiotemporal behavior and information transport in networks of excitatory and inhibitory neurons, by Alain Destexhe, published in Physical Review E 50: 1594-1606, 1994.
N=100, M=25, 1st neighb, 1.2ms between frames, 10 pixel/frame, 1000 frames, from t=0 to t=1.2 sec; -80 (white) to +50 mV (black). See Fig.4 in Physical Review E50:1594-1606, 1994.
N=100, M=25, 1st neighb, 1.2ms between frames, 10 pixel/frame, 1000 frames, from t=0 to t=1.2 sec; -80 (white) to +50 mV (black). See Fig.5 and 6a in Physical Review E50: 1594-1606, 1994.
N=6400, M=1600, 2nd neighb, 2ms between frames, 2 pixel/frame, 100 frames, from t=0.1 to t=0.2 sec; -80 (white) to +50 mV (black). See Fig.7 in Physical Review E50: 1594-1606, 1994.
Please cite the original papers if you use these movies.
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